Starting phenix.real_space_refine on Thu Feb 22 18:39:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgr_25116/02_2024/7sgr_25116_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgr_25116/02_2024/7sgr_25116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgr_25116/02_2024/7sgr_25116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgr_25116/02_2024/7sgr_25116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgr_25116/02_2024/7sgr_25116_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgr_25116/02_2024/7sgr_25116_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.104 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 6 5.49 5 S 80 5.16 5 C 22817 2.51 5 N 5907 2.21 5 O 6179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34989 Number of models: 1 Model: "" Number of chains: 21 Chain: "J" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4505 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 552} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 5549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5549 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 679} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 5543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5543 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 679} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4509 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 17, 'TRANS': 552} Chain: "E" Number of atoms: 5535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5535 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 679} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4509 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 17, 'TRANS': 552} Chain: "H" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "L" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "D" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "C" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1035 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "G" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1026 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 131 Chain: "K" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "J" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 82 Unusual residues: {'6OU': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'6OU:plan-1': 4, '6OU:plan-2': 6, '6OU:plan-3': 6} Unresolved non-hydrogen planarities: 60 Chain: "I" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 131 Unusual residues: {'6OU': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'6OU:plan-1': 7, '6OU:plan-2': 8, '6OU:plan-3': 8} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Unusual residues: {'6OU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'6OU:plan-1': 6, '6OU:plan-2': 3, '6OU:plan-3': 3} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'6OU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 2, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Unusual residues: {'6OU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'6OU:plan-1': 4, '6OU:plan-2': 4, '6OU:plan-3': 4} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'6OU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 2, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'6OU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'6OU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 2, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 19.26, per 1000 atoms: 0.55 Number of scatterers: 34989 At special positions: 0 Unit cell: (146.59, 149.8, 173.34, 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 80 16.00 P 6 15.00 O 6179 8.00 N 5907 7.00 C 22817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.78 Conformation dependent library (CDL) restraints added in 6.8 seconds 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 175 helices and 22 sheets defined 58.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.75 Creating SS restraints... Processing helix chain 'J' and resid 142 through 149 removed outlier: 4.015A pdb=" N ALA J 146 " --> pdb=" O TRP J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 181 removed outlier: 4.074A pdb=" N GLU J 156 " --> pdb=" O LYS J 152 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR J 171 " --> pdb=" O PHE J 167 " (cutoff:3.500A) Proline residue: J 172 - end of helix Processing helix chain 'J' and resid 189 through 236 removed outlier: 3.616A pdb=" N VAL J 200 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG J 222 " --> pdb=" O HIS J 218 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 244 Processing helix chain 'J' and resid 248 through 265 removed outlier: 4.126A pdb=" N LEU J 258 " --> pdb=" O ARG J 254 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP J 259 " --> pdb=" O VAL J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 277 Processing helix chain 'J' and resid 280 through 289 Processing helix chain 'J' and resid 291 through 338 Proline residue: J 302 - end of helix Proline residue: J 313 - end of helix Processing helix chain 'J' and resid 340 through 345 Processing helix chain 'J' and resid 350 through 401 Processing helix chain 'J' and resid 407 through 428 Proline residue: J 423 - end of helix Processing helix chain 'J' and resid 431 through 448 Processing helix chain 'J' and resid 508 through 515 removed outlier: 3.597A pdb=" N LEU J 511 " --> pdb=" O LYS J 508 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR J 512 " --> pdb=" O SER J 509 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE J 515 " --> pdb=" O THR J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 544 Processing helix chain 'J' and resid 559 through 563 Processing helix chain 'J' and resid 572 through 581 Processing helix chain 'J' and resid 584 through 589 Processing helix chain 'J' and resid 594 through 596 No H-bonds generated for 'chain 'J' and resid 594 through 596' Processing helix chain 'J' and resid 608 through 621 Processing helix chain 'J' and resid 638 through 646 Processing helix chain 'J' and resid 648 through 651 No H-bonds generated for 'chain 'J' and resid 648 through 651' Processing helix chain 'J' and resid 687 through 691 Processing helix chain 'J' and resid 697 through 705 Processing helix chain 'I' and resid 9 through 20 Processing helix chain 'I' and resid 27 through 34 Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 66 through 69 Processing helix chain 'I' and resid 111 through 117 Processing helix chain 'I' and resid 140 through 149 Proline residue: I 145 - end of helix Processing helix chain 'I' and resid 151 through 181 Proline residue: I 172 - end of helix removed outlier: 3.907A pdb=" N PHE I 175 " --> pdb=" O THR I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 236 removed outlier: 3.597A pdb=" N VAL I 193 " --> pdb=" O SER I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 244 Processing helix chain 'I' and resid 248 through 265 removed outlier: 4.104A pdb=" N LEU I 258 " --> pdb=" O ARG I 254 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP I 259 " --> pdb=" O VAL I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 277 Processing helix chain 'I' and resid 280 through 289 removed outlier: 3.606A pdb=" N ALA I 284 " --> pdb=" O PHE I 280 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL I 285 " --> pdb=" O ILE I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 291 through 338 removed outlier: 4.172A pdb=" N VAL I 296 " --> pdb=" O LYS I 292 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE I 297 " --> pdb=" O LEU I 293 " (cutoff:3.500A) Proline residue: I 302 - end of helix Proline residue: I 313 - end of helix Processing helix chain 'I' and resid 340 through 345 Processing helix chain 'I' and resid 349 through 402 Processing helix chain 'I' and resid 407 through 448 Proline residue: I 423 - end of helix removed outlier: 3.667A pdb=" N ILE I 430 " --> pdb=" O ARG I 426 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLN I 432 " --> pdb=" O ALA I 428 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP I 433 " --> pdb=" O GLN I 429 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR I 442 " --> pdb=" O GLY I 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 515 No H-bonds generated for 'chain 'I' and resid 512 through 515' Processing helix chain 'I' and resid 538 through 544 removed outlier: 3.899A pdb=" N GLN I 544 " --> pdb=" O TRP I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 563 Processing helix chain 'I' and resid 572 through 581 Processing helix chain 'I' and resid 585 through 590 Processing helix chain 'I' and resid 594 through 596 No H-bonds generated for 'chain 'I' and resid 594 through 596' Processing helix chain 'I' and resid 608 through 621 Processing helix chain 'I' and resid 641 through 651 removed outlier: 4.412A pdb=" N LYS I 650 " --> pdb=" O ARG I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 687 through 691 Processing helix chain 'I' and resid 697 through 705 Processing helix chain 'A' and resid 9 through 21 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 140 through 181 removed outlier: 3.848A pdb=" N ILE A 144 " --> pdb=" O THR A 141 " (cutoff:3.500A) Proline residue: A 145 - end of helix removed outlier: 4.195A pdb=" N ILE A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS A 149 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LYS A 152 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A 171 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 190 through 237 Processing helix chain 'A' and resid 240 through 245 removed outlier: 3.962A pdb=" N SER A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 removed outlier: 4.336A pdb=" N LEU A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 289 removed outlier: 3.837A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 337 Proline residue: A 302 - end of helix Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 349 through 402 Processing helix chain 'A' and resid 407 through 448 removed outlier: 3.976A pdb=" N VAL A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA A 422 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 4.177A pdb=" N GLN A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 435 " --> pdb=" O TRP A 431 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 515 No H-bonds generated for 'chain 'A' and resid 512 through 515' Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 538 through 544 removed outlier: 3.758A pdb=" N ARG A 543 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN A 544 " --> pdb=" O TRP A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 585 through 590 Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 638 through 651 removed outlier: 4.608A pdb=" N HIS A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LYS A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 667 removed outlier: 3.695A pdb=" N VAL A 667 " --> pdb=" O LEU A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 664 through 667' Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 697 through 705 Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 151 through 181 Proline residue: B 172 - end of helix Processing helix chain 'B' and resid 188 through 237 removed outlier: 3.540A pdb=" N VAL B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 248 through 265 removed outlier: 4.644A pdb=" N LEU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 289 removed outlier: 4.670A pdb=" N PHE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B 282 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 338 removed outlier: 3.739A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Proline residue: B 302 - end of helix Proline residue: B 313 - end of helix Processing helix chain 'B' and resid 340 through 345 Processing helix chain 'B' and resid 349 through 402 Processing helix chain 'B' and resid 407 through 448 Proline residue: B 423 - end of helix removed outlier: 4.197A pdb=" N ALA B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLN B 429 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 435 " --> pdb=" O TRP B 431 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 515 removed outlier: 3.672A pdb=" N LEU B 511 " --> pdb=" O LYS B 508 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR B 512 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 513 " --> pdb=" O THR B 510 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 515 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 538 through 544 Processing helix chain 'B' and resid 559 through 563 Processing helix chain 'B' and resid 572 through 582 Processing helix chain 'B' and resid 585 through 590 removed outlier: 3.766A pdb=" N GLU B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 596 No H-bonds generated for 'chain 'B' and resid 594 through 596' Processing helix chain 'B' and resid 608 through 619 Processing helix chain 'B' and resid 641 through 651 removed outlier: 4.713A pdb=" N HIS B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS B 650 " --> pdb=" O ARG B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 691 Processing helix chain 'B' and resid 697 through 705 Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 111 through 117 Processing helix chain 'E' and resid 140 through 149 Proline residue: E 145 - end of helix Processing helix chain 'E' and resid 151 through 181 removed outlier: 3.667A pdb=" N ILE E 170 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR E 171 " --> pdb=" O PHE E 167 " (cutoff:3.500A) Proline residue: E 172 - end of helix Processing helix chain 'E' and resid 191 through 237 removed outlier: 3.537A pdb=" N ALA E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 245 Processing helix chain 'E' and resid 248 through 265 removed outlier: 4.373A pdb=" N LEU E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 277 Processing helix chain 'E' and resid 280 through 289 removed outlier: 3.571A pdb=" N VAL E 285 " --> pdb=" O ILE E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 338 removed outlier: 3.718A pdb=" N VAL E 296 " --> pdb=" O LYS E 292 " (cutoff:3.500A) Proline residue: E 302 - end of helix Proline residue: E 313 - end of helix Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 349 through 401 Processing helix chain 'E' and resid 407 through 448 Proline residue: E 423 - end of helix removed outlier: 3.743A pdb=" N ILE E 430 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLN E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP E 433 " --> pdb=" O GLN E 429 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL E 447 " --> pdb=" O ARG E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 533 through 535 No H-bonds generated for 'chain 'E' and resid 533 through 535' Processing helix chain 'E' and resid 538 through 543 Processing helix chain 'E' and resid 559 through 563 Processing helix chain 'E' and resid 572 through 582 Processing helix chain 'E' and resid 585 through 589 Processing helix chain 'E' and resid 608 through 621 removed outlier: 3.806A pdb=" N GLN E 612 " --> pdb=" O GLY E 608 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG E 613 " --> pdb=" O GLY E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 634 No H-bonds generated for 'chain 'E' and resid 632 through 634' Processing helix chain 'E' and resid 638 through 651 removed outlier: 4.575A pdb=" N HIS E 649 " --> pdb=" O MET E 645 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYS E 650 " --> pdb=" O ARG E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 667 Processing helix chain 'E' and resid 687 through 691 Processing helix chain 'E' and resid 697 through 705 Processing helix chain 'F' and resid 141 through 149 Proline residue: F 145 - end of helix Processing helix chain 'F' and resid 151 through 181 Proline residue: F 172 - end of helix Processing helix chain 'F' and resid 190 through 237 removed outlier: 3.596A pdb=" N ILE F 223 " --> pdb=" O SER F 219 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA F 237 " --> pdb=" O ARG F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 244 Processing helix chain 'F' and resid 248 through 265 removed outlier: 3.964A pdb=" N ARG F 254 " --> pdb=" O ASP F 250 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL F 255 " --> pdb=" O THR F 251 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 277 Processing helix chain 'F' and resid 280 through 289 removed outlier: 3.784A pdb=" N TYR F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 338 Proline residue: F 302 - end of helix Proline residue: F 313 - end of helix Processing helix chain 'F' and resid 340 through 345 Processing helix chain 'F' and resid 350 through 401 Processing helix chain 'F' and resid 407 through 428 Proline residue: F 423 - end of helix Processing helix chain 'F' and resid 431 through 448 Processing helix chain 'F' and resid 512 through 515 No H-bonds generated for 'chain 'F' and resid 512 through 515' Processing helix chain 'F' and resid 533 through 535 No H-bonds generated for 'chain 'F' and resid 533 through 535' Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 559 through 563 Processing helix chain 'F' and resid 572 through 582 Processing helix chain 'F' and resid 585 through 590 Processing helix chain 'F' and resid 594 through 596 No H-bonds generated for 'chain 'F' and resid 594 through 596' Processing helix chain 'F' and resid 601 through 603 No H-bonds generated for 'chain 'F' and resid 601 through 603' Processing helix chain 'F' and resid 608 through 621 Processing helix chain 'F' and resid 638 through 651 removed outlier: 4.535A pdb=" N ILE F 643 " --> pdb=" O GLU F 639 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N HIS F 649 " --> pdb=" O MET F 645 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LYS F 650 " --> pdb=" O ARG F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 691 Processing helix chain 'F' and resid 697 through 705 Processing helix chain 'H' and resid 11 through 24 Processing helix chain 'H' and resid 36 through 40 Processing helix chain 'H' and resid 44 through 50 removed outlier: 3.662A pdb=" N LEU H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 76 Processing helix chain 'L' and resid 11 through 24 Processing helix chain 'L' and resid 36 through 40 Processing helix chain 'L' and resid 44 through 49 removed outlier: 3.817A pdb=" N LEU L 48 " --> pdb=" O ALA L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 76 Processing helix chain 'D' and resid 10 through 23 Processing helix chain 'D' and resid 36 through 40 Processing helix chain 'D' and resid 44 through 50 removed outlier: 3.693A pdb=" N LEU D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 76 Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 43 through 48 removed outlier: 3.506A pdb=" N LEU C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 77 Processing helix chain 'C' and resid 374 through 379 Processing helix chain 'C' and resid 395 through 398 No H-bonds generated for 'chain 'C' and resid 395 through 398' Processing helix chain 'C' and resid 459 through 469 Proline residue: C 466 - end of helix Processing helix chain 'G' and resid 35 through 41 removed outlier: 3.535A pdb=" N PHE G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 60 through 77 Processing helix chain 'G' and resid 374 through 379 Processing helix chain 'G' and resid 395 through 398 No H-bonds generated for 'chain 'G' and resid 395 through 398' Processing helix chain 'G' and resid 459 through 472 removed outlier: 3.941A pdb=" N SER G 465 " --> pdb=" O TYR G 462 " (cutoff:3.500A) Proline residue: G 466 - end of helix Processing helix chain 'K' and resid 35 through 41 removed outlier: 3.716A pdb=" N GLU K 40 " --> pdb=" O LYS K 36 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE K 41 " --> pdb=" O ASP K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 48 Processing helix chain 'K' and resid 59 through 75 Processing sheet with id= A, first strand: chain 'J' and resid 490 through 492 Processing sheet with id= B, first strand: chain 'J' and resid 680 through 685 removed outlier: 7.111A pdb=" N VAL J 675 " --> pdb=" O VAL J 682 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN J 684 " --> pdb=" O ILE J 673 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE J 673 " --> pdb=" O GLN J 684 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG J 672 " --> pdb=" O VAL J 497 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL J 657 " --> pdb=" O ILE J 498 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE J 500 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE J 659 " --> pdb=" O ILE J 500 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'I' and resid 55 through 61 Processing sheet with id= D, first strand: chain 'I' and resid 74 through 76 removed outlier: 3.540A pdb=" N PHE I 84 " --> pdb=" O VAL I 76 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'I' and resid 96 through 100 removed outlier: 3.545A pdb=" N ASN I 105 " --> pdb=" O ASP I 100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 490 through 492 Processing sheet with id= G, first strand: chain 'I' and resid 680 through 685 removed outlier: 6.995A pdb=" N VAL I 675 " --> pdb=" O VAL I 682 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN I 684 " --> pdb=" O ILE I 673 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE I 673 " --> pdb=" O GLN I 684 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG I 672 " --> pdb=" O VAL I 497 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL I 657 " --> pdb=" O ILE I 498 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE I 500 " --> pdb=" O VAL I 657 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE I 659 " --> pdb=" O ILE I 500 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N GLY I 502 " --> pdb=" O ILE I 659 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 56 through 61 Processing sheet with id= I, first strand: chain 'A' and resid 74 through 76 removed outlier: 3.764A pdb=" N PHE A 84 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 97 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL A 89 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG A 95 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 96 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 468 through 470 Processing sheet with id= K, first strand: chain 'A' and resid 680 through 683 removed outlier: 7.024A pdb=" N VAL A 675 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 672 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL A 657 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE A 500 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 659 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N GLY A 502 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 468 through 471 removed outlier: 3.620A pdb=" N ARG B 471 " --> pdb=" O GLN B 525 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 680 through 685 removed outlier: 7.314A pdb=" N VAL B 675 " --> pdb=" O VAL B 682 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN B 684 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 673 " --> pdb=" O GLN B 684 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 672 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 657 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE B 500 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 659 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 56 through 61 removed outlier: 3.524A pdb=" N ILE E 122 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 74 through 76 removed outlier: 3.634A pdb=" N PHE E 84 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL E 89 " --> pdb=" O ARG E 95 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ARG E 95 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 490 through 492 Processing sheet with id= Q, first strand: chain 'E' and resid 680 through 685 removed outlier: 7.100A pdb=" N VAL E 675 " --> pdb=" O VAL E 682 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN E 684 " --> pdb=" O ILE E 673 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 673 " --> pdb=" O GLN E 684 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 490 through 492 Processing sheet with id= S, first strand: chain 'F' and resid 681 through 685 removed outlier: 7.174A pdb=" N VAL F 675 " --> pdb=" O VAL F 682 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN F 684 " --> pdb=" O ILE F 673 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE F 673 " --> pdb=" O GLN F 684 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY F 502 " --> pdb=" O ALA F 661 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 79 through 81 Processing sheet with id= U, first strand: chain 'C' and resid 403 through 405 Processing sheet with id= V, first strand: chain 'G' and resid 403 through 405 1872 hydrogen bonds defined for protein. 5385 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: 13.07 Time building geometry restraints manager: 15.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5530 1.29 - 1.42: 8850 1.42 - 1.55: 20850 1.55 - 1.68: 224 1.68 - 1.81: 148 Bond restraints: 35602 Sorted by residual: bond pdb=" C40 6OU J 802 " pdb=" C41 6OU J 802 " ideal model delta sigma weight residual 1.333 1.559 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C40 6OU L 401 " pdb=" C41 6OU L 401 " ideal model delta sigma weight residual 1.333 1.559 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C40 6OU I 801 " pdb=" C41 6OU I 801 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C40 6OU J 801 " pdb=" C41 6OU J 801 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C40 6OU A 802 " pdb=" C41 6OU A 802 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 35597 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.59: 514 105.59 - 112.72: 19731 112.72 - 119.85: 11438 119.85 - 126.99: 16076 126.99 - 134.12: 347 Bond angle restraints: 48106 Sorted by residual: angle pdb=" N GLY F 403 " pdb=" CA GLY F 403 " pdb=" C GLY F 403 " ideal model delta sigma weight residual 115.30 125.45 -10.15 1.39e+00 5.18e-01 5.33e+01 angle pdb=" C40 6OU L 401 " pdb=" C41 6OU L 401 " pdb=" C42 6OU L 401 " ideal model delta sigma weight residual 127.56 108.43 19.13 3.00e+00 1.11e-01 4.07e+01 angle pdb=" C40 6OU J 802 " pdb=" C41 6OU J 802 " pdb=" C42 6OU J 802 " ideal model delta sigma weight residual 127.56 109.24 18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" C40 6OU F 802 " pdb=" C41 6OU F 802 " pdb=" C42 6OU F 802 " ideal model delta sigma weight residual 127.56 109.26 18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" C40 6OU J 801 " pdb=" C41 6OU J 801 " pdb=" C42 6OU J 801 " ideal model delta sigma weight residual 127.56 109.95 17.61 3.00e+00 1.11e-01 3.45e+01 ... (remaining 48101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 20931 33.71 - 67.42: 458 67.42 - 101.13: 67 101.13 - 134.84: 3 134.84 - 168.55: 8 Dihedral angle restraints: 21467 sinusoidal: 8691 harmonic: 12776 Sorted by residual: dihedral pdb=" CA VAL F 348 " pdb=" C VAL F 348 " pdb=" N SER F 349 " pdb=" CA SER F 349 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" C19 6OU A 801 " pdb=" C20 6OU A 801 " pdb=" C21 6OU A 801 " pdb=" O22 6OU A 801 " ideal model delta sinusoidal sigma weight residual 301.00 132.45 168.55 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C19 6OU K 401 " pdb=" C20 6OU K 401 " pdb=" C21 6OU K 401 " pdb=" O22 6OU K 401 " ideal model delta sinusoidal sigma weight residual -59.00 108.54 -167.54 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 21464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 5427 0.098 - 0.196: 212 0.196 - 0.294: 7 0.294 - 0.392: 1 0.392 - 0.491: 2 Chirality restraints: 5649 Sorted by residual: chirality pdb=" CA LEU A 301 " pdb=" N LEU A 301 " pdb=" C LEU A 301 " pdb=" CB LEU A 301 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA PHE A 299 " pdb=" N PHE A 299 " pdb=" C PHE A 299 " pdb=" CB PHE A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA ASP F 404 " pdb=" N ASP F 404 " pdb=" C ASP F 404 " pdb=" CB ASP F 404 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 5646 not shown) Planarity restraints: 6007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C39 6OU L 401 " -0.262 2.00e-02 2.50e+03 2.94e-01 8.64e+02 pdb=" C40 6OU L 401 " 0.477 2.00e-02 2.50e+03 pdb=" C41 6OU L 401 " -0.222 2.00e-02 2.50e+03 pdb=" C42 6OU L 401 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 6OU F 802 " 0.241 2.00e-02 2.50e+03 2.91e-01 8.45e+02 pdb=" C40 6OU F 802 " -0.459 2.00e-02 2.50e+03 pdb=" C41 6OU F 802 " 0.259 2.00e-02 2.50e+03 pdb=" C42 6OU F 802 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 6OU A 802 " 0.227 2.00e-02 2.50e+03 2.88e-01 8.29e+02 pdb=" C40 6OU A 802 " -0.444 2.00e-02 2.50e+03 pdb=" C41 6OU A 802 " 0.281 2.00e-02 2.50e+03 pdb=" C42 6OU A 802 " -0.063 2.00e-02 2.50e+03 ... (remaining 6004 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2945 2.74 - 3.28: 35236 3.28 - 3.82: 57149 3.82 - 4.36: 66477 4.36 - 4.90: 117469 Nonbonded interactions: 279276 Sorted by model distance: nonbonded pdb=" OE1 GLU I 257 " pdb=" OG SER I 440 " model vdw 2.202 2.440 nonbonded pdb=" O LEU E 41 " pdb=" OG SER E 45 " model vdw 2.220 2.440 nonbonded pdb=" OE1 GLU E 257 " pdb=" OG SER E 440 " model vdw 2.222 2.440 nonbonded pdb=" OE1 GLN J 176 " pdb=" OH TYR J 289 " model vdw 2.232 2.440 nonbonded pdb=" OG SER E 692 " pdb=" OE2 GLU E 693 " model vdw 2.238 2.440 ... (remaining 279271 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 7 through 130 or (resid 131 through 132 and (name N or nam \ e CA or name C or name O or name CB )) or resid 133 through 454 or (resid 455 th \ rough 456 and (name N or name CA or name C or name O or name CB )) or resid 457 \ or (resid 458 and (name N or name CA or name C or name O or name CB )) or resid \ 459 through 706)) selection = (chain 'E' and (resid 7 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 136 or (resid 137 and (name N or na \ me CA or name C or name O or name CB )) or resid 138 through 706)) selection = (chain 'I' and (resid 7 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 130 or (resid 131 through 132 and ( \ name N or name CA or name C or name O or name CB )) or (resid 133 through 137 an \ d (name N or name CA or name C or name O or name CB )) or resid 138 through 454 \ or (resid 455 through 456 and (name N or name CA or name C or name O or name CB \ )) or resid 457 through 706)) } ncs_group { reference = (chain 'B' and (resid 137 through 687 or (resid 688 and (name N or name CA or na \ me C or name O or name CB )) or resid 689 through 706 or resid 801)) selection = (chain 'F' and (resid 137 through 687 or (resid 688 and (name N or name CA or na \ me C or name O or name CB )) or resid 689 through 706 or (resid 801 and (name C3 \ 1 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name C45))) \ ) selection = (chain 'J' and (resid 137 through 706 or (resid 801 and (name C31 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43 or name C44 or name C45)))) } ncs_group { reference = (chain 'C' and (resid 29 through 80 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 363 through 471)) selection = (chain 'G' and resid 29 through 471) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 9 through 77) selection = (chain 'L' and resid 9 through 77) } 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: 2.890 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: 0.020 Extract box with map and model: 13.890 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 95.070 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.300 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:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 : 0.007 0.226 35602 Z= 0.471 Angle : 0.792 19.128 48106 Z= 0.385 Chirality : 0.043 0.491 5649 Planarity : 0.009 0.294 6007 Dihedral : 15.212 168.546 13195 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.89 (0.13), residues: 4369 helix: 1.80 (0.10), residues: 2658 sheet: -0.94 (0.29), residues: 346 loop : -1.43 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.001 TRP B 431 HIS 0.004 0.001 HIS E 662 PHE 0.030 0.001 PHE A 278 TYR 0.013 0.001 TYR C 462 ARG 0.007 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 702 time to evaluate : 4.368 Fit side-chains revert: symmetry clash REVERT: J 467 ASN cc_start: 0.6908 (m-40) cc_final: 0.6689 (t0) REVERT: J 550 GLN cc_start: 0.7729 (tt0) cc_final: 0.7388 (tt0) REVERT: J 630 ASP cc_start: 0.6874 (t70) cc_final: 0.6609 (t0) REVERT: J 673 ILE cc_start: 0.7760 (mp) cc_final: 0.7464 (mp) REVERT: I 69 PHE cc_start: 0.8286 (m-80) cc_final: 0.8049 (m-10) REVERT: I 328 ASP cc_start: 0.7578 (m-30) cc_final: 0.7327 (m-30) REVERT: I 369 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7861 (mttt) REVERT: I 498 ILE cc_start: 0.8208 (mm) cc_final: 0.7882 (mm) REVERT: I 663 ARG cc_start: 0.6401 (mpt180) cc_final: 0.5994 (mpt180) REVERT: A 8 ASP cc_start: 0.5433 (p0) cc_final: 0.5101 (p0) REVERT: A 358 LYS cc_start: 0.7093 (mttt) cc_final: 0.6883 (mppt) REVERT: A 433 ASP cc_start: 0.7073 (m-30) cc_final: 0.6453 (m-30) REVERT: A 645 MET cc_start: 0.8393 (mmm) cc_final: 0.8097 (mmm) REVERT: A 646 ARG cc_start: 0.7246 (mpt180) cc_final: 0.6992 (mpt180) REVERT: A 684 GLN cc_start: 0.8434 (pt0) cc_final: 0.8188 (pt0) REVERT: A 704 LEU cc_start: 0.8788 (tt) cc_final: 0.8560 (tp) REVERT: B 181 LYS cc_start: 0.8348 (mmtp) cc_final: 0.8115 (mmtp) REVERT: B 259 ASP cc_start: 0.7681 (t0) cc_final: 0.7230 (t70) REVERT: B 316 ARG cc_start: 0.7634 (tpm-80) cc_final: 0.7379 (tpm170) REVERT: B 474 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7616 (mtp-110) REVERT: B 512 THR cc_start: 0.8692 (t) cc_final: 0.8327 (m) REVERT: B 523 ASN cc_start: 0.7135 (t0) cc_final: 0.6912 (t0) REVERT: B 678 LYS cc_start: 0.8344 (mtpp) cc_final: 0.7734 (tptp) REVERT: E 31 LYS cc_start: 0.8095 (tttt) cc_final: 0.7810 (tttm) REVERT: E 224 ASP cc_start: 0.7885 (t70) cc_final: 0.7567 (t0) REVERT: E 663 ARG cc_start: 0.8213 (mtp-110) cc_final: 0.7613 (ttm110) REVERT: F 346 MET cc_start: 0.7809 (mtp) cc_final: 0.7605 (mtm) REVERT: F 586 ASP cc_start: 0.7283 (m-30) cc_final: 0.6782 (m-30) REVERT: F 601 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6276 (tt0) REVERT: F 625 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7888 (mmtm) REVERT: F 639 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6881 (tm-30) REVERT: F 645 MET cc_start: 0.7889 (mmm) cc_final: 0.7578 (mtp) REVERT: F 678 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7644 (mptt) REVERT: H 24 LYS cc_start: 0.7831 (mmtm) cc_final: 0.7535 (mmmt) REVERT: H 27 LYS cc_start: 0.8361 (mtmt) cc_final: 0.7930 (mtpp) REVERT: L 16 LYS cc_start: 0.7170 (mmmt) cc_final: 0.6640 (mmpt) REVERT: L 25 ILE cc_start: 0.7949 (tp) cc_final: 0.7719 (tp) REVERT: D 65 MET cc_start: 0.7392 (mtm) cc_final: 0.7173 (mtp) REVERT: K 37 ASP cc_start: 0.7705 (m-30) cc_final: 0.7464 (m-30) outliers start: 0 outliers final: 1 residues processed: 702 average time/residue: 1.3414 time to fit residues: 1136.3293 Evaluate side-chains 452 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 451 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 398 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 367 optimal weight: 2.9990 chunk 329 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 112 optimal weight: 0.1980 chunk 222 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 340 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 395 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 103 GLN I 185 HIS I 385 GLN I 398 HIS I 552 ASN I 612 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN A 467 ASN A 523 ASN B 192 ASN B 472 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 121 HIS E 192 ASN E 268 GLN E 525 GLN ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 622 ASN ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35602 Z= 0.279 Angle : 0.574 11.425 48106 Z= 0.297 Chirality : 0.043 0.228 5649 Planarity : 0.004 0.069 6007 Dihedral : 11.350 164.352 5262 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.68 % Allowed : 11.03 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.77 (0.13), residues: 4369 helix: 1.59 (0.10), residues: 2679 sheet: -0.90 (0.28), residues: 367 loop : -1.29 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 431 HIS 0.005 0.001 HIS F 218 PHE 0.025 0.002 PHE J 587 TYR 0.021 0.001 TYR E 700 ARG 0.007 0.001 ARG J 517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 467 time to evaluate : 4.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 321 ASP cc_start: 0.7364 (m-30) cc_final: 0.7159 (m-30) REVERT: J 346 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7921 (mtm) REVERT: J 467 ASN cc_start: 0.6942 (m-40) cc_final: 0.6698 (t0) REVERT: J 529 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: J 550 GLN cc_start: 0.8036 (tt0) cc_final: 0.7827 (tt0) REVERT: J 570 MET cc_start: 0.8684 (ptm) cc_final: 0.8326 (ptm) REVERT: I 97 LEU cc_start: 0.7921 (tp) cc_final: 0.7564 (tm) REVERT: A 8 ASP cc_start: 0.5644 (p0) cc_final: 0.5203 (p0) REVERT: A 165 GLN cc_start: 0.7281 (mp-120) cc_final: 0.7010 (mm110) REVERT: A 330 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7126 (mp10) REVERT: A 433 ASP cc_start: 0.7132 (m-30) cc_final: 0.6459 (m-30) REVERT: A 523 ASN cc_start: 0.7529 (m-40) cc_final: 0.7138 (m-40) REVERT: A 631 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.6937 (mm-30) REVERT: A 645 MET cc_start: 0.8416 (mmm) cc_final: 0.8071 (mmm) REVERT: A 646 ARG cc_start: 0.7176 (mpt180) cc_final: 0.6845 (mpt180) REVERT: B 179 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.7045 (ttp) REVERT: B 181 LYS cc_start: 0.8495 (mmtp) cc_final: 0.8264 (mmtp) REVERT: B 205 GLU cc_start: 0.6817 (tt0) cc_final: 0.6604 (tm-30) REVERT: B 256 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7731 (mtm110) REVERT: B 259 ASP cc_start: 0.7583 (t0) cc_final: 0.7263 (t70) REVERT: B 373 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8032 (mt) REVERT: B 427 LEU cc_start: 0.4312 (OUTLIER) cc_final: 0.4039 (tp) REVERT: B 474 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7523 (mtp-110) REVERT: B 488 ILE cc_start: 0.8503 (pp) cc_final: 0.8285 (pp) REVERT: B 523 ASN cc_start: 0.7110 (t0) cc_final: 0.6902 (t0) REVERT: B 574 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7566 (mtpp) REVERT: B 639 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7204 (pp20) REVERT: B 648 MET cc_start: 0.8618 (tpp) cc_final: 0.8087 (mmm) REVERT: E 31 LYS cc_start: 0.8427 (tttt) cc_final: 0.8109 (tttp) REVERT: E 95 ARG cc_start: 0.7209 (ptp-110) cc_final: 0.6654 (mtt180) REVERT: E 317 ARG cc_start: 0.7275 (ttp80) cc_final: 0.6989 (mtp-110) REVERT: E 663 ARG cc_start: 0.8189 (mtp-110) cc_final: 0.7600 (ttm110) REVERT: E 680 LYS cc_start: 0.8149 (mppt) cc_final: 0.7924 (mptt) REVERT: E 688 LYS cc_start: 0.8416 (mppt) cc_final: 0.8102 (mmtt) REVERT: F 586 ASP cc_start: 0.6929 (m-30) cc_final: 0.6704 (m-30) REVERT: F 601 GLU cc_start: 0.7598 (mm-30) cc_final: 0.6273 (tt0) REVERT: F 639 GLU cc_start: 0.7655 (mt-10) cc_final: 0.6844 (tm-30) REVERT: F 646 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6614 (ptp-170) REVERT: F 678 LYS cc_start: 0.7907 (mtmm) cc_final: 0.7594 (mptt) REVERT: H 24 LYS cc_start: 0.7883 (mmtm) cc_final: 0.7563 (mmmt) REVERT: L 16 LYS cc_start: 0.7340 (mmmt) cc_final: 0.6643 (mmpt) REVERT: L 55 ARG cc_start: 0.7211 (tpp-160) cc_final: 0.6955 (ttp80) REVERT: D 34 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.5991 (mtt-85) REVERT: C 47 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7718 (tp30) REVERT: K 37 ASP cc_start: 0.7672 (m-30) cc_final: 0.7437 (m-30) outliers start: 98 outliers final: 35 residues processed: 521 average time/residue: 1.3324 time to fit residues: 848.5664 Evaluate side-chains 466 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 420 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 346 MET Chi-restraints excluded: chain J residue 387 THR Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 529 ASP Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain J residue 643 ILE Chi-restraints excluded: chain J residue 681 ILE Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain I residue 399 LEU Chi-restraints excluded: chain I residue 553 VAL Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 646 ARG Chi-restraints excluded: chain F residue 706 SER Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain K residue 36 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 219 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 328 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 395 optimal weight: 6.9990 chunk 427 optimal weight: 40.0000 chunk 352 optimal weight: 1.9990 chunk 392 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 192 ASN I 185 HIS I 385 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS A 260 GLN A 449 ASN A 467 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN E 268 GLN E 398 HIS E 552 ASN E 622 ASN ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 35602 Z= 0.401 Angle : 0.604 10.941 48106 Z= 0.316 Chirality : 0.045 0.226 5649 Planarity : 0.004 0.061 6007 Dihedral : 10.952 167.293 5262 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.63 % Allowed : 13.57 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.50 (0.13), residues: 4369 helix: 1.33 (0.10), residues: 2681 sheet: -0.85 (0.27), residues: 370 loop : -1.35 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 431 HIS 0.006 0.001 HIS A 398 PHE 0.025 0.002 PHE D 67 TYR 0.019 0.002 TYR J 304 ARG 0.010 0.001 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 444 time to evaluate : 4.227 Fit side-chains REVERT: J 259 ASP cc_start: 0.7265 (m-30) cc_final: 0.7041 (m-30) REVERT: J 268 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7697 (mm-40) REVERT: J 283 PHE cc_start: 0.8364 (m-80) cc_final: 0.7805 (m-10) REVERT: J 346 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7992 (mtm) REVERT: J 467 ASN cc_start: 0.7500 (m-40) cc_final: 0.7082 (t0) REVERT: J 476 ARG cc_start: 0.7484 (mtp85) cc_final: 0.7267 (mtp85) REVERT: J 529 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8111 (m-30) REVERT: J 550 GLN cc_start: 0.8251 (tt0) cc_final: 0.8008 (tt0) REVERT: J 570 MET cc_start: 0.8681 (ptm) cc_final: 0.8339 (ptm) REVERT: J 638 TYR cc_start: 0.7671 (t80) cc_final: 0.7087 (t80) REVERT: J 643 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7734 (mp) REVERT: I 251 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7810 (m) REVERT: I 602 GLN cc_start: 0.8863 (mt0) cc_final: 0.8424 (mt0) REVERT: A 8 ASP cc_start: 0.5659 (p0) cc_final: 0.5256 (p0) REVERT: A 139 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: A 330 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7201 (mp10) REVERT: A 433 ASP cc_start: 0.7256 (m-30) cc_final: 0.6821 (m-30) REVERT: A 446 ASP cc_start: 0.8134 (t0) cc_final: 0.7860 (t0) REVERT: A 561 ASP cc_start: 0.7546 (t0) cc_final: 0.6871 (t0) REVERT: A 645 MET cc_start: 0.8433 (mmm) cc_final: 0.8021 (mmm) REVERT: B 259 ASP cc_start: 0.7625 (t0) cc_final: 0.7418 (t70) REVERT: B 373 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8081 (mt) REVERT: B 474 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7590 (mtp-110) REVERT: B 476 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6498 (mtp85) REVERT: B 488 ILE cc_start: 0.8582 (pp) cc_final: 0.8264 (pp) REVERT: B 543 ARG cc_start: 0.7681 (mmm160) cc_final: 0.7463 (mmm160) REVERT: B 639 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7161 (pp20) REVERT: B 645 MET cc_start: 0.8064 (mmm) cc_final: 0.7810 (mtm) REVERT: E 31 LYS cc_start: 0.8507 (tttt) cc_final: 0.8182 (tttp) REVERT: E 247 ARG cc_start: 0.7774 (mtm180) cc_final: 0.7310 (mtm180) REVERT: E 446 ASP cc_start: 0.7636 (m-30) cc_final: 0.7391 (m-30) REVERT: E 663 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7518 (ttm110) REVERT: E 688 LYS cc_start: 0.8439 (mppt) cc_final: 0.8135 (mmtt) REVERT: F 295 LEU cc_start: 0.8218 (mp) cc_final: 0.8002 (mm) REVERT: F 639 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6808 (tm-30) REVERT: H 24 LYS cc_start: 0.7946 (mmtm) cc_final: 0.7589 (mmmt) REVERT: H 40 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8236 (mt-10) REVERT: D 34 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.6113 (mtt-85) REVERT: C 47 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7786 (tp30) REVERT: G 462 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7344 (m-10) REVERT: K 37 ASP cc_start: 0.7790 (m-30) cc_final: 0.7509 (m-30) outliers start: 133 outliers final: 71 residues processed: 518 average time/residue: 1.2701 time to fit residues: 809.4034 Evaluate side-chains 494 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 410 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 268 GLN Chi-restraints excluded: chain J residue 346 MET Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 512 THR Chi-restraints excluded: chain J residue 529 ASP Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain J residue 643 ILE Chi-restraints excluded: chain J residue 681 ILE Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 399 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 526 VAL Chi-restraints excluded: chain I residue 553 VAL Chi-restraints excluded: chain I residue 643 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 706 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 462 TYR Chi-restraints excluded: chain K residue 36 LYS Chi-restraints excluded: chain K residue 54 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 390 optimal weight: 0.0980 chunk 297 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 188 optimal weight: 0.0070 chunk 265 optimal weight: 2.9990 chunk 397 optimal weight: 0.7980 chunk 420 optimal weight: 20.0000 chunk 207 optimal weight: 0.5980 chunk 376 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 185 HIS I 385 GLN A 330 GLN A 449 ASN A 467 ASN A 623 ASN B 523 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 622 ASN ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35602 Z= 0.149 Angle : 0.483 12.290 48106 Z= 0.254 Chirality : 0.040 0.204 5649 Planarity : 0.003 0.042 6007 Dihedral : 9.835 166.110 5262 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.54 % Allowed : 16.08 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.99 (0.13), residues: 4369 helix: 1.72 (0.10), residues: 2682 sheet: -0.58 (0.27), residues: 360 loop : -1.19 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 431 HIS 0.003 0.001 HIS F 218 PHE 0.018 0.001 PHE A 278 TYR 0.018 0.001 TYR J 700 ARG 0.006 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 443 time to evaluate : 3.974 Fit side-chains revert: symmetry clash REVERT: J 283 PHE cc_start: 0.8399 (m-80) cc_final: 0.7775 (m-10) REVERT: J 346 MET cc_start: 0.8186 (mtp) cc_final: 0.7859 (mtm) REVERT: J 467 ASN cc_start: 0.7322 (m-40) cc_final: 0.6848 (t0) REVERT: J 487 ASN cc_start: 0.6997 (m-40) cc_final: 0.6428 (t0) REVERT: J 493 LYS cc_start: 0.7169 (mppt) cc_final: 0.6539 (mmmt) REVERT: J 550 GLN cc_start: 0.8129 (tt0) cc_final: 0.7897 (tt0) REVERT: J 570 MET cc_start: 0.8710 (ptm) cc_final: 0.8360 (ptm) REVERT: J 638 TYR cc_start: 0.7613 (t80) cc_final: 0.6950 (t80) REVERT: J 643 ILE cc_start: 0.7935 (mm) cc_final: 0.7725 (mp) REVERT: I 88 LYS cc_start: 0.8289 (tptm) cc_final: 0.7989 (tptp) REVERT: I 97 LEU cc_start: 0.7938 (tp) cc_final: 0.7632 (tm) REVERT: I 111 GLN cc_start: 0.7435 (tt0) cc_final: 0.7148 (tp40) REVERT: I 602 GLN cc_start: 0.8682 (mt0) cc_final: 0.8293 (mt0) REVERT: A 139 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: A 179 MET cc_start: 0.6871 (OUTLIER) cc_final: 0.6626 (mtt) REVERT: A 250 ASP cc_start: 0.7697 (t0) cc_final: 0.7472 (t0) REVERT: A 330 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7148 (mp-120) REVERT: A 433 ASP cc_start: 0.7155 (m-30) cc_final: 0.6706 (m-30) REVERT: A 446 ASP cc_start: 0.8117 (t0) cc_final: 0.7832 (t0) REVERT: A 561 ASP cc_start: 0.7460 (t0) cc_final: 0.6714 (t0) REVERT: A 638 TYR cc_start: 0.7745 (t80) cc_final: 0.7487 (t80) REVERT: A 645 MET cc_start: 0.8329 (mmm) cc_final: 0.7944 (mmm) REVERT: B 427 LEU cc_start: 0.4552 (OUTLIER) cc_final: 0.4275 (tp) REVERT: B 474 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7553 (mtp-110) REVERT: B 476 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.5922 (mtp85) REVERT: B 639 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7110 (pp20) REVERT: B 698 TYR cc_start: 0.7762 (t80) cc_final: 0.7484 (t80) REVERT: E 31 LYS cc_start: 0.8431 (tttt) cc_final: 0.8112 (tttp) REVERT: E 663 ARG cc_start: 0.7998 (mtp-110) cc_final: 0.7497 (ttm110) REVERT: E 688 LYS cc_start: 0.8455 (mppt) cc_final: 0.8194 (mmtt) REVERT: F 601 GLU cc_start: 0.7680 (mm-30) cc_final: 0.6325 (tt0) REVERT: F 639 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6776 (tm-30) REVERT: H 24 LYS cc_start: 0.7796 (mmtm) cc_final: 0.7420 (mmmt) REVERT: D 34 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.6356 (mtt-85) REVERT: C 39 ASN cc_start: 0.7964 (m-40) cc_final: 0.7652 (m-40) REVERT: C 62 TYR cc_start: 0.7573 (t80) cc_final: 0.7335 (t80) REVERT: C 81 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7073 (mt-10) REVERT: C 464 LEU cc_start: 0.7373 (tt) cc_final: 0.7154 (pp) REVERT: G 462 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.7245 (m-10) REVERT: K 37 ASP cc_start: 0.7737 (m-30) cc_final: 0.7471 (m-30) REVERT: K 38 GLU cc_start: 0.8023 (tt0) cc_final: 0.7753 (mt-10) outliers start: 93 outliers final: 36 residues processed: 498 average time/residue: 1.2988 time to fit residues: 792.8773 Evaluate side-chains 457 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 413 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 553 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 465 ASN Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 462 TYR Chi-restraints excluded: chain K residue 54 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 350 optimal weight: 0.0270 chunk 238 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 chunk 173 optimal weight: 0.5980 chunk 358 optimal weight: 6.9990 chunk 290 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 377 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 185 HIS J 552 ASN J 612 GLN I 185 HIS I 329 ASN I 385 GLN A 260 GLN A 467 ASN B 467 ASN B 523 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN E 429 GLN ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 622 ASN F 185 HIS ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35602 Z= 0.148 Angle : 0.471 10.637 48106 Z= 0.246 Chirality : 0.040 0.219 5649 Planarity : 0.003 0.041 6007 Dihedral : 9.221 165.641 5262 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.84 % Allowed : 16.63 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.21 (0.13), residues: 4369 helix: 1.89 (0.10), residues: 2679 sheet: -0.45 (0.27), residues: 360 loop : -1.10 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 431 HIS 0.003 0.001 HIS I 185 PHE 0.017 0.001 PHE D 67 TYR 0.019 0.001 TYR J 700 ARG 0.010 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 428 time to evaluate : 4.046 Fit side-chains revert: symmetry clash REVERT: J 283 PHE cc_start: 0.8377 (m-80) cc_final: 0.7727 (m-10) REVERT: J 467 ASN cc_start: 0.7399 (m-40) cc_final: 0.6885 (t0) REVERT: J 487 ASN cc_start: 0.6987 (m-40) cc_final: 0.6384 (t0) REVERT: J 550 GLN cc_start: 0.8108 (tt0) cc_final: 0.7878 (tt0) REVERT: J 570 MET cc_start: 0.8710 (ptm) cc_final: 0.8254 (ptm) REVERT: J 638 TYR cc_start: 0.7632 (t80) cc_final: 0.6934 (t80) REVERT: J 643 ILE cc_start: 0.7884 (mm) cc_final: 0.7660 (mp) REVERT: I 88 LYS cc_start: 0.8376 (tptm) cc_final: 0.8056 (tptp) REVERT: I 97 LEU cc_start: 0.7934 (tp) cc_final: 0.7609 (tm) REVERT: I 111 GLN cc_start: 0.7447 (tt0) cc_final: 0.7132 (tp40) REVERT: I 132 THR cc_start: 0.2097 (OUTLIER) cc_final: 0.1849 (p) REVERT: I 602 GLN cc_start: 0.8574 (mt0) cc_final: 0.8217 (mt0) REVERT: A 8 ASP cc_start: 0.5533 (p0) cc_final: 0.5118 (p0) REVERT: A 179 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.6557 (mtt) REVERT: A 257 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: A 283 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.7234 (t80) REVERT: A 433 ASP cc_start: 0.7137 (m-30) cc_final: 0.6657 (m-30) REVERT: A 446 ASP cc_start: 0.8070 (t0) cc_final: 0.7813 (t0) REVERT: A 561 ASP cc_start: 0.7388 (t0) cc_final: 0.6699 (t0) REVERT: A 645 MET cc_start: 0.8200 (mmm) cc_final: 0.7817 (mmm) REVERT: B 169 LEU cc_start: 0.7827 (tt) cc_final: 0.7622 (tp) REVERT: B 205 GLU cc_start: 0.6786 (tt0) cc_final: 0.6495 (mt-10) REVERT: B 373 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7975 (mt) REVERT: B 427 LEU cc_start: 0.4433 (OUTLIER) cc_final: 0.4182 (tp) REVERT: B 474 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7479 (mtp-110) REVERT: B 476 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.5899 (mtp85) REVERT: B 639 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6882 (pp20) REVERT: B 643 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8050 (mp) REVERT: B 645 MET cc_start: 0.8102 (mmm) cc_final: 0.7894 (mmm) REVERT: B 698 TYR cc_start: 0.7803 (t80) cc_final: 0.7488 (t80) REVERT: E 31 LYS cc_start: 0.8456 (tttt) cc_final: 0.8122 (tttp) REVERT: E 111 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: E 247 ARG cc_start: 0.7576 (mtm180) cc_final: 0.7134 (mtm180) REVERT: E 663 ARG cc_start: 0.7998 (mtp-110) cc_final: 0.7486 (ttm110) REVERT: E 688 LYS cc_start: 0.8493 (mppt) cc_final: 0.8224 (mmtm) REVERT: F 601 GLU cc_start: 0.7689 (mm-30) cc_final: 0.6329 (tt0) REVERT: F 703 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8634 (tt0) REVERT: H 24 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7297 (mmmt) REVERT: D 34 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.6212 (mtt-85) REVERT: C 39 ASN cc_start: 0.7858 (m-40) cc_final: 0.7554 (m-40) REVERT: C 62 TYR cc_start: 0.7667 (t80) cc_final: 0.7444 (t80) REVERT: G 462 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.7302 (m-10) REVERT: K 37 ASP cc_start: 0.7732 (m-30) cc_final: 0.7458 (m-30) outliers start: 104 outliers final: 52 residues processed: 491 average time/residue: 1.2676 time to fit residues: 765.1574 Evaluate side-chains 469 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 405 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 399 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 553 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 111 GLN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 462 TYR Chi-restraints excluded: chain K residue 54 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 141 optimal weight: 0.5980 chunk 378 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 420 optimal weight: 20.0000 chunk 349 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 220 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 185 HIS I 385 GLN A 260 GLN A 467 ASN B 467 ASN B 523 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 567 ASN E 622 ASN ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 642 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 35602 Z= 0.379 Angle : 0.585 13.793 48106 Z= 0.304 Chirality : 0.044 0.240 5649 Planarity : 0.004 0.065 6007 Dihedral : 9.738 165.155 5262 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.30 % Allowed : 17.17 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.78 (0.13), residues: 4369 helix: 1.49 (0.10), residues: 2688 sheet: -0.57 (0.27), residues: 372 loop : -1.16 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 431 HIS 0.006 0.001 HIS A 398 PHE 0.025 0.002 PHE A 278 TYR 0.019 0.001 TYR J 304 ARG 0.013 0.001 ARG I 592 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 420 time to evaluate : 4.090 Fit side-chains revert: symmetry clash REVERT: J 268 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7645 (mm-40) REVERT: J 283 PHE cc_start: 0.8344 (m-80) cc_final: 0.7777 (m-10) REVERT: J 320 ASP cc_start: 0.7720 (m-30) cc_final: 0.7396 (m-30) REVERT: J 346 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7994 (mtm) REVERT: J 467 ASN cc_start: 0.7416 (m-40) cc_final: 0.7004 (t0) REVERT: J 550 GLN cc_start: 0.8179 (tt0) cc_final: 0.7958 (tt0) REVERT: J 570 MET cc_start: 0.8665 (ptm) cc_final: 0.8312 (ptm) REVERT: J 630 ASP cc_start: 0.7298 (t70) cc_final: 0.7078 (t0) REVERT: J 638 TYR cc_start: 0.7707 (t80) cc_final: 0.7094 (t80) REVERT: J 643 ILE cc_start: 0.8059 (mm) cc_final: 0.7825 (mp) REVERT: I 111 GLN cc_start: 0.7538 (tt0) cc_final: 0.7216 (tp40) REVERT: I 602 GLN cc_start: 0.8711 (mt0) cc_final: 0.8315 (mt0) REVERT: A 8 ASP cc_start: 0.5598 (p0) cc_final: 0.5145 (p0) REVERT: A 179 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6683 (mtm) REVERT: A 433 ASP cc_start: 0.7292 (m-30) cc_final: 0.6858 (m-30) REVERT: A 446 ASP cc_start: 0.8198 (t0) cc_final: 0.7892 (t0) REVERT: A 561 ASP cc_start: 0.7676 (t0) cc_final: 0.6897 (t0) REVERT: A 631 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: B 169 LEU cc_start: 0.7904 (tt) cc_final: 0.7610 (tp) REVERT: B 205 GLU cc_start: 0.6839 (tt0) cc_final: 0.6528 (mt-10) REVERT: B 427 LEU cc_start: 0.4796 (OUTLIER) cc_final: 0.4472 (tp) REVERT: B 474 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7612 (mtp-110) REVERT: B 476 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6251 (mtp85) REVERT: B 639 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7114 (pp20) REVERT: B 698 TYR cc_start: 0.7808 (t80) cc_final: 0.7532 (t80) REVERT: E 31 LYS cc_start: 0.8498 (tttt) cc_final: 0.8166 (tttp) REVERT: E 247 ARG cc_start: 0.7781 (mtm180) cc_final: 0.7244 (mtm180) REVERT: E 390 ILE cc_start: 0.8705 (mp) cc_final: 0.8453 (mt) REVERT: E 663 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7591 (ttm110) REVERT: E 688 LYS cc_start: 0.8400 (mppt) cc_final: 0.8156 (mmtt) REVERT: F 601 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6381 (tt0) REVERT: F 703 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8663 (tt0) REVERT: H 24 LYS cc_start: 0.7860 (mmtm) cc_final: 0.7445 (mmmt) REVERT: D 34 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.6146 (mtt-85) REVERT: C 62 TYR cc_start: 0.7639 (t80) cc_final: 0.7369 (t80) REVERT: G 462 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7379 (m-10) REVERT: K 37 ASP cc_start: 0.7772 (m-30) cc_final: 0.7493 (m-30) REVERT: K 38 GLU cc_start: 0.8024 (tt0) cc_final: 0.7744 (mt-10) outliers start: 121 outliers final: 70 residues processed: 492 average time/residue: 1.3044 time to fit residues: 793.4675 Evaluate side-chains 485 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 406 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 268 GLN Chi-restraints excluded: chain J residue 346 MET Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 446 ASP Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 308 SER Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 399 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 553 VAL Chi-restraints excluded: chain I residue 643 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain F residue 706 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 462 TYR Chi-restraints excluded: chain K residue 54 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 405 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 239 optimal weight: 1.9990 chunk 307 optimal weight: 0.7980 chunk 238 optimal weight: 2.9990 chunk 354 optimal weight: 0.9980 chunk 235 optimal weight: 0.1980 chunk 419 optimal weight: 4.9990 chunk 262 optimal weight: 0.8980 chunk 255 optimal weight: 0.7980 chunk 193 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 121 HIS I 185 HIS I 385 GLN A 260 GLN A 330 GLN A 467 ASN B 467 ASN B 523 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN E 552 ASN E 622 ASN F 585 HIS ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35602 Z= 0.154 Angle : 0.490 14.747 48106 Z= 0.255 Chirality : 0.040 0.188 5649 Planarity : 0.003 0.050 6007 Dihedral : 9.058 165.203 5262 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.51 % Allowed : 18.13 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.15 (0.13), residues: 4369 helix: 1.81 (0.10), residues: 2682 sheet: -0.48 (0.27), residues: 371 loop : -1.05 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 431 HIS 0.003 0.001 HIS F 218 PHE 0.015 0.001 PHE D 67 TYR 0.018 0.001 TYR G 62 ARG 0.012 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 434 time to evaluate : 4.402 Fit side-chains REVERT: J 283 PHE cc_start: 0.8306 (m-80) cc_final: 0.7705 (m-10) REVERT: J 346 MET cc_start: 0.8127 (mtp) cc_final: 0.7796 (mtm) REVERT: J 437 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8283 (p) REVERT: J 467 ASN cc_start: 0.7480 (m-40) cc_final: 0.7026 (t0) REVERT: J 487 ASN cc_start: 0.6941 (m-40) cc_final: 0.6321 (t0) REVERT: J 550 GLN cc_start: 0.8070 (tt0) cc_final: 0.7832 (tt0) REVERT: J 570 MET cc_start: 0.8702 (ptm) cc_final: 0.8338 (ptm) REVERT: J 638 TYR cc_start: 0.7707 (t80) cc_final: 0.7036 (t80) REVERT: J 643 ILE cc_start: 0.7983 (mm) cc_final: 0.7763 (mp) REVERT: J 689 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: I 97 LEU cc_start: 0.7985 (tp) cc_final: 0.7668 (tm) REVERT: I 111 GLN cc_start: 0.7494 (tt0) cc_final: 0.7193 (tp40) REVERT: I 132 THR cc_start: 0.2231 (OUTLIER) cc_final: 0.2016 (p) REVERT: I 602 GLN cc_start: 0.8604 (mt0) cc_final: 0.8199 (mt0) REVERT: A 8 ASP cc_start: 0.5531 (p0) cc_final: 0.5077 (p0) REVERT: A 330 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.6602 (mp-120) REVERT: A 433 ASP cc_start: 0.7155 (m-30) cc_final: 0.6699 (m-30) REVERT: A 446 ASP cc_start: 0.8101 (t0) cc_final: 0.7839 (t0) REVERT: A 561 ASP cc_start: 0.7523 (t0) cc_final: 0.6760 (t0) REVERT: A 645 MET cc_start: 0.8207 (mmm) cc_final: 0.7821 (mmm) REVERT: B 169 LEU cc_start: 0.7769 (tt) cc_final: 0.7561 (tp) REVERT: B 205 GLU cc_start: 0.6804 (tt0) cc_final: 0.6527 (mt-10) REVERT: B 373 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7966 (mt) REVERT: B 474 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7552 (mtp-110) REVERT: B 476 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.5825 (mtp85) REVERT: B 639 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6908 (pp20) REVERT: B 643 ILE cc_start: 0.8257 (mt) cc_final: 0.8014 (mp) REVERT: B 698 TYR cc_start: 0.7712 (t80) cc_final: 0.7470 (t80) REVERT: E 31 LYS cc_start: 0.8415 (tttt) cc_final: 0.8095 (tttp) REVERT: E 247 ARG cc_start: 0.7548 (mtm180) cc_final: 0.7159 (mtm180) REVERT: E 390 ILE cc_start: 0.8582 (mp) cc_final: 0.8344 (mt) REVERT: E 557 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.6224 (mtm180) REVERT: E 663 ARG cc_start: 0.8040 (mtp-110) cc_final: 0.7553 (ttm110) REVERT: E 688 LYS cc_start: 0.8501 (mppt) cc_final: 0.8275 (mmtm) REVERT: F 601 GLU cc_start: 0.7756 (mm-30) cc_final: 0.6420 (tt0) REVERT: F 630 ASP cc_start: 0.7430 (t0) cc_final: 0.7221 (t0) REVERT: F 703 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8633 (tt0) REVERT: H 24 LYS cc_start: 0.7678 (mmtm) cc_final: 0.7249 (mmmt) REVERT: L 16 LYS cc_start: 0.7308 (mmmt) cc_final: 0.7023 (mmpt) REVERT: D 34 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.6356 (mtt-85) REVERT: C 39 ASN cc_start: 0.7937 (m-40) cc_final: 0.7614 (m-40) REVERT: G 462 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.7322 (m-10) REVERT: K 38 GLU cc_start: 0.8032 (tt0) cc_final: 0.7757 (mt-10) outliers start: 92 outliers final: 49 residues processed: 486 average time/residue: 1.3042 time to fit residues: 776.7930 Evaluate side-chains 472 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 413 time to evaluate : 4.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain J residue 689 GLU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 553 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 462 TYR Chi-restraints excluded: chain K residue 54 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 259 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 250 optimal weight: 0.0050 chunk 126 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 266 optimal weight: 8.9990 chunk 285 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 39 optimal weight: 0.0470 chunk 329 optimal weight: 0.7980 overall best weight: 0.4492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 121 HIS I 185 HIS A 19 GLN A 260 GLN A 467 ASN A 649 HIS B 467 ASN B 523 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35602 Z= 0.147 Angle : 0.486 14.338 48106 Z= 0.252 Chirality : 0.040 0.221 5649 Planarity : 0.003 0.058 6007 Dihedral : 8.633 163.482 5262 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.16 % Allowed : 18.78 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.32 (0.13), residues: 4369 helix: 1.92 (0.10), residues: 2702 sheet: -0.36 (0.27), residues: 377 loop : -0.97 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 431 HIS 0.005 0.000 HIS I 185 PHE 0.029 0.001 PHE A 278 TYR 0.018 0.001 TYR C 462 ARG 0.015 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 449 time to evaluate : 4.033 Fit side-chains revert: symmetry clash REVERT: J 283 PHE cc_start: 0.8294 (m-80) cc_final: 0.7709 (m-10) REVERT: J 341 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8311 (m-40) REVERT: J 346 MET cc_start: 0.8127 (mtp) cc_final: 0.7790 (mtm) REVERT: J 437 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8240 (p) REVERT: J 467 ASN cc_start: 0.7469 (m-40) cc_final: 0.7023 (t0) REVERT: J 550 GLN cc_start: 0.8010 (tt0) cc_final: 0.7776 (tt0) REVERT: J 570 MET cc_start: 0.8703 (ptm) cc_final: 0.8342 (ptm) REVERT: J 638 TYR cc_start: 0.7617 (t80) cc_final: 0.6866 (t80) REVERT: J 643 ILE cc_start: 0.7961 (mm) cc_final: 0.7738 (mp) REVERT: J 689 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: I 88 LYS cc_start: 0.8345 (tptm) cc_final: 0.8022 (tptp) REVERT: I 97 LEU cc_start: 0.7987 (tp) cc_final: 0.7670 (tm) REVERT: I 111 GLN cc_start: 0.7469 (tt0) cc_final: 0.7175 (tp40) REVERT: I 602 GLN cc_start: 0.8563 (mt0) cc_final: 0.8183 (mt0) REVERT: A 8 ASP cc_start: 0.5522 (p0) cc_final: 0.5077 (p0) REVERT: A 250 ASP cc_start: 0.7474 (t0) cc_final: 0.7200 (t0) REVERT: A 433 ASP cc_start: 0.7123 (m-30) cc_final: 0.6651 (m-30) REVERT: A 446 ASP cc_start: 0.8075 (t0) cc_final: 0.7802 (t0) REVERT: A 561 ASP cc_start: 0.7518 (t0) cc_final: 0.6772 (t0) REVERT: A 645 MET cc_start: 0.8161 (mmm) cc_final: 0.7755 (mmm) REVERT: B 169 LEU cc_start: 0.7759 (tt) cc_final: 0.7550 (tp) REVERT: B 205 GLU cc_start: 0.6864 (tt0) cc_final: 0.6592 (mt-10) REVERT: B 256 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7752 (mtt180) REVERT: B 373 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7965 (mt) REVERT: B 439 ILE cc_start: 0.7985 (mt) cc_final: 0.7729 (tt) REVERT: B 474 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7548 (mtp-110) REVERT: B 476 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.5695 (mtp85) REVERT: B 639 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6889 (pp20) REVERT: B 643 ILE cc_start: 0.8329 (mt) cc_final: 0.8074 (mp) REVERT: B 698 TYR cc_start: 0.7706 (t80) cc_final: 0.7485 (t80) REVERT: E 31 LYS cc_start: 0.8408 (tttt) cc_final: 0.8081 (tttp) REVERT: E 95 ARG cc_start: 0.7293 (ptp-110) cc_final: 0.6449 (mtt180) REVERT: E 320 ASP cc_start: 0.7375 (m-30) cc_final: 0.7167 (m-30) REVERT: E 390 ILE cc_start: 0.8537 (mp) cc_final: 0.8303 (mt) REVERT: E 557 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6236 (mtm180) REVERT: E 663 ARG cc_start: 0.8026 (mtp-110) cc_final: 0.7531 (ttm110) REVERT: E 688 LYS cc_start: 0.8506 (mppt) cc_final: 0.8288 (mmtt) REVERT: F 601 GLU cc_start: 0.7717 (mm-30) cc_final: 0.6299 (tt0) REVERT: F 630 ASP cc_start: 0.7464 (t0) cc_final: 0.7242 (t0) REVERT: F 703 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8632 (tt0) REVERT: H 24 LYS cc_start: 0.7646 (mmtm) cc_final: 0.7213 (mmmt) REVERT: L 16 LYS cc_start: 0.7187 (mmmt) cc_final: 0.6943 (mmpt) REVERT: D 34 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.6199 (mtt-85) REVERT: C 39 ASN cc_start: 0.7839 (m-40) cc_final: 0.7522 (m-40) REVERT: G 456 MET cc_start: 0.8010 (mmt) cc_final: 0.7719 (mmt) REVERT: G 462 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.7217 (m-10) REVERT: K 38 GLU cc_start: 0.7997 (tt0) cc_final: 0.7717 (mt-10) outliers start: 79 outliers final: 43 residues processed: 501 average time/residue: 1.3287 time to fit residues: 821.7290 Evaluate side-chains 469 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 417 time to evaluate : 3.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 341 ASN Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain J residue 689 GLU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 553 VAL Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 462 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 381 optimal weight: 3.9990 chunk 401 optimal weight: 4.9990 chunk 366 optimal weight: 4.9990 chunk 390 optimal weight: 0.4980 chunk 235 optimal weight: 0.0060 chunk 170 optimal weight: 5.9990 chunk 306 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 353 optimal weight: 0.0870 chunk 369 optimal weight: 0.8980 chunk 389 optimal weight: 0.7980 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 121 HIS I 185 HIS A 19 GLN A 260 GLN A 330 GLN A 467 ASN B 467 ASN B 523 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 567 ASN ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35602 Z= 0.145 Angle : 0.486 15.155 48106 Z= 0.251 Chirality : 0.040 0.307 5649 Planarity : 0.003 0.060 6007 Dihedral : 8.324 161.390 5262 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.86 % Allowed : 19.36 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.46 (0.13), residues: 4369 helix: 2.04 (0.10), residues: 2681 sheet: -0.25 (0.27), residues: 372 loop : -0.93 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 431 HIS 0.006 0.001 HIS I 185 PHE 0.016 0.001 PHE H 63 TYR 0.019 0.001 TYR B 700 ARG 0.013 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 429 time to evaluate : 4.251 Fit side-chains REVERT: J 283 PHE cc_start: 0.8325 (m-80) cc_final: 0.7741 (m-10) REVERT: J 320 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: J 346 MET cc_start: 0.8101 (mtp) cc_final: 0.7756 (mtm) REVERT: J 467 ASN cc_start: 0.7443 (m-40) cc_final: 0.6960 (t0) REVERT: J 550 GLN cc_start: 0.8006 (tt0) cc_final: 0.7772 (tt0) REVERT: J 570 MET cc_start: 0.8688 (ptm) cc_final: 0.8324 (ptm) REVERT: J 630 ASP cc_start: 0.7263 (t70) cc_final: 0.7042 (t0) REVERT: J 638 TYR cc_start: 0.7611 (t80) cc_final: 0.6908 (t80) REVERT: J 643 ILE cc_start: 0.7938 (mm) cc_final: 0.7738 (mp) REVERT: I 88 LYS cc_start: 0.8343 (tptm) cc_final: 0.7994 (tptp) REVERT: I 97 LEU cc_start: 0.7969 (tp) cc_final: 0.7653 (tm) REVERT: I 111 GLN cc_start: 0.7471 (tt0) cc_final: 0.7155 (tp40) REVERT: I 570 MET cc_start: 0.8353 (ptp) cc_final: 0.8146 (ptm) REVERT: I 602 GLN cc_start: 0.8556 (mt0) cc_final: 0.8182 (mt0) REVERT: A 173 LEU cc_start: 0.8277 (mm) cc_final: 0.8073 (mt) REVERT: A 250 ASP cc_start: 0.7318 (t0) cc_final: 0.7089 (t0) REVERT: A 433 ASP cc_start: 0.7162 (m-30) cc_final: 0.6649 (m-30) REVERT: A 446 ASP cc_start: 0.8059 (t0) cc_final: 0.7778 (t0) REVERT: A 561 ASP cc_start: 0.7493 (t0) cc_final: 0.6759 (t0) REVERT: A 645 MET cc_start: 0.8160 (mmm) cc_final: 0.7718 (mmm) REVERT: B 205 GLU cc_start: 0.6870 (tt0) cc_final: 0.6597 (mt-10) REVERT: B 373 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7965 (mt) REVERT: B 439 ILE cc_start: 0.7896 (mt) cc_final: 0.7596 (tt) REVERT: B 474 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7522 (mtp-110) REVERT: B 476 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.5638 (mtp85) REVERT: B 639 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6899 (pp20) REVERT: B 643 ILE cc_start: 0.8300 (mt) cc_final: 0.8059 (mp) REVERT: E 31 LYS cc_start: 0.8411 (tttt) cc_final: 0.8085 (tttp) REVERT: E 320 ASP cc_start: 0.7336 (m-30) cc_final: 0.7132 (m-30) REVERT: E 663 ARG cc_start: 0.7944 (mtp-110) cc_final: 0.7444 (ttm110) REVERT: F 601 GLU cc_start: 0.7718 (mm-30) cc_final: 0.6304 (tt0) REVERT: F 630 ASP cc_start: 0.7445 (t0) cc_final: 0.7209 (t0) REVERT: F 703 GLN cc_start: 0.8911 (tm-30) cc_final: 0.8629 (tt0) REVERT: H 24 LYS cc_start: 0.7680 (mmtm) cc_final: 0.7264 (mmmt) REVERT: L 16 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6942 (mmpt) REVERT: C 39 ASN cc_start: 0.7811 (m-40) cc_final: 0.7500 (m-40) REVERT: G 462 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.7167 (m-10) REVERT: K 38 GLU cc_start: 0.7973 (tt0) cc_final: 0.7684 (mt-10) outliers start: 68 outliers final: 42 residues processed: 469 average time/residue: 1.2871 time to fit residues: 741.3877 Evaluate side-chains 458 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 410 time to evaluate : 3.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 320 ASP Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 462 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 256 optimal weight: 0.8980 chunk 413 optimal weight: 4.9990 chunk 252 optimal weight: 0.4980 chunk 195 optimal weight: 8.9990 chunk 287 optimal weight: 0.0670 chunk 433 optimal weight: 3.9990 chunk 398 optimal weight: 0.8980 chunk 345 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 266 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 523 ASN I 121 HIS I 185 HIS A 260 GLN A 467 ASN B 467 ASN B 523 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 567 ASN ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35602 Z= 0.157 Angle : 0.487 14.839 48106 Z= 0.252 Chirality : 0.040 0.198 5649 Planarity : 0.004 0.062 6007 Dihedral : 8.196 159.685 5262 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.69 % Allowed : 19.79 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.47 (0.13), residues: 4369 helix: 2.05 (0.10), residues: 2679 sheet: -0.28 (0.27), residues: 375 loop : -0.91 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 431 HIS 0.007 0.001 HIS I 185 PHE 0.031 0.001 PHE A 278 TYR 0.017 0.001 TYR B 700 ARG 0.016 0.000 ARG E 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 421 time to evaluate : 4.098 Fit side-chains REVERT: J 283 PHE cc_start: 0.8333 (m-80) cc_final: 0.7790 (m-10) REVERT: J 320 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7089 (m-30) REVERT: J 346 MET cc_start: 0.8122 (mtp) cc_final: 0.7781 (mtm) REVERT: J 467 ASN cc_start: 0.7460 (m-40) cc_final: 0.7012 (t0) REVERT: J 474 ARG cc_start: 0.7657 (ttm110) cc_final: 0.7350 (ttm110) REVERT: J 550 GLN cc_start: 0.8012 (tt0) cc_final: 0.7789 (tt0) REVERT: J 570 MET cc_start: 0.8690 (ptm) cc_final: 0.8326 (ptm) REVERT: J 638 TYR cc_start: 0.7602 (t80) cc_final: 0.6878 (t80) REVERT: J 689 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: I 97 LEU cc_start: 0.8036 (tp) cc_final: 0.7716 (tm) REVERT: I 111 GLN cc_start: 0.7461 (tt0) cc_final: 0.7146 (tp40) REVERT: I 602 GLN cc_start: 0.8552 (mt0) cc_final: 0.8197 (mt0) REVERT: A 173 LEU cc_start: 0.8269 (mm) cc_final: 0.8064 (mt) REVERT: A 250 ASP cc_start: 0.7295 (t0) cc_final: 0.7087 (t0) REVERT: A 433 ASP cc_start: 0.7166 (m-30) cc_final: 0.6658 (m-30) REVERT: A 446 ASP cc_start: 0.8088 (t0) cc_final: 0.7804 (t0) REVERT: A 561 ASP cc_start: 0.7530 (t0) cc_final: 0.6781 (t0) REVERT: A 645 MET cc_start: 0.8160 (mmm) cc_final: 0.7703 (mmm) REVERT: B 205 GLU cc_start: 0.6856 (tt0) cc_final: 0.6578 (mt-10) REVERT: B 373 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7969 (mt) REVERT: B 439 ILE cc_start: 0.7895 (mt) cc_final: 0.7597 (tt) REVERT: B 474 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7511 (mtp-110) REVERT: B 476 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.5664 (mtp85) REVERT: B 639 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6874 (pp20) REVERT: B 643 ILE cc_start: 0.8271 (mt) cc_final: 0.8037 (mp) REVERT: E 31 LYS cc_start: 0.8418 (tttt) cc_final: 0.8092 (tttp) REVERT: E 95 ARG cc_start: 0.7331 (ptp-110) cc_final: 0.6421 (mtt180) REVERT: E 320 ASP cc_start: 0.7343 (m-30) cc_final: 0.7139 (m-30) REVERT: E 663 ARG cc_start: 0.7945 (mtp-110) cc_final: 0.7446 (ttm110) REVERT: F 601 GLU cc_start: 0.7724 (mm-30) cc_final: 0.6308 (tt0) REVERT: F 630 ASP cc_start: 0.7460 (t0) cc_final: 0.7233 (t0) REVERT: F 703 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8644 (tt0) REVERT: H 24 LYS cc_start: 0.7633 (mmtm) cc_final: 0.7217 (mmmt) REVERT: L 16 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6947 (mmpt) REVERT: C 39 ASN cc_start: 0.7837 (m-40) cc_final: 0.7519 (m-40) REVERT: G 462 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: K 38 GLU cc_start: 0.7985 (tt0) cc_final: 0.7695 (mt-10) outliers start: 62 outliers final: 43 residues processed: 459 average time/residue: 1.3312 time to fit residues: 749.9609 Evaluate side-chains 457 residues out of total 3838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 407 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 320 ASP Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain J residue 689 GLU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 462 TYR Chi-restraints excluded: chain K residue 54 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 274 optimal weight: 1.9990 chunk 367 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 345 optimal weight: 0.7980 chunk 144 optimal weight: 0.0980 chunk 354 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 121 HIS I 185 HIS A 260 GLN A 467 ASN B 467 ASN B 523 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 567 ASN ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.150769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112240 restraints weight = 44500.403| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.32 r_work: 0.3221 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35602 Z= 0.161 Angle : 0.488 14.182 48106 Z= 0.253 Chirality : 0.040 0.191 5649 Planarity : 0.004 0.062 6007 Dihedral : 8.088 157.783 5262 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.77 % Allowed : 19.74 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.49 (0.13), residues: 4369 helix: 2.06 (0.10), residues: 2675 sheet: -0.18 (0.27), residues: 371 loop : -0.91 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 431 HIS 0.008 0.001 HIS I 185 PHE 0.018 0.001 PHE H 63 TYR 0.025 0.001 TYR G 62 ARG 0.015 0.000 ARG E 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12930.92 seconds wall clock time: 230 minutes 27.17 seconds (13827.17 seconds total)