Starting phenix.real_space_refine on Sat Mar 23 12:41:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcq_28990/03_2024/8fcq_28990_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcq_28990/03_2024/8fcq_28990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcq_28990/03_2024/8fcq_28990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcq_28990/03_2024/8fcq_28990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcq_28990/03_2024/8fcq_28990_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcq_28990/03_2024/8fcq_28990_updated.pdb" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 189 5.16 5 C 23162 2.51 5 N 6477 2.21 5 O 7052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "E PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 357": "OE1" <-> "OE2" Residue "G TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36904 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "A" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "F" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "E" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "D" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "C" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "G" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2740 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.18, per 1000 atoms: 0.52 Number of scatterers: 36904 At special positions: 0 Unit cell: (182.646, 190.152, 117.594, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 189 16.00 P 24 15.00 O 7052 8.00 N 6477 7.00 C 23162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.79 Conformation dependent library (CDL) restraints added in 6.5 seconds 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8730 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 233 helices and 33 sheets defined 43.7% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.78 Creating SS restraints... Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.587A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 319 through 336 removed outlier: 3.562A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LYS B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 383 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 426 Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 493 Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 663 removed outlier: 5.013A pdb=" N LYS B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.779A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.785A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 130 through 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 225 removed outlier: 5.043A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 319 through 336 removed outlier: 3.560A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A 336 " --> pdb=" O MET A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 493 Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 663 removed outlier: 4.980A pdb=" N LYS A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 706 removed outlier: 3.832A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.779A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 761 Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 130 through 133 No H-bonds generated for 'chain 'F' and resid 130 through 133' Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 225 removed outlier: 4.027A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 231 Processing helix chain 'F' and resid 251 through 262 removed outlier: 3.580A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 319 through 336 removed outlier: 3.886A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LYS F 336 " --> pdb=" O MET F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 387 removed outlier: 5.267A pdb=" N ASN F 387 " --> pdb=" O ILE F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 430 removed outlier: 4.476A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 removed outlier: 3.694A pdb=" N VAL F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 524 through 534 removed outlier: 3.512A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 599 through 610 removed outlier: 3.873A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 615 No H-bonds generated for 'chain 'F' and resid 613 through 615' Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 706 Processing helix chain 'F' and resid 733 through 741 removed outlier: 3.681A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 762 Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 130 through 133 No H-bonds generated for 'chain 'E' and resid 130 through 133' Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.716A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 251 through 262 removed outlier: 3.535A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.533A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 319 through 336 removed outlier: 3.769A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 385 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 430 removed outlier: 3.676A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 493 Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 524 through 534 removed outlier: 3.512A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 removed outlier: 3.515A pdb=" N PHE E 563 " --> pdb=" O ARG E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 613 through 615 No H-bonds generated for 'chain 'E' and resid 613 through 615' Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 663 removed outlier: 5.045A pdb=" N LYS E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 706 removed outlier: 3.705A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.754A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 761 removed outlier: 4.200A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 130 through 139 removed outlier: 4.268A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 225 removed outlier: 4.698A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 319 through 336 removed outlier: 3.629A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS D 336 " --> pdb=" O MET D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 430 removed outlier: 3.672A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 493 Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 613 through 615 No H-bonds generated for 'chain 'D' and resid 613 through 615' Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 663 removed outlier: 5.072A pdb=" N LYS D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.680A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.732A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 761 removed outlier: 3.871A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.758A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 319 through 336 removed outlier: 3.547A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS C 336 " --> pdb=" O MET C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 430 removed outlier: 4.283A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 443 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 493 Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.585A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.828A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 761 Processing helix chain 'G' and resid 50 through 67 Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.721A pdb=" N PHE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N SER G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 168 through 187 Processing helix chain 'G' and resid 192 through 194 No H-bonds generated for 'chain 'G' and resid 192 through 194' Processing helix chain 'G' and resid 202 through 207 removed outlier: 3.934A pdb=" N GLU G 206 " --> pdb=" O LYS G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 220 Processing helix chain 'G' and resid 244 through 247 No H-bonds generated for 'chain 'G' and resid 244 through 247' Processing helix chain 'G' and resid 250 through 261 Processing helix chain 'G' and resid 281 through 284 Processing helix chain 'G' and resid 290 through 293 Processing helix chain 'G' and resid 297 through 315 Processing helix chain 'G' and resid 320 through 330 removed outlier: 3.953A pdb=" N GLU G 326 " --> pdb=" O MET G 322 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG G 329 " --> pdb=" O LYS G 325 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY G 330 " --> pdb=" O GLU G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 369 Processing helix chain 'G' and resid 412 through 420 removed outlier: 4.230A pdb=" N ASP G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 436 removed outlier: 5.227A pdb=" N ALA G 436 " --> pdb=" O GLU G 432 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 81 through 84 removed outlier: 7.895A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.792A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= D, first strand: chain 'B' and resid 365 through 368 removed outlier: 4.179A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 641 through 644 removed outlier: 4.163A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 81 through 84 removed outlier: 7.207A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.921A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.692A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 365 through 368 removed outlier: 4.041A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 641 through 644 removed outlier: 3.602A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.394A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 181 through 183 removed outlier: 6.739A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= N, first strand: chain 'F' and resid 365 through 368 removed outlier: 9.325A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 641 through 645 removed outlier: 8.870A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 81 through 84 removed outlier: 7.802A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP E 74 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 181 through 183 removed outlier: 6.831A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.753A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.821A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 641 through 644 removed outlier: 3.617A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 81 through 84 removed outlier: 7.430A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.808A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= X, first strand: chain 'D' and resid 365 through 368 removed outlier: 3.788A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 641 through 644 removed outlier: 3.669A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 81 through 83 removed outlier: 7.441A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.823A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= AC, first strand: chain 'C' and resid 365 through 368 removed outlier: 3.779A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.520A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 122 through 124 Processing sheet with id= AF, first strand: chain 'G' and resid 196 through 198 Processing sheet with id= AG, first strand: chain 'G' and resid 438 through 440 1305 hydrogen bonds defined for protein. 3651 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.14 Time building geometry restraints manager: 15.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7661 1.33 - 1.45: 7790 1.45 - 1.57: 21739 1.57 - 1.69: 36 1.69 - 1.81: 301 Bond restraints: 37527 Sorted by residual: bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 37522 not shown) Histogram of bond angle deviations from ideal: 100.85 - 107.87: 1539 107.87 - 114.89: 22521 114.89 - 121.91: 19115 121.91 - 128.93: 7401 128.93 - 135.95: 170 Bond angle restraints: 50746 Sorted by residual: angle pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" C LEU G 331 " ideal model delta sigma weight residual 113.28 123.95 -10.67 1.22e+00 6.72e-01 7.64e+01 angle pdb=" N ARG G 332 " pdb=" CA ARG G 332 " pdb=" C ARG G 332 " ideal model delta sigma weight residual 111.87 122.42 -10.55 1.41e+00 5.03e-01 5.60e+01 angle pdb=" CA GLY D 591 " pdb=" C GLY D 591 " pdb=" O GLY D 591 " ideal model delta sigma weight residual 122.23 118.56 3.67 6.90e-01 2.10e+00 2.83e+01 angle pdb=" N LYS G 333 " pdb=" CA LYS G 333 " pdb=" C LYS G 333 " ideal model delta sigma weight residual 112.23 118.42 -6.19 1.26e+00 6.30e-01 2.41e+01 angle pdb=" C LEU A 429 " pdb=" N ILE A 430 " pdb=" CA ILE A 430 " ideal model delta sigma weight residual 122.66 127.29 -4.63 9.70e-01 1.06e+00 2.28e+01 ... (remaining 50741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 22929 35.37 - 70.75: 242 70.75 - 106.12: 45 106.12 - 141.49: 9 141.49 - 176.87: 8 Dihedral angle restraints: 23233 sinusoidal: 9775 harmonic: 13458 Sorted by residual: dihedral pdb=" O1B ADP D 901 " pdb=" O3A ADP D 901 " pdb=" PB ADP D 901 " pdb=" PA ADP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 116.87 -176.87 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual 300.00 123.88 176.11 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 115.25 -175.25 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 23230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4074 0.047 - 0.094: 990 0.094 - 0.142: 463 0.142 - 0.189: 184 0.189 - 0.236: 12 Chirality restraints: 5723 Sorted by residual: chirality pdb=" CA ILE A 590 " pdb=" N ILE A 590 " pdb=" C ILE A 590 " pdb=" CB ILE A 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE E 590 " pdb=" N ILE E 590 " pdb=" C ILE E 590 " pdb=" CB ILE E 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE F 590 " pdb=" N ILE F 590 " pdb=" C ILE F 590 " pdb=" CB ILE F 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 5720 not shown) Planarity restraints: 6650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 254 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C GLU G 254 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU G 254 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG G 255 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 534 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C GLU F 534 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU F 534 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS F 535 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 360 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C PHE C 360 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE C 360 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY C 361 " 0.013 2.00e-02 2.50e+03 ... (remaining 6647 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 13726 2.89 - 3.39: 36184 3.39 - 3.89: 63852 3.89 - 4.40: 73538 4.40 - 4.90: 118345 Nonbonded interactions: 305645 Sorted by model distance: nonbonded pdb=" OD2 ASP E 368 " pdb=" NZ LYS E 565 " model vdw 2.387 2.520 nonbonded pdb=" OD2 ASP C 368 " pdb=" NZ LYS C 565 " model vdw 2.401 2.520 nonbonded pdb=" OD2 ASP D 368 " pdb=" NZ LYS D 565 " model vdw 2.408 2.520 nonbonded pdb=" NZ LYS C 62 " pdb=" OD2 ASP C 98 " model vdw 2.413 2.520 nonbonded pdb=" OE2 GLU E 30 " pdb=" NZ LYS E 217 " model vdw 2.424 2.520 ... (remaining 305640 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.750 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 96.750 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5684 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.111 37527 Z= 0.712 Angle : 0.848 12.426 50746 Z= 0.520 Chirality : 0.058 0.236 5723 Planarity : 0.004 0.033 6650 Dihedral : 12.291 176.869 14503 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.70 % Favored : 98.23 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.11), residues: 4639 helix: -0.25 (0.10), residues: 2069 sheet: 0.68 (0.17), residues: 778 loop : 0.89 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 476 HIS 0.001 0.000 HIS D 406 PHE 0.001 0.000 PHE C 52 TYR 0.001 0.000 TYR D 173 ARG 0.001 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1442 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1441 time to evaluate : 4.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 VAL cc_start: 0.7923 (t) cc_final: 0.7379 (t) REVERT: B 244 TYR cc_start: 0.6516 (p90) cc_final: 0.6227 (p90) REVERT: B 332 MET cc_start: 0.7472 (mmm) cc_final: 0.6880 (mmm) REVERT: B 654 VAL cc_start: 0.6785 (t) cc_final: 0.6577 (t) REVERT: A 252 THR cc_start: 0.7013 (p) cc_final: 0.6533 (t) REVERT: A 302 PHE cc_start: 0.5466 (t80) cc_final: 0.4905 (t80) REVERT: F 133 VAL cc_start: 0.7334 (t) cc_final: 0.7121 (t) REVERT: F 188 PRO cc_start: 0.7304 (Cg_exo) cc_final: 0.7039 (Cg_endo) REVERT: F 198 LEU cc_start: 0.7056 (mt) cc_final: 0.6801 (mt) REVERT: F 371 ILE cc_start: 0.8324 (mt) cc_final: 0.7848 (mp) REVERT: F 430 ILE cc_start: 0.7756 (mt) cc_final: 0.7358 (mm) REVERT: E 153 LEU cc_start: 0.5934 (tp) cc_final: 0.5427 (tp) REVERT: E 244 TYR cc_start: 0.7631 (p90) cc_final: 0.7269 (p90) REVERT: E 332 MET cc_start: 0.7866 (mmm) cc_final: 0.7579 (mmm) REVERT: D 201 VAL cc_start: 0.7321 (t) cc_final: 0.7009 (t) REVERT: D 399 VAL cc_start: 0.8141 (t) cc_final: 0.7869 (t) REVERT: D 644 TYR cc_start: 0.6779 (t80) cc_final: 0.6435 (t80) REVERT: C 51 LEU cc_start: 0.5447 (pp) cc_final: 0.5224 (pp) REVERT: C 275 MET cc_start: 0.6891 (mmm) cc_final: 0.6489 (mmm) REVERT: C 363 PHE cc_start: 0.6807 (m-80) cc_final: 0.6552 (m-10) outliers start: 1 outliers final: 0 residues processed: 1442 average time/residue: 0.5495 time to fit residues: 1219.2938 Evaluate side-chains 732 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 732 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 393 optimal weight: 6.9990 chunk 353 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 365 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 222 optimal weight: 0.9980 chunk 271 optimal weight: 7.9990 chunk 423 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 ASN ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN F 226 HIS F 660 ASN E 285 ASN E 296 ASN E 458 GLN ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS D 327 GLN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS D 602 ASN D 763 GLN C 115 HIS C 443 ASN G 53 GLN G 67 GLN G 148 HIS G 328 GLN G 371 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 37527 Z= 0.264 Angle : 0.751 11.577 50746 Z= 0.365 Chirality : 0.047 0.239 5723 Planarity : 0.005 0.088 6650 Dihedral : 9.905 174.366 5191 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.25 % Favored : 98.73 % Rotamer: Outliers : 2.80 % Allowed : 12.47 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.12), residues: 4639 helix: 0.88 (0.11), residues: 2036 sheet: 0.62 (0.17), residues: 788 loop : 1.12 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP D 476 HIS 0.010 0.001 HIS D 404 PHE 0.025 0.002 PHE B 618 TYR 0.035 0.003 TYR C 495 ARG 0.014 0.001 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 778 time to evaluate : 3.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 THR cc_start: 0.7752 (p) cc_final: 0.7113 (t) REVERT: B 268 LEU cc_start: 0.8227 (tt) cc_final: 0.7993 (tt) REVERT: B 382 GLN cc_start: 0.7163 (mt0) cc_final: 0.6870 (mt0) REVERT: A 244 TYR cc_start: 0.4756 (p90) cc_final: 0.4113 (p90) REVERT: F 198 LEU cc_start: 0.6799 (mt) cc_final: 0.5813 (mt) REVERT: F 307 ASP cc_start: 0.7407 (p0) cc_final: 0.7176 (p0) REVERT: F 650 GLU cc_start: 0.5873 (tm-30) cc_final: 0.5445 (tm-30) REVERT: E 332 MET cc_start: 0.8028 (mmm) cc_final: 0.7635 (mmm) REVERT: E 543 LYS cc_start: 0.6983 (mtmm) cc_final: 0.6709 (mtmm) REVERT: D 366 GLU cc_start: 0.7557 (pp20) cc_final: 0.7261 (pp20) REVERT: C 172 PRO cc_start: 0.7213 (Cg_endo) cc_final: 0.6923 (Cg_exo) REVERT: C 275 MET cc_start: 0.6984 (mmm) cc_final: 0.6385 (mmm) REVERT: C 327 GLN cc_start: 0.8000 (tp40) cc_final: 0.7592 (tp40) REVERT: G 134 LYS cc_start: 0.6411 (tptt) cc_final: 0.6096 (tptt) outliers start: 111 outliers final: 69 residues processed: 846 average time/residue: 0.4968 time to fit residues: 670.1770 Evaluate side-chains 651 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 582 time to evaluate : 4.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 565 LYS Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 674 PHE Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 538 ASN Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 315 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 235 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 352 optimal weight: 9.9990 chunk 288 optimal weight: 30.0000 chunk 116 optimal weight: 0.9990 chunk 423 optimal weight: 6.9990 chunk 457 optimal weight: 8.9990 chunk 377 optimal weight: 6.9990 chunk 420 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN A 624 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS F 443 ASN F 735 HIS E 384 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN G 278 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 37527 Z= 0.461 Angle : 0.848 12.956 50746 Z= 0.420 Chirality : 0.049 0.266 5723 Planarity : 0.006 0.066 6650 Dihedral : 9.877 171.525 5191 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.28 % Allowed : 13.37 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.12), residues: 4639 helix: 0.42 (0.11), residues: 2060 sheet: 0.39 (0.17), residues: 785 loop : 0.78 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 476 HIS 0.010 0.002 HIS A 735 PHE 0.031 0.003 PHE B 563 TYR 0.025 0.003 TYR C 495 ARG 0.007 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 583 time to evaluate : 3.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 489 LEU cc_start: 0.7664 (mt) cc_final: 0.7463 (mm) REVERT: A 388 MET cc_start: 0.4507 (mtt) cc_final: 0.4257 (mtt) REVERT: F 275 MET cc_start: 0.8244 (mpp) cc_final: 0.7782 (mmp) REVERT: F 691 CYS cc_start: 0.5569 (OUTLIER) cc_final: 0.5324 (t) REVERT: D 84 MET cc_start: 0.5061 (pmm) cc_final: 0.4810 (ptp) REVERT: C 275 MET cc_start: 0.7301 (mmm) cc_final: 0.6647 (mmm) REVERT: G 162 TYR cc_start: 0.4544 (m-80) cc_final: 0.4310 (m-10) REVERT: G 270 LEU cc_start: 0.6054 (tt) cc_final: 0.5171 (mp) outliers start: 170 outliers final: 120 residues processed: 702 average time/residue: 0.4792 time to fit residues: 547.7292 Evaluate side-chains 609 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 488 time to evaluate : 3.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 565 LYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 295 LYS Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 674 PHE Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 691 CYS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 538 ASN Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 543 LYS Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 691 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 418 optimal weight: 1.9990 chunk 318 optimal weight: 0.9980 chunk 220 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 284 optimal weight: 9.9990 chunk 425 optimal weight: 10.0000 chunk 450 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 403 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 ASN B 296 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS F 603 GLN E 616 ASN D 103 GLN D 404 HIS ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37527 Z= 0.209 Angle : 0.689 12.880 50746 Z= 0.328 Chirality : 0.046 0.244 5723 Planarity : 0.004 0.052 6650 Dihedral : 9.429 171.277 5191 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.37 % Allowed : 15.13 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.12), residues: 4639 helix: 0.69 (0.11), residues: 2072 sheet: 0.49 (0.18), residues: 767 loop : 0.84 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 454 HIS 0.006 0.001 HIS D 404 PHE 0.028 0.002 PHE B 563 TYR 0.024 0.002 TYR D 495 ARG 0.009 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 585 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 606 THR cc_start: 0.8019 (p) cc_final: 0.7745 (t) REVERT: B 633 ILE cc_start: 0.7041 (mp) cc_final: 0.6543 (mm) REVERT: A 388 MET cc_start: 0.4405 (mtt) cc_final: 0.4114 (mtt) REVERT: F 219 MET cc_start: 0.7480 (mtt) cc_final: 0.7244 (mtm) REVERT: E 755 TYR cc_start: 0.4528 (m-80) cc_final: 0.4223 (m-80) REVERT: D 531 ILE cc_start: 0.7106 (tp) cc_final: 0.6894 (tp) REVERT: C 153 LEU cc_start: 0.7868 (tp) cc_final: 0.7622 (tt) REVERT: C 244 TYR cc_start: 0.7425 (p90) cc_final: 0.7181 (p90) REVERT: C 275 MET cc_start: 0.7256 (mmm) cc_final: 0.6596 (mmm) REVERT: G 270 LEU cc_start: 0.5981 (tt) cc_final: 0.5211 (mp) outliers start: 134 outliers final: 88 residues processed: 680 average time/residue: 0.4703 time to fit residues: 521.8208 Evaluate side-chains 587 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 499 time to evaluate : 4.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 565 LYS Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 454 TRP Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 691 CYS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 538 ASN Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 239 PHE Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 311 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 375 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 335 optimal weight: 4.9990 chunk 185 optimal weight: 0.2980 chunk 384 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 230 optimal weight: 20.0000 chunk 404 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN D 404 HIS ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37527 Z= 0.238 Angle : 0.696 12.265 50746 Z= 0.332 Chirality : 0.046 0.244 5723 Planarity : 0.004 0.051 6650 Dihedral : 9.243 175.637 5191 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.83 % Allowed : 15.74 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.12), residues: 4639 helix: 0.76 (0.11), residues: 2062 sheet: 0.39 (0.18), residues: 773 loop : 0.84 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 476 HIS 0.007 0.001 HIS A 735 PHE 0.021 0.001 PHE B 563 TYR 0.029 0.002 TYR D 495 ARG 0.010 0.001 ARG G 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 535 time to evaluate : 4.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 633 ILE cc_start: 0.7050 (mp) cc_final: 0.6601 (mm) REVERT: A 388 MET cc_start: 0.4255 (mtt) cc_final: 0.3972 (mtt) REVERT: A 442 MET cc_start: 0.6604 (OUTLIER) cc_final: 0.6364 (mmt) REVERT: F 740 MET cc_start: 0.4883 (ppp) cc_final: 0.4011 (tmm) REVERT: D 531 ILE cc_start: 0.7075 (tp) cc_final: 0.6852 (tp) REVERT: C 153 LEU cc_start: 0.7884 (tp) cc_final: 0.7671 (tt) REVERT: C 158 MET cc_start: 0.6349 (mmp) cc_final: 0.5468 (mmp) REVERT: C 275 MET cc_start: 0.7253 (mmm) cc_final: 0.6720 (mmm) REVERT: C 348 ASN cc_start: 0.7227 (p0) cc_final: 0.6778 (p0) REVERT: C 508 MET cc_start: 0.4317 (tpp) cc_final: 0.3872 (mmt) REVERT: G 167 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7936 (p0) REVERT: G 270 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.5460 (mp) outliers start: 152 outliers final: 110 residues processed: 644 average time/residue: 0.4623 time to fit residues: 491.4938 Evaluate side-chains 589 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 476 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 565 LYS Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 454 TRP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 691 CYS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 538 ASN Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 543 LYS Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 691 CYS Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 239 PHE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 151 optimal weight: 10.0000 chunk 405 optimal weight: 0.0370 chunk 89 optimal weight: 0.0470 chunk 264 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 450 optimal weight: 0.3980 chunk 374 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 236 optimal weight: 0.6980 overall best weight: 1.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 458 GLN ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 HIS ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN D 404 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37527 Z= 0.191 Angle : 0.689 12.482 50746 Z= 0.325 Chirality : 0.045 0.240 5723 Planarity : 0.004 0.049 6650 Dihedral : 8.991 177.933 5191 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.37 % Allowed : 17.00 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.12), residues: 4639 helix: 0.82 (0.11), residues: 2080 sheet: 0.37 (0.18), residues: 781 loop : 0.80 (0.16), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP E 476 HIS 0.005 0.001 HIS B 499 PHE 0.026 0.001 PHE E 302 TYR 0.036 0.002 TYR D 495 ARG 0.007 0.000 ARG G 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 554 time to evaluate : 4.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 606 THR cc_start: 0.7929 (p) cc_final: 0.7564 (t) REVERT: B 633 ILE cc_start: 0.6912 (mp) cc_final: 0.6467 (mm) REVERT: A 388 MET cc_start: 0.4438 (mtt) cc_final: 0.4142 (mtt) REVERT: A 442 MET cc_start: 0.6576 (mmp) cc_final: 0.6309 (mmt) REVERT: F 740 MET cc_start: 0.4821 (ppp) cc_final: 0.3929 (tmm) REVERT: D 275 MET cc_start: 0.7021 (mmm) cc_final: 0.6806 (mmm) REVERT: D 531 ILE cc_start: 0.6949 (tp) cc_final: 0.6744 (tp) REVERT: C 153 LEU cc_start: 0.7844 (tp) cc_final: 0.7107 (tt) REVERT: C 275 MET cc_start: 0.7226 (mmm) cc_final: 0.6683 (mmm) REVERT: G 167 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7928 (p0) REVERT: G 270 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.5496 (mp) outliers start: 134 outliers final: 101 residues processed: 650 average time/residue: 0.4685 time to fit residues: 501.9297 Evaluate side-chains 598 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 495 time to evaluate : 4.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 565 LYS Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 517 TYR Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 674 PHE Chi-restraints excluded: chain F residue 691 CYS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 538 ASN Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 543 LYS Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 239 PHE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 434 optimal weight: 0.0370 chunk 50 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 chunk 329 optimal weight: 9.9990 chunk 255 optimal weight: 4.9990 chunk 379 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 449 optimal weight: 10.0000 chunk 281 optimal weight: 20.0000 chunk 273 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 ASN A 735 HIS ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN D 115 HIS D 404 HIS ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 760 GLN C 384 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37527 Z= 0.219 Angle : 0.703 16.599 50746 Z= 0.333 Chirality : 0.046 0.241 5723 Planarity : 0.004 0.059 6650 Dihedral : 8.779 172.786 5191 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.60 % Allowed : 17.30 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.12), residues: 4639 helix: 0.69 (0.11), residues: 2111 sheet: 0.23 (0.17), residues: 793 loop : 0.75 (0.16), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 454 HIS 0.005 0.001 HIS D 183 PHE 0.030 0.002 PHE B 363 TYR 0.034 0.002 TYR B 244 ARG 0.012 0.001 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 513 time to evaluate : 4.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 411 LEU cc_start: 0.8177 (mt) cc_final: 0.7514 (mt) REVERT: B 606 THR cc_start: 0.7969 (p) cc_final: 0.7461 (t) REVERT: B 633 ILE cc_start: 0.6928 (mp) cc_final: 0.6537 (mm) REVERT: A 388 MET cc_start: 0.4378 (mtt) cc_final: 0.4105 (mtt) REVERT: F 193 ASP cc_start: 0.6211 (p0) cc_final: 0.5947 (p0) REVERT: F 740 MET cc_start: 0.4851 (ppp) cc_final: 0.3994 (tmm) REVERT: D 368 ASP cc_start: 0.6930 (t0) cc_final: 0.6632 (t0) REVERT: D 388 MET cc_start: 0.6120 (ptm) cc_final: 0.5855 (ptm) REVERT: D 602 ASN cc_start: 0.7275 (p0) cc_final: 0.6968 (p0) REVERT: C 153 LEU cc_start: 0.7794 (tp) cc_final: 0.7489 (tt) REVERT: C 275 MET cc_start: 0.7232 (mmm) cc_final: 0.6804 (mmm) REVERT: C 678 MET cc_start: 0.6367 (mmm) cc_final: 0.6087 (mmt) REVERT: G 167 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7930 (p0) REVERT: G 270 LEU cc_start: 0.6395 (tt) cc_final: 0.5538 (mp) outliers start: 143 outliers final: 117 residues processed: 618 average time/residue: 0.4698 time to fit residues: 480.4523 Evaluate side-chains 601 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 483 time to evaluate : 4.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 565 LYS Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 517 TYR Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 674 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 538 ASN Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 543 LYS Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 277 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 285 optimal weight: 9.9990 chunk 306 optimal weight: 7.9990 chunk 222 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 353 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN G 215 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 37527 Z= 0.298 Angle : 0.747 12.361 50746 Z= 0.357 Chirality : 0.047 0.252 5723 Planarity : 0.005 0.055 6650 Dihedral : 8.778 169.612 5191 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.80 % Allowed : 17.43 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.12), residues: 4639 helix: 0.53 (0.11), residues: 2101 sheet: 0.10 (0.17), residues: 790 loop : 0.58 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 454 HIS 0.005 0.001 HIS B 499 PHE 0.023 0.002 PHE B 363 TYR 0.042 0.002 TYR B 244 ARG 0.011 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 497 time to evaluate : 4.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 351 ASN cc_start: 0.7159 (p0) cc_final: 0.6737 (p0) REVERT: B 633 ILE cc_start: 0.7028 (mp) cc_final: 0.6637 (mm) REVERT: A 388 MET cc_start: 0.4511 (mtt) cc_final: 0.4207 (mtt) REVERT: F 193 ASP cc_start: 0.6392 (p0) cc_final: 0.6120 (p0) REVERT: F 740 MET cc_start: 0.4950 (ppp) cc_final: 0.4062 (tmm) REVERT: D 336 LYS cc_start: 0.6759 (mmtt) cc_final: 0.6334 (mmtt) REVERT: D 602 ASN cc_start: 0.7339 (p0) cc_final: 0.6925 (p0) REVERT: C 96 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6426 (tp) REVERT: C 275 MET cc_start: 0.7264 (mmm) cc_final: 0.6942 (mmm) REVERT: C 509 THR cc_start: 0.8136 (m) cc_final: 0.7576 (t) REVERT: C 678 MET cc_start: 0.6371 (mmm) cc_final: 0.6101 (mmt) REVERT: G 167 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7923 (p0) REVERT: G 270 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.5497 (mp) outliers start: 151 outliers final: 123 residues processed: 610 average time/residue: 0.4476 time to fit residues: 455.1171 Evaluate side-chains 596 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 470 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 565 LYS Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 517 TYR Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 538 ASN Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 543 LYS Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 408 optimal weight: 7.9990 chunk 430 optimal weight: 0.0870 chunk 392 optimal weight: 3.9990 chunk 418 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 328 optimal weight: 7.9990 chunk 128 optimal weight: 20.0000 chunk 378 optimal weight: 0.0870 chunk 395 optimal weight: 5.9990 chunk 417 optimal weight: 10.0000 overall best weight: 2.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 ASN A 43 GLN ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS D 406 HIS D 458 GLN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.6694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37527 Z= 0.237 Angle : 0.737 13.235 50746 Z= 0.348 Chirality : 0.046 0.247 5723 Planarity : 0.005 0.060 6650 Dihedral : 8.607 163.608 5191 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.35 % Allowed : 18.38 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.12), residues: 4639 helix: 0.56 (0.11), residues: 2097 sheet: 0.12 (0.18), residues: 787 loop : 0.61 (0.16), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 454 HIS 0.005 0.001 HIS B 499 PHE 0.048 0.002 PHE B 363 TYR 0.043 0.002 TYR B 244 ARG 0.007 0.000 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 491 time to evaluate : 4.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 351 ASN cc_start: 0.7094 (p0) cc_final: 0.6678 (p0) REVERT: B 633 ILE cc_start: 0.6972 (mp) cc_final: 0.6579 (mm) REVERT: A 388 MET cc_start: 0.4576 (mtt) cc_final: 0.4274 (mtt) REVERT: F 120 ASP cc_start: 0.6339 (OUTLIER) cc_final: 0.5881 (p0) REVERT: F 193 ASP cc_start: 0.6292 (p0) cc_final: 0.5952 (p0) REVERT: F 740 MET cc_start: 0.4971 (ppp) cc_final: 0.4081 (tmm) REVERT: E 162 GLU cc_start: 0.4739 (mm-30) cc_final: 0.4527 (mm-30) REVERT: D 221 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5926 (pp20) REVERT: D 602 ASN cc_start: 0.7244 (p0) cc_final: 0.6812 (p0) REVERT: C 96 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6344 (tp) REVERT: C 275 MET cc_start: 0.7276 (mmm) cc_final: 0.6933 (mmm) REVERT: C 678 MET cc_start: 0.6321 (mmm) cc_final: 0.6094 (mmt) REVERT: G 167 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7889 (p0) REVERT: G 270 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.5565 (mp) outliers start: 133 outliers final: 112 residues processed: 592 average time/residue: 0.4552 time to fit residues: 446.9875 Evaluate side-chains 581 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 464 time to evaluate : 4.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 565 LYS Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 538 ASN Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 543 LYS Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 274 optimal weight: 8.9990 chunk 442 optimal weight: 1.9990 chunk 270 optimal weight: 0.6980 chunk 209 optimal weight: 0.1980 chunk 307 optimal weight: 0.9980 chunk 464 optimal weight: 1.9990 chunk 427 optimal weight: 7.9990 chunk 369 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 285 optimal weight: 9.9990 chunk 226 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 763 GLN D 404 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37527 Z= 0.198 Angle : 0.748 14.073 50746 Z= 0.350 Chirality : 0.046 0.240 5723 Planarity : 0.005 0.053 6650 Dihedral : 8.343 153.637 5191 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.69 % Allowed : 19.09 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.12), residues: 4639 helix: 0.68 (0.11), residues: 2081 sheet: 0.20 (0.18), residues: 783 loop : 0.61 (0.16), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 454 HIS 0.004 0.001 HIS B 499 PHE 0.029 0.002 PHE B 563 TYR 0.042 0.002 TYR B 244 ARG 0.006 0.000 ARG G 318 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 524 time to evaluate : 4.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.3961 (OUTLIER) cc_final: 0.3209 (mtmm) REVERT: B 332 MET cc_start: 0.7544 (mmm) cc_final: 0.7106 (mmm) REVERT: B 351 ASN cc_start: 0.7009 (p0) cc_final: 0.6682 (p0) REVERT: B 633 ILE cc_start: 0.6832 (mp) cc_final: 0.6469 (mm) REVERT: A 84 MET cc_start: 0.4945 (ptp) cc_final: 0.4620 (mtp) REVERT: A 388 MET cc_start: 0.4427 (mtt) cc_final: 0.4158 (mtt) REVERT: F 193 ASP cc_start: 0.6280 (p0) cc_final: 0.6015 (p0) REVERT: F 740 MET cc_start: 0.4906 (ppp) cc_final: 0.4049 (tmm) REVERT: D 336 LYS cc_start: 0.6553 (mmtt) cc_final: 0.6070 (mmtt) REVERT: D 602 ASN cc_start: 0.7210 (p0) cc_final: 0.6848 (p0) REVERT: C 96 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6302 (tp) REVERT: C 275 MET cc_start: 0.7246 (mmm) cc_final: 0.6873 (mmm) REVERT: G 167 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7912 (p0) REVERT: G 270 LEU cc_start: 0.6520 (OUTLIER) cc_final: 0.5598 (mp) outliers start: 107 outliers final: 97 residues processed: 601 average time/residue: 0.4763 time to fit residues: 475.3905 Evaluate side-chains 590 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 489 time to evaluate : 4.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 565 LYS Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 538 ASN Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 239 PHE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 293 optimal weight: 9.9990 chunk 393 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 340 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 370 optimal weight: 0.9990 chunk 154 optimal weight: 0.0970 chunk 380 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.096221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.075982 restraints weight = 144759.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.078101 restraints weight = 83014.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.079480 restraints weight = 56094.722| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37527 Z= 0.189 Angle : 0.748 14.748 50746 Z= 0.352 Chirality : 0.046 0.234 5723 Planarity : 0.005 0.062 6650 Dihedral : 8.102 149.097 5191 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.54 % Allowed : 19.42 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.13), residues: 4639 helix: 0.71 (0.11), residues: 2094 sheet: 0.30 (0.18), residues: 770 loop : 0.67 (0.16), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 454 HIS 0.004 0.001 HIS B 499 PHE 0.025 0.001 PHE A 452 TYR 0.039 0.001 TYR B 244 ARG 0.015 0.000 ARG B 700 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9663.58 seconds wall clock time: 176 minutes 47.35 seconds (10607.35 seconds total)