Starting phenix.real_space_refine on Fri Feb 23 06:28:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcr_28991/02_2024/8fcr_28991_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcr_28991/02_2024/8fcr_28991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcr_28991/02_2024/8fcr_28991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcr_28991/02_2024/8fcr_28991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcr_28991/02_2024/8fcr_28991_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcr_28991/02_2024/8fcr_28991_updated.pdb" } resolution = 4.12 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= 0.043 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 188 5.16 5 C 23170 2.51 5 N 6487 2.21 5 O 7062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 110": "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 PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "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 GLU 546": "OE1" <-> "OE2" 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 "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 TYR 173": "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 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 "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "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 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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 GLU 200": "OE1" <-> "OE2" 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 "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 GLU 200": "OE1" <-> "OE2" 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 TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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 TYR 143": "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 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 452": "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 "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 292": "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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36931 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5637 Classifications: {'peptide': 721} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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: "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: "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: "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: "F" Number of atoms: 5565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5565 Classifications: {'peptide': 712} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 674} Chain breaks: 2 Chain: "G" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2845 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 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: "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: "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} 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: "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: "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} Time building chain proxies: 18.98, per 1000 atoms: 0.51 Number of scatterers: 36931 At special positions: 0 Unit cell: (183.48, 191.82, 115.092, 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 188 16.00 P 24 15.00 O 7062 8.00 N 6487 7.00 C 23170 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: 14.74 Conformation dependent library (CDL) restraints added in 6.9 seconds 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8756 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 233 helices and 33 sheets defined 43.8% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.02 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 86 through 91 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: 4.551A 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: 3.586A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.749A 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 579 through 585 removed outlier: 3.845A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) 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: 5.123A 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: 3.710A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.661A 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 'B' and resid 43 through 48 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' 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: 4.639A 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: 3.600A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 427 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 removed outlier: 3.535A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 579 through 585 removed outlier: 4.280A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) 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 660 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.762A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.804A 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 '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: 4.788A 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: 3.620A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 4.893A 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: 3.678A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 4.578A 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 663 removed outlier: 5.073A pdb=" N LYS C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.796A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.812A 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 'D' and resid 43 through 48 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 130 through 133 No H-bonds generated for 'chain 'D' and resid 130 through 133' Processing helix chain 'D' and resid 135 through 139 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: 4.691A 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: 3.642A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 4.895A 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 385 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 430 removed outlier: 3.705A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 5.114A 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: 3.521A pdb=" N ARG D 662 " --> pdb=" O LYS D 658 " (cutoff:3.500A) removed outlier: 5.061A 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: 3.792A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.735A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 761 removed outlier: 3.897A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) 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: 4.704A 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 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 295 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: 3.602A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) 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 427 removed outlier: 3.769A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (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 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 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: 5.015A 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: 3.692A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.734A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 761 removed outlier: 4.017A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 86 through 92 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: 4.811A 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 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: 3.528A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 4.822A 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: 5.139A 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: 4.435A 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 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 524 through 534 removed outlier: 3.508A 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: 3.855A 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 'G' and resid 50 through 67 Processing helix chain 'G' and resid 75 through 93 Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.771A pdb=" N PHE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 163 Processing helix chain 'G' and resid 168 through 187 removed outlier: 3.515A pdb=" N ILE G 185 " --> pdb=" O TYR G 181 " (cutoff:3.500A) 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 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 251 through 261 Processing helix chain 'G' and resid 281 through 284 Processing helix chain 'G' and resid 290 through 293 removed outlier: 4.413A pdb=" N PHE G 293 " --> pdb=" O GLY G 290 " (cutoff:3.500A) No H-bonds generated for '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: 4.008A pdb=" N ARG G 329 " --> pdb=" O LYS G 325 " (cutoff:3.500A) removed outlier: 4.750A 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: 3.577A pdb=" N ASP G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 436 removed outlier: 5.089A pdb=" N ALA G 436 " --> pdb=" O GLU G 432 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 81 through 84 removed outlier: 7.259A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.933A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.674A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.833A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 641 through 644 removed outlier: 4.177A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 81 through 84 removed outlier: 7.940A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 74 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.784A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= I, first strand: chain 'B' and resid 365 through 368 removed outlier: 4.235A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.462A 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: 7.685A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 641 through 644 removed outlier: 3.583A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 81 through 83 removed outlier: 7.484A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.522A pdb=" N HIS C 115 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= N, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.773A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 641 through 644 removed outlier: 8.630A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 81 through 83 removed outlier: 7.111A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP D 55 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.837A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= S, first strand: chain 'D' and resid 365 through 368 removed outlier: 3.894A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 641 through 644 removed outlier: 4.123A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 81 through 84 removed outlier: 7.950A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP E 74 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 181 through 183 removed outlier: 6.862A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.743A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 365 through 368 removed outlier: 9.098A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.620A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.224A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 181 through 183 removed outlier: 6.718A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AC, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.864A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 641 through 645 removed outlier: 8.607A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE F 540 " --> pdb=" O PHE F 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 275 through 277 1322 hydrogen bonds defined for protein. 3684 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: 14.12 Time building geometry restraints manager: 15.78 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: 7600 1.33 - 1.45: 7846 1.45 - 1.57: 21768 1.57 - 1.69: 36 1.69 - 1.81: 299 Bond restraints: 37549 Sorted by residual: bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 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 C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 ... (remaining 37544 not shown) Histogram of bond angle deviations from ideal: 100.82 - 107.83: 1527 107.83 - 114.84: 22361 114.84 - 121.86: 19141 121.86 - 128.87: 7583 128.87 - 135.88: 168 Bond angle restraints: 50780 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 113.28 123.96 -10.68 1.22e+00 6.72e-01 7.67e+01 angle pdb=" N ARG G 332 " pdb=" CA ARG G 332 " pdb=" C ARG G 332 " ideal model delta sigma weight residual 112.92 122.47 -9.55 1.23e+00 6.61e-01 6.03e+01 angle pdb=" CA ASP F 592 " pdb=" C ASP F 592 " pdb=" O ASP F 592 " ideal model delta sigma weight residual 117.94 121.86 -3.92 5.80e-01 2.97e+00 4.57e+01 angle pdb=" N LYS G 333 " pdb=" CA LYS G 333 " pdb=" C LYS G 333 " ideal model delta sigma weight residual 111.82 118.44 -6.62 1.16e+00 7.43e-01 3.26e+01 angle pdb=" C ASP F 592 " pdb=" CA ASP F 592 " pdb=" CB ASP F 592 " ideal model delta sigma weight residual 117.07 110.15 6.92 1.44e+00 4.82e-01 2.31e+01 ... (remaining 50775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 22928 34.86 - 69.71: 258 69.71 - 104.57: 42 104.57 - 139.43: 8 139.43 - 174.28: 9 Dihedral angle restraints: 23245 sinusoidal: 9751 harmonic: 13494 Sorted by residual: 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 -60.00 114.28 -174.28 1 2.00e+01 2.50e-03 4.79e+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 300.00 126.06 173.93 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual 300.00 126.70 173.29 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 23242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4072 0.048 - 0.095: 999 0.095 - 0.143: 477 0.143 - 0.191: 173 0.191 - 0.239: 13 Chirality restraints: 5734 Sorted by residual: 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 1.42e+00 chirality pdb=" CA ILE B 590 " pdb=" N ILE B 590 " pdb=" C ILE B 590 " pdb=" CB ILE B 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE C 590 " pdb=" N ILE C 590 " pdb=" C ILE C 590 " pdb=" CB ILE C 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 5731 not shown) Planarity restraints: 6656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 144 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" C ARG E 144 " 0.044 2.00e-02 2.50e+03 pdb=" O ARG E 144 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO E 145 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 82 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C GLN G 82 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN G 82 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL G 83 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 254 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C GLU G 254 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU G 254 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG G 255 " -0.013 2.00e-02 2.50e+03 ... (remaining 6653 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 12381 2.85 - 3.36: 35347 3.36 - 3.88: 63325 3.88 - 4.39: 74508 4.39 - 4.90: 119902 Nonbonded interactions: 305463 Sorted by model distance: nonbonded pdb=" O LYS A 696 " pdb=" CG1 ILE A 699 " model vdw 2.340 3.440 nonbonded pdb=" OD2 ASP B 368 " pdb=" NZ LYS B 565 " model vdw 2.387 2.520 nonbonded pdb=" OD2 ASP E 368 " pdb=" NZ LYS E 565 " model vdw 2.408 2.520 nonbonded pdb=" OD2 ASP A 368 " pdb=" NZ LYS A 565 " model vdw 2.424 2.520 nonbonded pdb=" O ALA D 583 " pdb=" N GLY D 588 " model vdw 2.425 2.520 ... (remaining 305458 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' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 902)) selection = (chain 'B' and (resid 23 through 499 or resid 509 through 696 or (resid 697 thro \ ugh 698 and (name N or name CA or name C or name O or name CB )) or resid 699 th \ rough 763 or resid 901 through 902)) selection = (chain 'C' and (resid 23 through 499 or resid 509 through 696 or (resid 697 thro \ ugh 698 and (name N or name CA or name C or name O or name CB )) or resid 699 th \ rough 763 or resid 901 through 902)) selection = (chain 'D' and (resid 23 through 499 or resid 509 through 696 or (resid 697 thro \ ugh 698 and (name N or name CA or name C or name O or name CB )) or resid 699 th \ rough 763 or resid 901 through 902)) selection = (chain 'E' and (resid 23 through 499 or resid 509 through 696 or (resid 697 thro \ ugh 698 and (name N or name CA or name C or name O or name CB )) or resid 699 th \ rough 763 or resid 901 through 902)) selection = (chain 'F' and (resid 23 through 696 or (resid 697 through 698 and (name N or na \ me CA or name C or name O or name CB )) or resid 699 through 763 or resid 901 th \ rough 902)) } 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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 15.420 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 97.760 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.160 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 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 0.112 37549 Z= 0.705 Angle : 0.854 12.374 50780 Z= 0.526 Chirality : 0.058 0.239 5734 Planarity : 0.004 0.035 6656 Dihedral : 12.235 174.283 14489 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.70 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 0.38 (0.11), residues: 4647 helix: -0.15 (0.10), residues: 2068 sheet: 0.68 (0.17), residues: 802 loop : 0.88 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 551 HIS 0.001 0.000 HIS G 215 PHE 0.002 0.000 PHE D 267 TYR 0.001 0.000 TYR C 203 ARG 0.001 0.000 ARG F 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1473 time to evaluate : 4.788 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: A 88 VAL cc_start: 0.7015 (t) cc_final: 0.5759 (t) REVERT: A 206 ILE cc_start: 0.7943 (mt) cc_final: 0.7526 (mt) REVERT: A 335 LEU cc_start: 0.7970 (mt) cc_final: 0.7405 (mt) REVERT: A 367 VAL cc_start: 0.6445 (t) cc_final: 0.6167 (t) REVERT: A 383 ILE cc_start: 0.8142 (mt) cc_final: 0.7766 (mm) REVERT: A 414 LEU cc_start: 0.8167 (mt) cc_final: 0.7859 (tp) REVERT: B 138 TYR cc_start: 0.7345 (t80) cc_final: 0.6972 (t80) REVERT: B 618 PHE cc_start: 0.6974 (t80) cc_final: 0.6518 (t80) REVERT: C 161 VAL cc_start: 0.6947 (t) cc_final: 0.6707 (t) REVERT: C 260 ASN cc_start: 0.6942 (m-40) cc_final: 0.5460 (m110) REVERT: C 373 ASP cc_start: 0.5554 (p0) cc_final: 0.5292 (p0) REVERT: C 581 SER cc_start: 0.8138 (p) cc_final: 0.7740 (t) REVERT: D 153 LEU cc_start: 0.7389 (tp) cc_final: 0.7126 (mp) REVERT: D 363 PHE cc_start: 0.6866 (m-80) cc_final: 0.6039 (m-80) REVERT: D 364 ASP cc_start: 0.6813 (p0) cc_final: 0.6370 (p0) REVERT: D 485 VAL cc_start: 0.7876 (t) cc_final: 0.7487 (t) REVERT: D 644 TYR cc_start: 0.6964 (t80) cc_final: 0.6742 (t80) REVERT: E 216 ILE cc_start: 0.8946 (mt) cc_final: 0.8735 (mt) REVERT: E 252 THR cc_start: 0.8349 (p) cc_final: 0.8090 (t) REVERT: E 268 LEU cc_start: 0.8163 (tp) cc_final: 0.7942 (tt) REVERT: E 341 VAL cc_start: 0.8234 (t) cc_final: 0.7995 (p) REVERT: E 373 ASP cc_start: 0.4585 (p0) cc_final: 0.3295 (p0) REVERT: E 456 LEU cc_start: 0.8175 (mt) cc_final: 0.7776 (mt) REVERT: E 559 VAL cc_start: 0.7183 (t) cc_final: 0.6655 (t) REVERT: E 564 ASP cc_start: 0.4591 (t70) cc_final: 0.4355 (t70) REVERT: F 335 LEU cc_start: 0.7675 (mt) cc_final: 0.6925 (mt) REVERT: F 380 ILE cc_start: 0.8583 (mt) cc_final: 0.8331 (mm) REVERT: F 432 LEU cc_start: 0.6229 (tp) cc_final: 0.5982 (tt) REVERT: G 396 ASN cc_start: 0.8239 (p0) cc_final: 0.7681 (p0) outliers start: 0 outliers final: 0 residues processed: 1473 average time/residue: 0.5560 time to fit residues: 1263.9257 Evaluate side-chains 801 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 801 time to evaluate : 3.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 0.9980 chunk 353 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 366 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 424 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN A 494 GLN A 538 ASN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 91 ASN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 GLN F 384 HIS ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37549 Z= 0.228 Angle : 0.682 13.360 50780 Z= 0.334 Chirality : 0.045 0.198 5734 Planarity : 0.005 0.069 6656 Dihedral : 9.847 171.556 5201 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.12 % Favored : 98.84 % Rotamer: Outliers : 0.20 % Allowed : 2.95 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.38 (0.12), residues: 4647 helix: 1.00 (0.11), residues: 2044 sheet: 0.77 (0.17), residues: 800 loop : 1.17 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 476 HIS 0.013 0.001 HIS E 340 PHE 0.026 0.002 PHE C 563 TYR 0.034 0.002 TYR E 495 ARG 0.022 0.001 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 972 time to evaluate : 4.771 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.7037 (t) cc_final: 0.6141 (t) REVERT: B 92 LEU cc_start: 0.7772 (mt) cc_final: 0.7515 (mt) REVERT: B 348 ASN cc_start: 0.6508 (t0) cc_final: 0.6266 (t0) REVERT: B 550 MET cc_start: 0.5445 (mmp) cc_final: 0.5207 (mmp) REVERT: B 618 PHE cc_start: 0.6989 (t80) cc_final: 0.6663 (t80) REVERT: C 53 ARG cc_start: 0.6247 (ttt90) cc_final: 0.5907 (mpt180) REVERT: C 581 SER cc_start: 0.8313 (p) cc_final: 0.7899 (t) REVERT: D 179 ASP cc_start: 0.6806 (p0) cc_final: 0.6547 (p0) REVERT: D 244 TYR cc_start: 0.6044 (p90) cc_final: 0.5658 (p90) REVERT: D 261 GLU cc_start: 0.6253 (mm-30) cc_final: 0.5883 (mm-30) REVERT: D 364 ASP cc_start: 0.6891 (p0) cc_final: 0.6621 (p0) REVERT: D 568 GLN cc_start: 0.6228 (pt0) cc_final: 0.5749 (pt0) REVERT: E 268 LEU cc_start: 0.8160 (tp) cc_final: 0.7940 (tt) REVERT: E 333 ASP cc_start: 0.7314 (m-30) cc_final: 0.7085 (m-30) REVERT: E 456 LEU cc_start: 0.8512 (mt) cc_final: 0.7993 (mt) REVERT: E 601 ILE cc_start: 0.6813 (pt) cc_final: 0.6497 (pt) REVERT: F 332 MET cc_start: 0.7472 (tpt) cc_final: 0.7114 (mmm) REVERT: F 368 ASP cc_start: 0.7182 (t0) cc_final: 0.6844 (t70) REVERT: F 619 ILE cc_start: 0.7804 (mp) cc_final: 0.7475 (mp) REVERT: G 292 PHE cc_start: 0.5995 (t80) cc_final: 0.5755 (t80) REVERT: G 397 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7745 (mp0) outliers start: 8 outliers final: 2 residues processed: 979 average time/residue: 0.5081 time to fit residues: 792.9191 Evaluate side-chains 677 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 675 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 235 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 352 optimal weight: 0.1980 chunk 288 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 424 optimal weight: 7.9990 chunk 458 optimal weight: 9.9990 chunk 378 optimal weight: 8.9990 chunk 421 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 chunk 340 optimal weight: 9.9990 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN C 458 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN C 760 GLN D 337 GLN D 384 HIS ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 760 GLN F 90 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 HIS G 273 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 37549 Z= 0.454 Angle : 0.848 12.286 50780 Z= 0.423 Chirality : 0.047 0.216 5734 Planarity : 0.006 0.071 6656 Dihedral : 9.755 179.819 5201 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.15 % Allowed : 3.89 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 0.83 (0.12), residues: 4647 helix: 0.63 (0.11), residues: 2044 sheet: 0.51 (0.17), residues: 791 loop : 0.74 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP F 454 HIS 0.013 0.002 HIS E 340 PHE 0.041 0.003 PHE E 563 TYR 0.047 0.003 TYR E 495 ARG 0.029 0.001 ARG C 638 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 746 time to evaluate : 4.706 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: A 26 LEU cc_start: 0.7246 (mt) cc_final: 0.7037 (mt) REVERT: A 88 VAL cc_start: 0.7231 (t) cc_final: 0.6651 (t) REVERT: A 332 MET cc_start: 0.6688 (tpt) cc_final: 0.6168 (tpt) REVERT: B 275 MET cc_start: 0.8231 (mmp) cc_final: 0.7770 (mmt) REVERT: B 348 ASN cc_start: 0.6856 (t0) cc_final: 0.6418 (t0) REVERT: B 618 PHE cc_start: 0.7139 (t80) cc_final: 0.6770 (t80) REVERT: D 690 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7744 (tp) REVERT: F 335 LEU cc_start: 0.8188 (mt) cc_final: 0.7639 (mt) REVERT: F 364 ASP cc_start: 0.7288 (p0) cc_final: 0.6912 (p0) REVERT: F 368 ASP cc_start: 0.7659 (t0) cc_final: 0.7344 (t0) REVERT: G 158 ILE cc_start: 0.4254 (mm) cc_final: 0.4039 (mm) REVERT: G 292 PHE cc_start: 0.6301 (t80) cc_final: 0.5956 (t80) outliers start: 6 outliers final: 2 residues processed: 752 average time/residue: 0.5027 time to fit residues: 607.4291 Evaluate side-chains 554 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 551 time to evaluate : 4.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 9.9990 chunk 319 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 chunk 426 optimal weight: 9.9990 chunk 451 optimal weight: 0.9980 chunk 222 optimal weight: 9.9990 chunk 404 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 285 ASN C 327 GLN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS D 317 HIS D 406 HIS ** D 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 HIS ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 37549 Z= 0.352 Angle : 0.726 11.749 50780 Z= 0.360 Chirality : 0.046 0.275 5734 Planarity : 0.005 0.100 6656 Dihedral : 9.424 171.743 5201 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.73 (0.12), residues: 4647 helix: 0.64 (0.11), residues: 2048 sheet: 0.44 (0.17), residues: 789 loop : 0.59 (0.15), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 476 HIS 0.014 0.002 HIS E 340 PHE 0.025 0.002 PHE E 563 TYR 0.028 0.002 TYR F 203 ARG 0.014 0.001 ARG G 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 721 time to evaluate : 4.630 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: A 88 VAL cc_start: 0.7115 (t) cc_final: 0.6136 (t) REVERT: A 380 ILE cc_start: 0.7313 (mt) cc_final: 0.6929 (tt) REVERT: B 275 MET cc_start: 0.8130 (mmp) cc_final: 0.7615 (mmt) REVERT: B 348 ASN cc_start: 0.6894 (t0) cc_final: 0.6560 (t0) REVERT: B 415 CYS cc_start: 0.6891 (p) cc_final: 0.6602 (p) REVERT: B 438 ASP cc_start: 0.6617 (t70) cc_final: 0.6088 (t70) REVERT: B 618 PHE cc_start: 0.7314 (t80) cc_final: 0.7005 (t80) REVERT: D 261 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6512 (mm-30) REVERT: D 414 LEU cc_start: 0.8373 (tp) cc_final: 0.7996 (tp) REVERT: E 601 ILE cc_start: 0.6791 (pt) cc_final: 0.6588 (pt) REVERT: F 329 LEU cc_start: 0.8061 (mt) cc_final: 0.7668 (mt) REVERT: F 332 MET cc_start: 0.7265 (tpp) cc_final: 0.7030 (tpp) REVERT: F 335 LEU cc_start: 0.8237 (mt) cc_final: 0.7760 (mt) REVERT: F 364 ASP cc_start: 0.7222 (p0) cc_final: 0.6959 (p0) REVERT: F 368 ASP cc_start: 0.7600 (t0) cc_final: 0.6768 (t0) REVERT: G 292 PHE cc_start: 0.6362 (t80) cc_final: 0.5830 (t80) outliers start: 4 outliers final: 0 residues processed: 724 average time/residue: 0.4914 time to fit residues: 573.3833 Evaluate side-chains 537 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 537 time to evaluate : 4.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 375 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 336 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 385 optimal weight: 0.0570 chunk 312 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 405 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 overall best weight: 3.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 91 ASN B 406 HIS B 473 GLN B 603 GLN C 91 ASN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN E 260 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 406 HIS F 602 ASN ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 37549 Z= 0.286 Angle : 0.683 11.002 50780 Z= 0.335 Chirality : 0.045 0.195 5734 Planarity : 0.005 0.076 6656 Dihedral : 9.182 176.748 5201 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.05 % Allowed : 2.80 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.69 (0.12), residues: 4647 helix: 0.69 (0.11), residues: 2061 sheet: 0.40 (0.17), residues: 775 loop : 0.45 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 551 HIS 0.014 0.001 HIS E 340 PHE 0.021 0.002 PHE E 230 TYR 0.044 0.002 TYR F 203 ARG 0.009 0.001 ARG G 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 722 time to evaluate : 4.360 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: B 348 ASN cc_start: 0.6778 (t0) cc_final: 0.6469 (t0) REVERT: B 415 CYS cc_start: 0.6767 (p) cc_final: 0.6566 (p) REVERT: B 488 GLU cc_start: 0.6501 (pp20) cc_final: 0.5983 (pp20) REVERT: B 618 PHE cc_start: 0.7326 (t80) cc_final: 0.7048 (t80) REVERT: C 275 MET cc_start: 0.6732 (mmt) cc_final: 0.6476 (mmm) REVERT: D 261 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6349 (mm-30) REVERT: D 275 MET cc_start: 0.7809 (mmm) cc_final: 0.6849 (mmm) REVERT: D 317 HIS cc_start: 0.6145 (p90) cc_final: 0.5765 (p-80) REVERT: D 414 LEU cc_start: 0.8359 (tp) cc_final: 0.8034 (tp) REVERT: D 420 LEU cc_start: 0.8156 (mt) cc_final: 0.7624 (mt) REVERT: E 275 MET cc_start: 0.8139 (mmm) cc_final: 0.7652 (mmm) REVERT: E 333 ASP cc_start: 0.7363 (m-30) cc_final: 0.7145 (m-30) REVERT: F 335 LEU cc_start: 0.8203 (mt) cc_final: 0.7601 (mt) REVERT: F 368 ASP cc_start: 0.7513 (t0) cc_final: 0.7255 (t0) REVERT: F 604 ILE cc_start: 0.7658 (mt) cc_final: 0.7303 (mt) REVERT: F 614 LYS cc_start: 0.8061 (pptt) cc_final: 0.7708 (ttpp) REVERT: F 634 LEU cc_start: 0.7162 (mt) cc_final: 0.6935 (mt) outliers start: 2 outliers final: 1 residues processed: 724 average time/residue: 0.4864 time to fit residues: 572.4118 Evaluate side-chains 540 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 539 time to evaluate : 4.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 151 optimal weight: 10.0000 chunk 406 optimal weight: 9.9990 chunk 89 optimal weight: 0.1980 chunk 265 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 451 optimal weight: 1.9990 chunk 375 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 237 optimal weight: 7.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS A 538 ASN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 327 GLN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 GLN C 763 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN E 260 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 602 ASN ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 37549 Z= 0.343 Angle : 0.734 10.936 50780 Z= 0.360 Chirality : 0.046 0.255 5734 Planarity : 0.005 0.064 6656 Dihedral : 8.988 179.363 5201 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.48 (0.12), residues: 4647 helix: 0.64 (0.11), residues: 2013 sheet: 0.24 (0.17), residues: 781 loop : 0.21 (0.15), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 454 HIS 0.014 0.002 HIS E 340 PHE 0.028 0.002 PHE F 131 TYR 0.028 0.002 TYR G 334 ARG 0.010 0.001 ARG G 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 694 time to evaluate : 4.297 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: A 606 THR cc_start: 0.8282 (p) cc_final: 0.7983 (p) REVERT: B 348 ASN cc_start: 0.6863 (t0) cc_final: 0.6532 (t0) REVERT: B 414 LEU cc_start: 0.8373 (tp) cc_final: 0.8141 (tt) REVERT: B 488 GLU cc_start: 0.6586 (pp20) cc_final: 0.6066 (pp20) REVERT: D 414 LEU cc_start: 0.8392 (tp) cc_final: 0.7738 (tt) REVERT: E 332 MET cc_start: 0.6775 (tpt) cc_final: 0.6490 (tpp) REVERT: E 333 ASP cc_start: 0.7401 (m-30) cc_final: 0.6900 (m-30) REVERT: E 403 THR cc_start: 0.8336 (p) cc_final: 0.8128 (p) REVERT: F 335 LEU cc_start: 0.8217 (mt) cc_final: 0.7572 (mt) REVERT: F 560 ARG cc_start: 0.6612 (ttp-110) cc_final: 0.6365 (ttm110) REVERT: F 576 PHE cc_start: 0.5880 (m-10) cc_final: 0.5551 (m-10) REVERT: F 608 MET cc_start: 0.6003 (ptp) cc_final: 0.5797 (ptt) REVERT: F 614 LYS cc_start: 0.8072 (pptt) cc_final: 0.7772 (ttpp) REVERT: F 634 LEU cc_start: 0.7225 (mt) cc_final: 0.6978 (mt) outliers start: 0 outliers final: 0 residues processed: 694 average time/residue: 0.4929 time to fit residues: 558.0957 Evaluate side-chains 512 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 435 optimal weight: 30.0000 chunk 50 optimal weight: 7.9990 chunk 257 optimal weight: 6.9990 chunk 329 optimal weight: 9.9990 chunk 255 optimal weight: 0.7980 chunk 380 optimal weight: 4.9990 chunk 252 optimal weight: 9.9990 chunk 450 optimal weight: 9.9990 chunk 281 optimal weight: 5.9990 chunk 274 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 183 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS F 404 HIS F 602 ASN ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 37549 Z= 0.351 Angle : 0.740 13.150 50780 Z= 0.367 Chirality : 0.046 0.210 5734 Planarity : 0.005 0.123 6656 Dihedral : 8.884 179.834 5201 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.30 (0.12), residues: 4647 helix: 0.57 (0.11), residues: 2008 sheet: 0.08 (0.17), residues: 793 loop : 0.05 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 454 HIS 0.014 0.002 HIS E 340 PHE 0.037 0.002 PHE F 131 TYR 0.049 0.002 TYR F 203 ARG 0.014 0.001 ARG E 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 688 time to evaluate : 4.093 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: A 332 MET cc_start: 0.6811 (tpt) cc_final: 0.6499 (tpt) REVERT: A 423 ILE cc_start: 0.7569 (tt) cc_final: 0.6814 (tt) REVERT: A 606 THR cc_start: 0.8198 (p) cc_final: 0.7967 (p) REVERT: B 153 LEU cc_start: 0.8475 (tp) cc_final: 0.7444 (tp) REVERT: B 273 GLU cc_start: 0.6947 (pt0) cc_final: 0.6482 (pt0) REVERT: B 275 MET cc_start: 0.8122 (mmp) cc_final: 0.7791 (mmt) REVERT: B 488 GLU cc_start: 0.6583 (pp20) cc_final: 0.6107 (pp20) REVERT: B 618 PHE cc_start: 0.7266 (t80) cc_final: 0.6684 (t80) REVERT: D 542 ILE cc_start: 0.8277 (mm) cc_final: 0.8072 (mm) REVERT: E 231 LYS cc_start: 0.8574 (pttm) cc_final: 0.8155 (tptt) REVERT: E 275 MET cc_start: 0.7931 (mmm) cc_final: 0.7557 (mmm) REVERT: E 307 ASP cc_start: 0.8496 (p0) cc_final: 0.8284 (p0) REVERT: E 332 MET cc_start: 0.6752 (tpt) cc_final: 0.6497 (tpp) REVERT: E 344 MET cc_start: 0.6428 (mtp) cc_final: 0.6203 (mtp) REVERT: E 606 THR cc_start: 0.8096 (p) cc_final: 0.7851 (p) REVERT: F 335 LEU cc_start: 0.8266 (mt) cc_final: 0.7604 (mt) REVERT: F 560 ARG cc_start: 0.6464 (ttp-110) cc_final: 0.6235 (ttm110) REVERT: F 634 LEU cc_start: 0.7254 (mt) cc_final: 0.6932 (mt) outliers start: 0 outliers final: 0 residues processed: 688 average time/residue: 0.4892 time to fit residues: 545.8278 Evaluate side-chains 514 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 514 time to evaluate : 4.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 278 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 268 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 286 optimal weight: 20.0000 chunk 306 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 353 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN D 406 HIS ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 602 ASN ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 37549 Z= 0.300 Angle : 0.715 12.321 50780 Z= 0.351 Chirality : 0.046 0.216 5734 Planarity : 0.005 0.071 6656 Dihedral : 8.566 178.745 5201 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.38 (0.12), residues: 4647 helix: 0.67 (0.12), residues: 2008 sheet: 0.05 (0.18), residues: 788 loop : 0.07 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 454 HIS 0.013 0.002 HIS E 340 PHE 0.038 0.002 PHE F 131 TYR 0.043 0.002 TYR E 244 ARG 0.014 0.001 ARG E 365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 679 time to evaluate : 4.378 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: A 332 MET cc_start: 0.6938 (tpt) cc_final: 0.6515 (tpt) REVERT: A 335 LEU cc_start: 0.7999 (mt) cc_final: 0.7788 (mt) REVERT: A 423 ILE cc_start: 0.7464 (tt) cc_final: 0.6749 (tt) REVERT: A 606 THR cc_start: 0.8148 (p) cc_final: 0.7838 (p) REVERT: B 198 LEU cc_start: 0.8184 (tt) cc_final: 0.7875 (tt) REVERT: B 348 ASN cc_start: 0.6788 (t0) cc_final: 0.6241 (t0) REVERT: B 363 PHE cc_start: 0.7715 (m-80) cc_final: 0.7505 (m-80) REVERT: B 488 GLU cc_start: 0.6566 (pp20) cc_final: 0.6085 (pp20) REVERT: B 618 PHE cc_start: 0.7336 (t80) cc_final: 0.6733 (t80) REVERT: C 633 ILE cc_start: 0.7596 (mt) cc_final: 0.7378 (mt) REVERT: D 414 LEU cc_start: 0.8368 (tp) cc_final: 0.7673 (tt) REVERT: E 231 LYS cc_start: 0.8437 (pttm) cc_final: 0.8173 (tptt) REVERT: E 275 MET cc_start: 0.7969 (mmm) cc_final: 0.7499 (mmm) REVERT: E 332 MET cc_start: 0.6713 (tpt) cc_final: 0.6489 (tpp) REVERT: E 344 MET cc_start: 0.6274 (mtp) cc_final: 0.6026 (mtp) REVERT: F 335 LEU cc_start: 0.8296 (mt) cc_final: 0.7568 (mt) REVERT: F 364 ASP cc_start: 0.7296 (p0) cc_final: 0.7078 (p0) REVERT: F 560 ARG cc_start: 0.6615 (ttp-110) cc_final: 0.6273 (ttm110) REVERT: F 576 PHE cc_start: 0.6013 (m-10) cc_final: 0.5680 (m-10) REVERT: F 614 LYS cc_start: 0.7982 (pptt) cc_final: 0.7642 (ttpp) REVERT: F 634 LEU cc_start: 0.7192 (mt) cc_final: 0.6918 (mt) outliers start: 0 outliers final: 0 residues processed: 679 average time/residue: 0.4865 time to fit residues: 540.3815 Evaluate side-chains 504 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 409 optimal weight: 0.0980 chunk 431 optimal weight: 3.9990 chunk 393 optimal weight: 5.9990 chunk 419 optimal weight: 7.9990 chunk 252 optimal weight: 10.0000 chunk 182 optimal weight: 0.0570 chunk 329 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 379 optimal weight: 4.9990 chunk 396 optimal weight: 6.9990 chunk 417 optimal weight: 1.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN D 602 ASN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN F 183 HIS ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 602 ASN ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 37549 Z= 0.194 Angle : 0.686 11.639 50780 Z= 0.332 Chirality : 0.046 0.211 5734 Planarity : 0.004 0.073 6656 Dihedral : 8.164 176.069 5201 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 0.67 (0.12), residues: 4647 helix: 0.90 (0.12), residues: 2024 sheet: 0.17 (0.18), residues: 793 loop : 0.25 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 454 HIS 0.009 0.001 HIS E 340 PHE 0.029 0.002 PHE F 563 TYR 0.049 0.002 TYR E 203 ARG 0.009 0.000 ARG G 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 707 time to evaluate : 4.740 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: A 423 ILE cc_start: 0.7366 (tt) cc_final: 0.6754 (tt) REVERT: A 606 THR cc_start: 0.8160 (p) cc_final: 0.7752 (p) REVERT: B 88 VAL cc_start: 0.7264 (t) cc_final: 0.6844 (t) REVERT: B 123 VAL cc_start: 0.8507 (m) cc_final: 0.8270 (p) REVERT: B 198 LEU cc_start: 0.8067 (tt) cc_final: 0.7808 (tt) REVERT: B 219 MET cc_start: 0.6669 (mtt) cc_final: 0.6404 (mtp) REVERT: B 440 GLU cc_start: 0.7435 (pm20) cc_final: 0.7128 (pm20) REVERT: B 488 GLU cc_start: 0.6354 (pp20) cc_final: 0.5863 (pp20) REVERT: B 618 PHE cc_start: 0.7151 (t80) cc_final: 0.6754 (t80) REVERT: D 268 LEU cc_start: 0.8420 (tp) cc_final: 0.8197 (tt) REVERT: D 275 MET cc_start: 0.7737 (mmm) cc_final: 0.7196 (mmp) REVERT: D 420 LEU cc_start: 0.7938 (mt) cc_final: 0.7422 (mt) REVERT: E 231 LYS cc_start: 0.8299 (pttm) cc_final: 0.8001 (tptt) REVERT: E 275 MET cc_start: 0.7989 (mmm) cc_final: 0.7388 (mmm) REVERT: F 335 LEU cc_start: 0.8296 (mt) cc_final: 0.7567 (mt) REVERT: F 560 ARG cc_start: 0.6477 (ttp-110) cc_final: 0.6124 (ttm110) REVERT: F 614 LYS cc_start: 0.7877 (pptt) cc_final: 0.7535 (ttpp) REVERT: G 339 LEU cc_start: 0.8374 (mt) cc_final: 0.8168 (mt) outliers start: 0 outliers final: 0 residues processed: 707 average time/residue: 0.4823 time to fit residues: 559.5648 Evaluate side-chains 541 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 4.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 275 optimal weight: 5.9990 chunk 443 optimal weight: 20.0000 chunk 270 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 308 optimal weight: 0.7980 chunk 465 optimal weight: 8.9990 chunk 428 optimal weight: 10.0000 chunk 370 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN A 538 ASN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 602 ASN ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.7157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 37549 Z= 0.279 Angle : 0.721 10.779 50780 Z= 0.352 Chirality : 0.046 0.259 5734 Planarity : 0.005 0.072 6656 Dihedral : 8.078 176.617 5201 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 0.45 (0.12), residues: 4647 helix: 0.74 (0.12), residues: 2017 sheet: 0.10 (0.18), residues: 792 loop : 0.10 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 454 HIS 0.011 0.001 HIS E 340 PHE 0.029 0.002 PHE F 563 TYR 0.031 0.002 TYR G 334 ARG 0.010 0.001 ARG G 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 671 time to evaluate : 4.587 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: A 244 TYR cc_start: 0.5177 (p90) cc_final: 0.4780 (p90) REVERT: A 423 ILE cc_start: 0.7437 (tt) cc_final: 0.6699 (tt) REVERT: A 606 THR cc_start: 0.8170 (p) cc_final: 0.7749 (p) REVERT: B 198 LEU cc_start: 0.8166 (tt) cc_final: 0.7560 (tt) REVERT: B 488 GLU cc_start: 0.6406 (pp20) cc_final: 0.5928 (pp20) REVERT: B 618 PHE cc_start: 0.7246 (t80) cc_final: 0.6753 (t80) REVERT: C 633 ILE cc_start: 0.7617 (mt) cc_final: 0.7366 (mt) REVERT: D 268 LEU cc_start: 0.8490 (tp) cc_final: 0.8267 (tt) REVERT: D 275 MET cc_start: 0.7883 (mmm) cc_final: 0.7106 (mmm) REVERT: D 414 LEU cc_start: 0.8310 (tp) cc_final: 0.7819 (tt) REVERT: D 420 LEU cc_start: 0.7938 (mt) cc_final: 0.7498 (mt) REVERT: E 231 LYS cc_start: 0.8390 (pttm) cc_final: 0.8120 (tptt) REVERT: E 275 MET cc_start: 0.7988 (mmm) cc_final: 0.7460 (mmm) REVERT: E 344 MET cc_start: 0.6269 (mtp) cc_final: 0.6067 (mtp) REVERT: F 335 LEU cc_start: 0.8309 (mt) cc_final: 0.7572 (mt) REVERT: F 560 ARG cc_start: 0.6487 (ttp-110) cc_final: 0.6266 (ttm110) REVERT: F 608 MET cc_start: 0.6240 (ptp) cc_final: 0.5987 (ptp) REVERT: F 614 LYS cc_start: 0.7898 (pptt) cc_final: 0.7593 (ttpp) outliers start: 0 outliers final: 0 residues processed: 671 average time/residue: 0.4772 time to fit residues: 524.4129 Evaluate side-chains 501 residues out of total 3982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 4.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 294 optimal weight: 2.9990 chunk 394 optimal weight: 0.0980 chunk 113 optimal weight: 1.9990 chunk 341 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 371 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 381 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 340 HIS ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 ASN D 602 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 602 ASN ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.086471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.063553 restraints weight = 161906.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.065386 restraints weight = 99463.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.066659 restraints weight = 70796.827| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37549 Z= 0.193 Angle : 0.681 10.868 50780 Z= 0.329 Chirality : 0.046 0.203 5734 Planarity : 0.004 0.069 6656 Dihedral : 7.812 178.277 5201 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 0.62 (0.13), residues: 4647 helix: 0.80 (0.12), residues: 2047 sheet: 0.13 (0.18), residues: 781 loop : 0.30 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 454 HIS 0.009 0.001 HIS E 340 PHE 0.041 0.002 PHE C 363 TYR 0.028 0.002 TYR G 334 ARG 0.019 0.000 ARG E 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10564.61 seconds wall clock time: 191 minutes 7.76 seconds (11467.76 seconds total)