Starting phenix.real_space_refine on Thu Feb 22 14:31:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fct_28992/02_2024/8fct_28992_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fct_28992/02_2024/8fct_28992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fct_28992/02_2024/8fct_28992.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fct_28992/02_2024/8fct_28992.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fct_28992/02_2024/8fct_28992_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fct_28992/02_2024/8fct_28992_updated.pdb" } resolution = 3.42 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= -0.002 sd= 0.030 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 180 5.16 5 C 21517 2.51 5 N 6036 2.21 5 O 6572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 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 "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "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 PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C 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 267": "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 PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "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 PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34329 Number of models: 1 Model: "" Number of chains: 13 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: "A" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "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: "G" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 240 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 38} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 6 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: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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} Time building chain proxies: 18.08, per 1000 atoms: 0.53 Number of scatterers: 34329 At special positions: 0 Unit cell: (180.978, 168.468, 101.748, 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 180 16.00 P 24 15.00 O 6572 8.00 N 6036 7.00 C 21517 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: 11.99 Conformation dependent library (CDL) restraints added in 5.7 seconds 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 219 helices and 30 sheets defined 43.4% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.45 Creating SS restraints... 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: 4.728A 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 removed outlier: 3.740A pdb=" N LYS F 231 " --> pdb=" O ALA F 228 " (cutoff:3.500A) 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 removed outlier: 3.587A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) 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: 3.644A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LYS F 336 " --> pdb=" O MET F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 430 removed outlier: 3.508A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 4.608A 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 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 Processing helix chain 'F' and resid 579 through 585 removed outlier: 4.260A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS F 584 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 610 removed outlier: 3.826A 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 663 removed outlier: 5.107A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) 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: 3.531A 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 '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: 4.553A 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 removed outlier: 3.664A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' 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: 3.650A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.834A 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 430 removed outlier: 4.285A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) 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 removed outlier: 3.579A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 660 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 706 removed outlier: 3.937A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.717A 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 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: 4.665A 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 231 Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 282 through 295 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' 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: 3.596A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 430 removed outlier: 4.176A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) 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: 3.504A 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 581 through 585 Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 660 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.727A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.799A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 removed outlier: 3.556A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 86 through 91 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: 4.610A 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 removed outlier: 3.528A pdb=" N ALA C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 282 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: 3.599A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 4.897A 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 383 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 430 removed outlier: 4.526A 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 removed outlier: 3.535A pdb=" N PHE C 563 " --> pdb=" O ARG C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.682A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.728A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 761 removed outlier: 4.107A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) 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: 4.632A 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 removed outlier: 3.866A pdb=" N ALA D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.503A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' 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: 3.589A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 4.819A 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: 4.289A 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 660 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.742A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.706A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 761 removed outlier: 3.506A 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 91 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 139 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: 4.430A 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 231 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 282 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: 3.598A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 385 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 430 removed outlier: 4.088A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 492 Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 524 through 534 removed outlier: 3.538A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 removed outlier: 3.559A pdb=" N PHE E 563 " --> pdb=" O ARG E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 613 through 615 No H-bonds generated for 'chain 'E' and resid 613 through 615' Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 660 Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 706 removed outlier: 3.783A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.772A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 761 Processing helix chain 'G' and resid 50 through 67 Processing helix chain 'G' and resid 76 through 92 Processing sheet with id= A, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.480A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 181 through 183 removed outlier: 6.760A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= D, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.831A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 641 through 644 removed outlier: 8.559A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 81 through 84 removed outlier: 8.008A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP A 74 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.865A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= I, first strand: chain 'A' and resid 365 through 368 removed outlier: 3.590A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 469 through 471 removed outlier: 6.558A pdb=" N GLN A 641 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N TYR A 517 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 643 " --> pdb=" O TYR A 517 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 81 through 84 removed outlier: 7.936A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP B 74 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.575A pdb=" N GLU B 167 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= N, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.668A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.639A 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= O, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.658A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 81 through 84 removed outlier: 7.958A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C 74 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.537A pdb=" N GLU C 167 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= S, first strand: chain 'C' and resid 365 through 368 removed outlier: 3.617A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 641 through 645 removed outlier: 4.017A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 81 through 84 removed outlier: 7.945A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP D 74 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.773A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= X, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.760A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.653A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 81 through 84 removed outlier: 7.943A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP E 74 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.514A pdb=" N GLU E 167 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= AC, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.715A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.680A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) 1202 hydrogen bonds defined for protein. 3360 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: 12.15 Time building geometry restraints manager: 12.88 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: 7024 1.33 - 1.45: 7281 1.45 - 1.57: 20270 1.57 - 1.69: 36 1.69 - 1.81: 288 Bond restraints: 34899 Sorted by residual: bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.09e+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 3.07e+01 bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 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 ... (remaining 34894 not shown) Histogram of bond angle deviations from ideal: 100.85 - 107.86: 1444 107.86 - 114.87: 20881 114.87 - 121.88: 17799 121.88 - 128.89: 6920 128.89 - 135.90: 158 Bond angle restraints: 47202 Sorted by residual: angle pdb=" N ILE E 590 " pdb=" CA ILE E 590 " pdb=" C ILE E 590 " ideal model delta sigma weight residual 111.67 106.68 4.99 9.50e-01 1.11e+00 2.76e+01 angle pdb=" N ILE C 590 " pdb=" CA ILE C 590 " pdb=" C ILE C 590 " ideal model delta sigma weight residual 111.67 106.68 4.99 9.50e-01 1.11e+00 2.76e+01 angle pdb=" N ILE D 590 " pdb=" CA ILE D 590 " pdb=" C ILE D 590 " ideal model delta sigma weight residual 111.67 106.70 4.97 9.50e-01 1.11e+00 2.74e+01 angle pdb=" N ILE A 590 " pdb=" CA ILE A 590 " pdb=" C ILE A 590 " ideal model delta sigma weight residual 111.67 106.72 4.95 9.50e-01 1.11e+00 2.72e+01 angle pdb=" N ILE B 590 " pdb=" CA ILE B 590 " pdb=" C ILE B 590 " ideal model delta sigma weight residual 111.67 106.72 4.95 9.50e-01 1.11e+00 2.71e+01 ... (remaining 47197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.72: 21268 32.72 - 65.44: 272 65.44 - 98.16: 42 98.16 - 130.88: 18 130.88 - 163.60: 6 Dihedral angle restraints: 21606 sinusoidal: 9061 harmonic: 12545 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 300.00 136.40 163.60 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O2A ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PA ADP F 901 " pdb=" PB ADP F 901 " ideal model delta sinusoidal sigma weight residual 300.00 153.24 146.76 1 2.00e+01 2.50e-03 4.41e+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 300.00 160.01 139.99 1 2.00e+01 2.50e-03 4.24e+01 ... (remaining 21603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3828 0.048 - 0.095: 890 0.095 - 0.143: 460 0.143 - 0.191: 147 0.191 - 0.239: 12 Chirality restraints: 5337 Sorted by residual: 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 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE E 590 " pdb=" N ILE E 590 " pdb=" C ILE E 590 " pdb=" CB ILE E 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+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 1.41e+00 ... (remaining 5334 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN G 82 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.07e+00 pdb=" C GLN G 82 " -0.043 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 F 534 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C GLU F 534 " -0.039 2.00e-02 2.50e+03 pdb=" O GLU F 534 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS F 535 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 360 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C PHE F 360 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE F 360 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY F 361 " 0.013 2.00e-02 2.50e+03 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 14080 2.92 - 3.42: 33773 3.42 - 3.91: 59225 3.91 - 4.41: 66197 4.41 - 4.90: 106523 Nonbonded interactions: 279798 Sorted by model distance: nonbonded pdb=" OD2 ASP D 368 " pdb=" NZ LYS D 565 " model vdw 2.429 2.520 nonbonded pdb=" NZ LYS F 512 " pdb=" O GLY F 637 " model vdw 2.453 2.520 nonbonded pdb=" OD2 ASP D 580 " pdb=" NZ LYS D 584 " model vdw 2.454 2.520 nonbonded pdb=" NZ LYS C 112 " pdb=" OD2 ASP C 179 " model vdw 2.459 2.520 nonbonded pdb=" NZ LYS C 63 " pdb=" OE1 GLU C 194 " model vdw 2.464 2.520 ... (remaining 279793 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 763 or resid 901 throu \ gh 902)) selection = (chain 'C' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 902)) selection = (chain 'D' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 902)) selection = (chain 'E' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 902)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.190 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 84.400 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.120 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 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 34899 Z= 0.707 Angle : 0.815 12.438 47202 Z= 0.489 Chirality : 0.058 0.239 5337 Planarity : 0.003 0.029 6186 Dihedral : 12.054 163.600 13468 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.34 % Favored : 98.52 % Rotamer: Outliers : 0.05 % Allowed : 0.30 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 0.46 (0.12), residues: 4326 helix: -0.14 (0.10), residues: 1911 sheet: 0.74 (0.17), residues: 749 loop : 0.99 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 551 HIS 0.001 0.000 HIS F 735 PHE 0.001 0.000 PHE B 758 TYR 0.001 0.000 TYR D 755 ARG 0.001 0.000 ARG F 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 791 time to evaluate : 4.023 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: E 508 MET cc_start: -0.0799 (ttt) cc_final: -0.3105 (mtt) outliers start: 2 outliers final: 0 residues processed: 793 average time/residue: 0.5679 time to fit residues: 671.6936 Evaluate side-chains 374 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 366 optimal weight: 3.9990 chunk 328 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 340 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 206 optimal weight: 0.9990 chunk 253 optimal weight: 0.9990 chunk 394 optimal weight: 0.9980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 421 GLN B 340 HIS B 660 ASN C 568 GLN D 406 HIS D 660 ASN E 43 GLN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS E 660 ASN E 680 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34899 Z= 0.211 Angle : 0.668 8.384 47202 Z= 0.321 Chirality : 0.045 0.171 5337 Planarity : 0.005 0.069 6186 Dihedral : 9.133 161.890 4846 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.20 % Favored : 98.77 % Rotamer: Outliers : 1.44 % Allowed : 8.01 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.62 (0.13), residues: 4326 helix: 1.13 (0.11), residues: 1929 sheet: 0.86 (0.18), residues: 739 loop : 1.40 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 454 HIS 0.005 0.001 HIS A 499 PHE 0.030 0.001 PHE A 674 TYR 0.022 0.002 TYR A 495 ARG 0.009 0.001 ARG C 560 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 410 time to evaluate : 4.344 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: F 550 MET cc_start: 0.4612 (mmp) cc_final: 0.4038 (mtm) REVERT: E 508 MET cc_start: -0.0745 (ttt) cc_final: -0.3200 (mmt) outliers start: 53 outliers final: 25 residues processed: 443 average time/residue: 0.4870 time to fit residues: 343.6127 Evaluate side-chains 353 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 328 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 619 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 219 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 328 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 394 optimal weight: 9.9990 chunk 426 optimal weight: 3.9990 chunk 351 optimal weight: 0.5980 chunk 391 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 316 optimal weight: 0.0060 overall best weight: 3.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 GLN F 340 HIS A 285 ASN A 327 GLN A 558 ASN B 660 ASN C 406 HIS C 421 GLN C 660 ASN D 317 HIS ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS E 760 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5741 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34899 Z= 0.284 Angle : 0.677 11.310 47202 Z= 0.322 Chirality : 0.045 0.157 5337 Planarity : 0.004 0.053 6186 Dihedral : 8.527 162.950 4846 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.44 % Allowed : 8.61 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.78 (0.13), residues: 4326 helix: 1.42 (0.12), residues: 1937 sheet: 0.78 (0.18), residues: 744 loop : 1.36 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 551 HIS 0.005 0.001 HIS E 226 PHE 0.038 0.002 PHE A 674 TYR 0.032 0.002 TYR A 203 ARG 0.013 0.001 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 331 time to evaluate : 4.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 550 MET cc_start: 0.4565 (mmp) cc_final: 0.4124 (mtm) REVERT: E 508 MET cc_start: -0.0464 (ttt) cc_final: -0.3136 (mmt) REVERT: G 50 ASN cc_start: 0.7350 (t0) cc_final: 0.7004 (t0) outliers start: 53 outliers final: 33 residues processed: 368 average time/residue: 0.4961 time to fit residues: 293.2885 Evaluate side-chains 321 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 288 time to evaluate : 3.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 619 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 390 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 204 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 188 optimal weight: 0.0870 chunk 265 optimal weight: 4.9990 chunk 396 optimal weight: 10.0000 chunk 419 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 375 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 ASN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34899 Z= 0.174 Angle : 0.630 9.883 47202 Z= 0.294 Chirality : 0.044 0.148 5337 Planarity : 0.004 0.045 6186 Dihedral : 8.012 160.630 4846 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.33 % Allowed : 9.20 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.92 (0.13), residues: 4326 helix: 1.59 (0.12), residues: 1924 sheet: 0.87 (0.18), residues: 741 loop : 1.33 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 551 HIS 0.006 0.001 HIS E 226 PHE 0.015 0.001 PHE D 139 TYR 0.027 0.001 TYR A 203 ARG 0.008 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 332 time to evaluate : 4.227 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: F 550 MET cc_start: 0.4536 (mmp) cc_final: 0.4151 (mtm) REVERT: A 230 PHE cc_start: 0.6184 (m-80) cc_final: 0.5859 (m-80) REVERT: A 611 MET cc_start: 0.4876 (tpp) cc_final: 0.4486 (mtt) REVERT: E 305 GLU cc_start: 0.6074 (mp0) cc_final: 0.5217 (mp0) REVERT: E 508 MET cc_start: -0.0398 (ttt) cc_final: -0.3000 (mmt) outliers start: 49 outliers final: 30 residues processed: 367 average time/residue: 0.4628 time to fit residues: 276.1057 Evaluate side-chains 325 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 295 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 619 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 349 optimal weight: 5.9990 chunk 238 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 312 optimal weight: 0.0980 chunk 173 optimal weight: 7.9990 chunk 357 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 376 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 HIS E 340 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34899 Z= 0.258 Angle : 0.659 11.206 47202 Z= 0.310 Chirality : 0.044 0.143 5337 Planarity : 0.004 0.053 6186 Dihedral : 7.668 158.547 4846 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.41 % Allowed : 9.69 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.92 (0.13), residues: 4326 helix: 1.66 (0.12), residues: 1904 sheet: 0.92 (0.18), residues: 743 loop : 1.21 (0.16), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 454 HIS 0.005 0.001 HIS E 226 PHE 0.026 0.001 PHE E 674 TYR 0.032 0.002 TYR B 138 ARG 0.007 0.000 ARG E 560 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 288 time to evaluate : 5.188 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: F 550 MET cc_start: 0.4668 (mmp) cc_final: 0.4046 (mtm) REVERT: E 508 MET cc_start: -0.0250 (ttt) cc_final: -0.2967 (mmt) outliers start: 52 outliers final: 41 residues processed: 329 average time/residue: 0.4771 time to fit residues: 257.2176 Evaluate side-chains 306 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 265 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain G residue 49 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 7.9990 chunk 377 optimal weight: 6.9990 chunk 82 optimal weight: 0.0370 chunk 246 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 419 optimal weight: 9.9990 chunk 348 optimal weight: 0.0970 chunk 194 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 overall best weight: 2.8262 ------------------------------------------------------------------------------- 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** B 602 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34899 Z= 0.251 Angle : 0.668 11.330 47202 Z= 0.312 Chirality : 0.044 0.260 5337 Planarity : 0.004 0.048 6186 Dihedral : 7.408 154.735 4846 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.47 % Allowed : 10.43 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.90 (0.13), residues: 4326 helix: 1.67 (0.12), residues: 1904 sheet: 0.93 (0.18), residues: 744 loop : 1.15 (0.16), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 551 HIS 0.004 0.001 HIS B 183 PHE 0.037 0.001 PHE E 363 TYR 0.026 0.001 TYR B 138 ARG 0.011 0.001 ARG E 560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 279 time to evaluate : 3.896 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: F 550 MET cc_start: 0.4659 (mmp) cc_final: 0.4101 (mtm) REVERT: F 634 LEU cc_start: 0.0910 (OUTLIER) cc_final: 0.0443 (pp) REVERT: A 611 MET cc_start: 0.4898 (tpp) cc_final: 0.4506 (mtt) REVERT: C 351 ASN cc_start: 0.6223 (p0) cc_final: 0.5375 (p0) REVERT: E 508 MET cc_start: -0.0211 (ttt) cc_final: -0.3031 (mmt) outliers start: 54 outliers final: 44 residues processed: 320 average time/residue: 0.4649 time to fit residues: 242.1685 Evaluate side-chains 302 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 257 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 619 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 404 optimal weight: 7.9990 chunk 47 optimal weight: 40.0000 chunk 239 optimal weight: 7.9990 chunk 306 optimal weight: 0.9980 chunk 237 optimal weight: 0.5980 chunk 353 optimal weight: 5.9990 chunk 234 optimal weight: 0.7980 chunk 418 optimal weight: 0.0370 chunk 261 optimal weight: 0.7980 chunk 255 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN C 660 ASN D 43 GLN E 43 GLN E 351 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5746 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34899 Z= 0.158 Angle : 0.646 11.496 47202 Z= 0.300 Chirality : 0.044 0.167 5337 Planarity : 0.004 0.046 6186 Dihedral : 7.226 152.752 4846 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.14 % Allowed : 11.21 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.94 (0.13), residues: 4326 helix: 1.72 (0.12), residues: 1904 sheet: 0.99 (0.19), residues: 731 loop : 1.13 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 454 HIS 0.004 0.001 HIS A 499 PHE 0.026 0.001 PHE A 674 TYR 0.020 0.001 TYR C 203 ARG 0.008 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 280 time to evaluate : 4.344 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: F 550 MET cc_start: 0.4596 (mmp) cc_final: 0.4119 (mtm) REVERT: F 634 LEU cc_start: 0.0879 (OUTLIER) cc_final: 0.0415 (pp) REVERT: A 611 MET cc_start: 0.4760 (tpp) cc_final: 0.4489 (mtt) REVERT: E 315 LYS cc_start: 0.5568 (pttp) cc_final: 0.5275 (pttm) REVERT: E 508 MET cc_start: -0.0115 (ttt) cc_final: -0.2933 (mmt) outliers start: 42 outliers final: 34 residues processed: 314 average time/residue: 0.4671 time to fit residues: 239.6597 Evaluate side-chains 295 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 260 time to evaluate : 4.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 619 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 258 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 249 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 284 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 328 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 ASN D 43 GLN D 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34899 Z= 0.303 Angle : 0.692 11.083 47202 Z= 0.325 Chirality : 0.044 0.166 5337 Planarity : 0.004 0.046 6186 Dihedral : 7.176 149.488 4846 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.41 % Allowed : 11.32 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.86 (0.13), residues: 4326 helix: 1.69 (0.12), residues: 1908 sheet: 0.92 (0.19), residues: 740 loop : 1.05 (0.16), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 454 HIS 0.005 0.001 HIS A 499 PHE 0.019 0.001 PHE A 674 TYR 0.024 0.002 TYR C 517 ARG 0.018 0.001 ARG E 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 249 time to evaluate : 4.422 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: F 550 MET cc_start: 0.4748 (mmp) cc_final: 0.4155 (mtm) REVERT: F 634 LEU cc_start: 0.0926 (OUTLIER) cc_final: 0.0474 (pp) REVERT: E 508 MET cc_start: -0.0219 (ttt) cc_final: -0.3183 (mmt) REVERT: E 611 MET cc_start: 0.5685 (tpp) cc_final: 0.5453 (tpt) outliers start: 52 outliers final: 44 residues processed: 289 average time/residue: 0.4526 time to fit residues: 216.8865 Evaluate side-chains 281 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 236 time to evaluate : 3.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 740 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 380 optimal weight: 20.0000 chunk 400 optimal weight: 0.4980 chunk 365 optimal weight: 4.9990 chunk 389 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 306 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 368 optimal weight: 5.9990 chunk 388 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34899 Z= 0.221 Angle : 0.664 11.995 47202 Z= 0.309 Chirality : 0.044 0.160 5337 Planarity : 0.004 0.046 6186 Dihedral : 7.023 145.306 4846 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.28 % Allowed : 11.62 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.89 (0.13), residues: 4326 helix: 1.76 (0.12), residues: 1886 sheet: 0.92 (0.19), residues: 753 loop : 1.04 (0.16), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 454 HIS 0.004 0.001 HIS A 499 PHE 0.020 0.001 PHE A 674 TYR 0.024 0.001 TYR C 517 ARG 0.027 0.000 ARG E 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 256 time to evaluate : 3.620 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: F 550 MET cc_start: 0.4863 (mmp) cc_final: 0.4248 (mtm) REVERT: F 634 LEU cc_start: 0.0972 (OUTLIER) cc_final: 0.0516 (pp) REVERT: A 611 MET cc_start: 0.4914 (tpp) cc_final: 0.4520 (mtt) REVERT: E 508 MET cc_start: 0.0017 (ttt) cc_final: -0.2855 (mmt) outliers start: 47 outliers final: 43 residues processed: 291 average time/residue: 0.4358 time to fit residues: 208.8494 Evaluate side-chains 284 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 240 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 255 optimal weight: 0.9990 chunk 412 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 286 optimal weight: 0.9980 chunk 432 optimal weight: 1.9990 chunk 397 optimal weight: 0.2980 chunk 344 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5779 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34899 Z= 0.170 Angle : 0.669 12.886 47202 Z= 0.308 Chirality : 0.044 0.182 5337 Planarity : 0.004 0.047 6186 Dihedral : 6.839 142.685 4846 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.22 % Allowed : 11.70 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.97 (0.13), residues: 4326 helix: 1.82 (0.12), residues: 1878 sheet: 0.96 (0.19), residues: 753 loop : 1.09 (0.16), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 454 HIS 0.004 0.001 HIS A 499 PHE 0.021 0.001 PHE A 674 TYR 0.029 0.001 TYR C 517 ARG 0.017 0.000 ARG E 560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 264 time to evaluate : 4.331 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: F 550 MET cc_start: 0.4853 (mmp) cc_final: 0.4274 (mtm) REVERT: F 634 LEU cc_start: 0.1039 (OUTLIER) cc_final: 0.0610 (pp) REVERT: F 740 MET cc_start: 0.2820 (mmm) cc_final: 0.2485 (mmm) REVERT: A 515 LEU cc_start: 0.6345 (tt) cc_final: 0.6095 (tp) REVERT: A 611 MET cc_start: 0.4778 (tpp) cc_final: 0.4462 (mtt) REVERT: E 508 MET cc_start: 0.0125 (ttt) cc_final: -0.2832 (mmt) outliers start: 45 outliers final: 36 residues processed: 297 average time/residue: 0.4443 time to fit residues: 218.8243 Evaluate side-chains 291 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 254 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 273 optimal weight: 6.9990 chunk 366 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 chunk 50 optimal weight: 30.0000 chunk 95 optimal weight: 0.7980 chunk 344 optimal weight: 0.9980 chunk 144 optimal weight: 0.0070 chunk 354 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 421 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.079787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.053914 restraints weight = 135313.517| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 6.20 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34899 Z= 0.189 Angle : 0.668 12.817 47202 Z= 0.309 Chirality : 0.044 0.170 5337 Planarity : 0.004 0.048 6186 Dihedral : 6.716 140.001 4846 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.06 % Allowed : 11.97 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.97 (0.13), residues: 4326 helix: 1.81 (0.12), residues: 1878 sheet: 0.97 (0.19), residues: 753 loop : 1.10 (0.16), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 454 HIS 0.004 0.001 HIS A 499 PHE 0.019 0.001 PHE A 674 TYR 0.031 0.001 TYR C 517 ARG 0.017 0.000 ARG E 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7077.85 seconds wall clock time: 129 minutes 38.57 seconds (7778.57 seconds total)