Starting phenix.real_space_refine on Tue Sep 24 18:35:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/09_2024/7adc_11723.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/09_2024/7adc_11723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/09_2024/7adc_11723.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/09_2024/7adc_11723.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/09_2024/7adc_11723.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adc_11723/09_2024/7adc_11723.cif" } resolution = 4.0 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= 0.003 sd= 0.016 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 96 5.49 5 Mg 6 5.21 5 S 223 5.16 5 Be 5 3.05 5 C 32003 2.51 5 N 9111 2.21 5 O 10104 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 159 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 51565 Number of models: 1 Model: "" Number of chains: 21 Chain: "a" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3852 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 480} Chain: "U" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1825 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Chain: "V" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2504 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 303} Chain: "W" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "X" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "Y" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10545 Classifications: {'peptide': 1358} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Chain: "K" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 515 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 682 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "R" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 590 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 12} Link IDs: {'rna2p': 7, 'rna3p': 20} Chain breaks: 1 Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39504 SG CYS Y 70 55.781 119.368 118.676 1.00132.17 S ATOM 39518 SG CYS Y 72 55.851 116.963 121.610 1.00141.56 S ATOM 39650 SG CYS Y 88 56.884 119.450 123.963 1.00131.23 S ATOM 45338 SG CYS Y 814 70.313 185.472 120.093 1.00 77.05 S ATOM 45903 SG CYS Y 888 71.680 181.458 120.146 1.00 71.20 S ATOM 45954 SG CYS Y 895 70.584 182.742 116.905 1.00 70.90 S ATOM 45975 SG CYS Y 898 73.251 184.751 118.230 1.00 63.61 S Restraints were copied for chains: b, c, d, e, f Time building chain proxies: 22.20, per 1000 atoms: 0.43 Number of scatterers: 51565 At special positions: 0 Unit cell: (161.2, 226.92, 194.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 223 16.00 P 96 15.00 Mg 6 11.99 F 15 9.00 O 10104 8.00 N 9111 7.00 C 32003 6.00 Be 5 4.00 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 - 3.00 Amino acid : True - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.16 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y1502 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 72 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 88 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 70 " pdb=" ZN Y1503 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 888 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 898 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 814 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 895 " Number of angles added : 6 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11746 Finding SS restraints... Secondary structure from input PDB file: 231 helices and 74 sheets defined 41.4% alpha, 17.4% beta 30 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 14.93 Creating SS restraints... Processing helix chain 'f' and resid 3 through 8 Processing helix chain 'f' and resid 10 through 21 removed outlier: 3.506A pdb=" N LEU f 14 " --> pdb=" O PRO f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 45 removed outlier: 3.809A pdb=" N SER f 45 " --> pdb=" O GLN f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 90 removed outlier: 3.644A pdb=" N ILE f 86 " --> pdb=" O SER f 82 " (cutoff:3.500A) Processing helix chain 'f' and resid 123 through 129 Processing helix chain 'f' and resid 156 through 161 Processing helix chain 'f' and resid 161 through 166 Processing helix chain 'f' and resid 183 through 199 Processing helix chain 'f' and resid 212 through 221 Processing helix chain 'f' and resid 235 through 256 removed outlier: 3.926A pdb=" N HIS f 239 " --> pdb=" O PRO f 235 " (cutoff:3.500A) Processing helix chain 'f' and resid 266 through 278 removed outlier: 3.581A pdb=" N LEU f 270 " --> pdb=" O SER f 266 " (cutoff:3.500A) Processing helix chain 'f' and resid 294 through 303 Processing helix chain 'f' and resid 325 through 335 Processing helix chain 'f' and resid 346 through 352 removed outlier: 3.654A pdb=" N LYS f 352 " --> pdb=" O LYS f 348 " (cutoff:3.500A) Processing helix chain 'f' and resid 373 through 388 Processing helix chain 'f' and resid 392 through 406 removed outlier: 3.684A pdb=" N THR f 406 " --> pdb=" O LYS f 402 " (cutoff:3.500A) Processing helix chain 'f' and resid 408 through 416 removed outlier: 3.802A pdb=" N PHE f 412 " --> pdb=" O THR f 408 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 8 Processing helix chain 'a' and resid 10 through 21 removed outlier: 3.506A pdb=" N LEU a 14 " --> pdb=" O PRO a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 45 removed outlier: 3.808A pdb=" N SER a 45 " --> pdb=" O GLN a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 82 through 90 removed outlier: 3.644A pdb=" N ILE a 86 " --> pdb=" O SER a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 129 Processing helix chain 'a' and resid 156 through 161 Processing helix chain 'a' and resid 161 through 166 Processing helix chain 'a' and resid 183 through 199 Processing helix chain 'a' and resid 212 through 221 Processing helix chain 'a' and resid 235 through 256 removed outlier: 3.925A pdb=" N HIS a 239 " --> pdb=" O PRO a 235 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 278 removed outlier: 3.582A pdb=" N LEU a 270 " --> pdb=" O SER a 266 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 303 Processing helix chain 'a' and resid 325 through 335 Processing helix chain 'a' and resid 346 through 352 removed outlier: 3.654A pdb=" N LYS a 352 " --> pdb=" O LYS a 348 " (cutoff:3.500A) Processing helix chain 'a' and resid 373 through 388 Processing helix chain 'a' and resid 392 through 406 removed outlier: 3.685A pdb=" N THR a 406 " --> pdb=" O LYS a 402 " (cutoff:3.500A) Processing helix chain 'a' and resid 408 through 416 removed outlier: 3.802A pdb=" N PHE a 412 " --> pdb=" O THR a 408 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 8 Processing helix chain 'b' and resid 10 through 21 removed outlier: 3.506A pdb=" N LEU b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 45 removed outlier: 3.809A pdb=" N SER b 45 " --> pdb=" O GLN b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 90 removed outlier: 3.643A pdb=" N ILE b 86 " --> pdb=" O SER b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 129 Processing helix chain 'b' and resid 156 through 161 Processing helix chain 'b' and resid 161 through 166 Processing helix chain 'b' and resid 183 through 199 Processing helix chain 'b' and resid 212 through 221 Processing helix chain 'b' and resid 235 through 256 removed outlier: 3.925A pdb=" N HIS b 239 " --> pdb=" O PRO b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 266 through 278 removed outlier: 3.582A pdb=" N LEU b 270 " --> pdb=" O SER b 266 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 303 Processing helix chain 'b' and resid 325 through 335 Processing helix chain 'b' and resid 346 through 352 removed outlier: 3.654A pdb=" N LYS b 352 " --> pdb=" O LYS b 348 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 388 Processing helix chain 'b' and resid 392 through 406 removed outlier: 3.684A pdb=" N THR b 406 " --> pdb=" O LYS b 402 " (cutoff:3.500A) Processing helix chain 'b' and resid 408 through 416 removed outlier: 3.803A pdb=" N PHE b 412 " --> pdb=" O THR b 408 " (cutoff:3.500A) Processing helix chain 'c' and resid 3 through 8 Processing helix chain 'c' and resid 10 through 21 removed outlier: 3.507A pdb=" N LEU c 14 " --> pdb=" O PRO c 10 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 45 removed outlier: 3.809A pdb=" N SER c 45 " --> pdb=" O GLN c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 90 removed outlier: 3.644A pdb=" N ILE c 86 " --> pdb=" O SER c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 129 Processing helix chain 'c' and resid 156 through 161 Processing helix chain 'c' and resid 161 through 166 Processing helix chain 'c' and resid 183 through 199 Processing helix chain 'c' and resid 212 through 221 Processing helix chain 'c' and resid 235 through 256 removed outlier: 3.926A pdb=" N HIS c 239 " --> pdb=" O PRO c 235 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 278 removed outlier: 3.583A pdb=" N LEU c 270 " --> pdb=" O SER c 266 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 303 Processing helix chain 'c' and resid 325 through 335 Processing helix chain 'c' and resid 346 through 352 removed outlier: 3.654A pdb=" N LYS c 352 " --> pdb=" O LYS c 348 " (cutoff:3.500A) Processing helix chain 'c' and resid 373 through 388 Processing helix chain 'c' and resid 392 through 406 removed outlier: 3.684A pdb=" N THR c 406 " --> pdb=" O LYS c 402 " (cutoff:3.500A) Processing helix chain 'c' and resid 408 through 416 removed outlier: 3.803A pdb=" N PHE c 412 " --> pdb=" O THR c 408 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 8 Processing helix chain 'd' and resid 10 through 21 removed outlier: 3.506A pdb=" N LEU d 14 " --> pdb=" O PRO d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 45 removed outlier: 3.809A pdb=" N SER d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 90 removed outlier: 3.645A pdb=" N ILE d 86 " --> pdb=" O SER d 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 129 Processing helix chain 'd' and resid 156 through 161 Processing helix chain 'd' and resid 161 through 166 Processing helix chain 'd' and resid 183 through 199 Processing helix chain 'd' and resid 212 through 221 Processing helix chain 'd' and resid 235 through 256 removed outlier: 3.925A pdb=" N HIS d 239 " --> pdb=" O PRO d 235 " (cutoff:3.500A) Processing helix chain 'd' and resid 266 through 278 removed outlier: 3.581A pdb=" N LEU d 270 " --> pdb=" O SER d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 294 through 303 Processing helix chain 'd' and resid 325 through 335 Processing helix chain 'd' and resid 346 through 352 removed outlier: 3.654A pdb=" N LYS d 352 " --> pdb=" O LYS d 348 " (cutoff:3.500A) Processing helix chain 'd' and resid 373 through 388 Processing helix chain 'd' and resid 392 through 406 removed outlier: 3.683A pdb=" N THR d 406 " --> pdb=" O LYS d 402 " (cutoff:3.500A) Processing helix chain 'd' and resid 408 through 416 removed outlier: 3.803A pdb=" N PHE d 412 " --> pdb=" O THR d 408 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 8 Processing helix chain 'e' and resid 10 through 21 removed outlier: 3.506A pdb=" N LEU e 14 " --> pdb=" O PRO e 10 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 45 removed outlier: 3.809A pdb=" N SER e 45 " --> pdb=" O GLN e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 90 removed outlier: 3.645A pdb=" N ILE e 86 " --> pdb=" O SER e 82 " (cutoff:3.500A) Processing helix chain 'e' and resid 123 through 129 Processing helix chain 'e' and resid 156 through 161 Processing helix chain 'e' and resid 161 through 166 Processing helix chain 'e' and resid 183 through 199 Processing helix chain 'e' and resid 212 through 221 Processing helix chain 'e' and resid 235 through 256 removed outlier: 3.926A pdb=" N HIS e 239 " --> pdb=" O PRO e 235 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 278 removed outlier: 3.583A pdb=" N LEU e 270 " --> pdb=" O SER e 266 " (cutoff:3.500A) Processing helix chain 'e' and resid 294 through 303 Processing helix chain 'e' and resid 325 through 335 Processing helix chain 'e' and resid 346 through 352 removed outlier: 3.654A pdb=" N LYS e 352 " --> pdb=" O LYS e 348 " (cutoff:3.500A) Processing helix chain 'e' and resid 373 through 388 Processing helix chain 'e' and resid 392 through 406 removed outlier: 3.684A pdb=" N THR e 406 " --> pdb=" O LYS e 402 " (cutoff:3.500A) Processing helix chain 'e' and resid 408 through 416 removed outlier: 3.802A pdb=" N PHE e 412 " --> pdb=" O THR e 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 19 through 39 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 103 through 132 removed outlier: 3.973A pdb=" N PHE A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 213 removed outlier: 3.595A pdb=" N LEU A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 330 removed outlier: 4.044A pdb=" N ALA A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.686A pdb=" N TYR A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 426 Processing helix chain 'A' and resid 431 through 436 removed outlier: 3.517A pdb=" N ASN A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 removed outlier: 3.562A pdb=" N GLY A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.530A pdb=" N GLU A 461 " --> pdb=" O ASP A 458 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN A 462 " --> pdb=" O LEU A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 458 through 462' Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 474 through 490 Processing helix chain 'U' and resid 34 through 50 removed outlier: 3.590A pdb=" N THR U 38 " --> pdb=" O GLY U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 88 Processing helix chain 'U' and resid 212 through 233 removed outlier: 3.959A pdb=" N ASP U 233 " --> pdb=" O GLU U 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 18 through 21 Processing helix chain 'V' and resid 34 through 49 removed outlier: 3.703A pdb=" N THR V 38 " --> pdb=" O GLY V 34 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER V 49 " --> pdb=" O ARG V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 87 Processing helix chain 'V' and resid 113 through 115 No H-bonds generated for 'chain 'V' and resid 113 through 115' Processing helix chain 'V' and resid 154 through 165 removed outlier: 4.147A pdb=" N GLU V 165 " --> pdb=" O SER V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 212 through 229 Processing helix chain 'V' and resid 230 through 232 No H-bonds generated for 'chain 'V' and resid 230 through 232' Processing helix chain 'V' and resid 250 through 255 removed outlier: 4.017A pdb=" N LEU V 254 " --> pdb=" O ASP V 250 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG V 255 " --> pdb=" O PRO V 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 250 through 255' Processing helix chain 'V' and resid 256 through 260 removed outlier: 3.627A pdb=" N LEU V 260 " --> pdb=" O VAL V 257 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 273 removed outlier: 3.813A pdb=" N GLU V 273 " --> pdb=" O CYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 278 through 283 removed outlier: 3.761A pdb=" N GLN V 283 " --> pdb=" O GLY V 279 " (cutoff:3.500A) Processing helix chain 'V' and resid 285 through 289 Processing helix chain 'V' and resid 297 through 309 removed outlier: 3.519A pdb=" N ALA V 308 " --> pdb=" O LYS V 304 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 13 Processing helix chain 'W' and resid 16 through 32 Processing helix chain 'W' and resid 45 through 56 Processing helix chain 'W' and resid 60 through 80 Processing helix chain 'X' and resid 4 through 10 removed outlier: 3.529A pdb=" N ARG X 10 " --> pdb=" O THR X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 39 Processing helix chain 'X' and resid 49 through 57 Processing helix chain 'X' and resid 81 through 89 Processing helix chain 'X' and resid 206 through 212 Processing helix chain 'X' and resid 216 through 225 Processing helix chain 'X' and resid 270 through 280 removed outlier: 3.814A pdb=" N ASP X 280 " --> pdb=" O GLN X 276 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 293 removed outlier: 4.369A pdb=" N ILE X 292 " --> pdb=" O PRO X 288 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA X 293 " --> pdb=" O VAL X 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 288 through 293' Processing helix chain 'X' and resid 318 through 329 removed outlier: 3.705A pdb=" N GLY X 329 " --> pdb=" O LEU X 325 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 353 Processing helix chain 'X' and resid 358 through 371 Processing helix chain 'X' and resid 377 through 390 removed outlier: 3.657A pdb=" N SER X 383 " --> pdb=" O GLU X 379 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU X 384 " --> pdb=" O ALA X 380 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE X 385 " --> pdb=" O ALA X 381 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE X 389 " --> pdb=" O PHE X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 398 through 409 Processing helix chain 'X' and resid 421 through 438 Processing helix chain 'X' and resid 455 through 479 removed outlier: 3.573A pdb=" N MET X 459 " --> pdb=" O SER X 455 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG X 470 " --> pdb=" O VAL X 466 " (cutoff:3.500A) Processing helix chain 'X' and resid 495 through 508 Processing helix chain 'X' and resid 519 through 528 Processing helix chain 'X' and resid 539 through 543 removed outlier: 3.982A pdb=" N ALA X 543 " --> pdb=" O ARG X 540 " (cutoff:3.500A) Processing helix chain 'X' and resid 544 through 549 removed outlier: 3.886A pdb=" N ARG X 548 " --> pdb=" O GLY X 544 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP X 549 " --> pdb=" O PHE X 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 544 through 549' Processing helix chain 'X' and resid 551 through 555 Processing helix chain 'X' and resid 608 through 612 removed outlier: 3.577A pdb=" N GLU X 611 " --> pdb=" O ALA X 608 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY X 612 " --> pdb=" O ILE X 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 608 through 612' Processing helix chain 'X' and resid 662 through 667 removed outlier: 3.917A pdb=" N LEU X 667 " --> pdb=" O VAL X 663 " (cutoff:3.500A) Processing helix chain 'X' and resid 670 through 674 Processing helix chain 'X' and resid 675 through 687 removed outlier: 3.746A pdb=" N ARG X 687 " --> pdb=" O ALA X 683 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 712 removed outlier: 3.515A pdb=" N ALA X 709 " --> pdb=" O GLU X 705 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL X 710 " --> pdb=" O ARG X 706 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER X 712 " --> pdb=" O VAL X 708 " (cutoff:3.500A) Processing helix chain 'X' and resid 820 through 825 Processing helix chain 'X' and resid 896 through 906 Processing helix chain 'X' and resid 942 through 979 Processing helix chain 'X' and resid 982 through 990 Processing helix chain 'X' and resid 992 through 996 removed outlier: 4.109A pdb=" N ASP X 995 " --> pdb=" O LEU X 992 " (cutoff:3.500A) Processing helix chain 'X' and resid 1003 through 1038 removed outlier: 5.201A pdb=" N ASN X1009 " --> pdb=" O GLU X1005 " (cutoff:3.500A) Processing helix chain 'X' and resid 1099 through 1103 Processing helix chain 'X' and resid 1109 through 1134 removed outlier: 3.570A pdb=" N LEU X1113 " --> pdb=" O ILE X1109 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN X1134 " --> pdb=" O ALA X1130 " (cutoff:3.500A) Processing helix chain 'X' and resid 1137 through 1150 Processing helix chain 'X' and resid 1167 through 1177 removed outlier: 3.713A pdb=" N ARG X1171 " --> pdb=" O GLU X1167 " (cutoff:3.500A) Processing helix chain 'X' and resid 1191 through 1202 removed outlier: 3.693A pdb=" N GLY X1202 " --> pdb=" O LEU X1198 " (cutoff:3.500A) Processing helix chain 'X' and resid 1238 through 1242 Processing helix chain 'X' and resid 1271 through 1281 Processing helix chain 'X' and resid 1283 through 1292 removed outlier: 3.654A pdb=" N THR X1292 " --> pdb=" O GLN X1288 " (cutoff:3.500A) Processing helix chain 'X' and resid 1299 through 1310 removed outlier: 3.857A pdb=" N LYS X1303 " --> pdb=" O ASN X1299 " (cutoff:3.500A) Processing helix chain 'X' and resid 1320 through 1333 Processing helix chain 'Y' and resid 26 through 33 Processing helix chain 'Y' and resid 94 through 100 removed outlier: 3.531A pdb=" N VAL Y 97 " --> pdb=" O GLN Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 113 through 118 Processing helix chain 'Y' and resid 122 through 128 Processing helix chain 'Y' and resid 131 through 140 Processing helix chain 'Y' and resid 161 through 170 removed outlier: 3.789A pdb=" N ALA Y 168 " --> pdb=" O GLN Y 164 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU Y 170 " --> pdb=" O LEU Y 166 " (cutoff:3.500A) Processing helix chain 'Y' and resid 181 through 191 removed outlier: 3.685A pdb=" N ILE Y 185 " --> pdb=" O GLY Y 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 208 Processing helix chain 'Y' and resid 211 through 230 Processing helix chain 'Y' and resid 233 through 236 Processing helix chain 'Y' and resid 263 through 285 removed outlier: 3.554A pdb=" N ASP Y 267 " --> pdb=" O SER Y 263 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 308 Processing helix chain 'Y' and resid 327 through 331 Processing helix chain 'Y' and resid 332 through 335 removed outlier: 3.944A pdb=" N GLN Y 335 " --> pdb=" O LYS Y 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 332 through 335' Processing helix chain 'Y' and resid 336 through 341 Processing helix chain 'Y' and resid 370 through 377 Processing helix chain 'Y' and resid 377 through 388 Processing helix chain 'Y' and resid 393 through 404 removed outlier: 3.577A pdb=" N ALA Y 397 " --> pdb=" O THR Y 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 408 through 416 Processing helix chain 'Y' and resid 430 through 432 No H-bonds generated for 'chain 'Y' and resid 430 through 432' Processing helix chain 'Y' and resid 450 through 458 removed outlier: 3.662A pdb=" N CYS Y 454 " --> pdb=" O HIS Y 450 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA Y 455 " --> pdb=" O PRO Y 451 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ALA Y 456 " --> pdb=" O LEU Y 452 " (cutoff:3.500A) Processing helix chain 'Y' and resid 473 through 483 Processing helix chain 'Y' and resid 503 through 515 Processing helix chain 'Y' and resid 529 through 539 Processing helix chain 'Y' and resid 574 through 580 Processing helix chain 'Y' and resid 588 through 592 removed outlier: 3.878A pdb=" N ILE Y 591 " --> pdb=" O PRO Y 588 " (cutoff:3.500A) Processing helix chain 'Y' and resid 597 through 613 Processing helix chain 'Y' and resid 614 through 636 removed outlier: 4.339A pdb=" N ILE Y 619 " --> pdb=" O LYS Y 615 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY Y 636 " --> pdb=" O ALA Y 632 " (cutoff:3.500A) Processing helix chain 'Y' and resid 649 through 670 Processing helix chain 'Y' and resid 674 through 703 Processing helix chain 'Y' and resid 720 through 728 Processing helix chain 'Y' and resid 733 through 742 Processing helix chain 'Y' and resid 768 through 804 removed outlier: 3.861A pdb=" N LYS Y 781 " --> pdb=" O HIS Y 777 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY Y 782 " --> pdb=" O GLY Y 778 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR Y 786 " --> pdb=" O GLY Y 782 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA Y 787 " --> pdb=" O LEU Y 783 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ALA Y 791 " --> pdb=" O ALA Y 787 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN Y 792 " --> pdb=" O LEU Y 788 " (cutoff:3.500A) Processing helix chain 'Y' and resid 835 through 839 Processing helix chain 'Y' and resid 865 through 875 Processing helix chain 'Y' and resid 896 through 900 removed outlier: 3.977A pdb=" N GLY Y 900 " --> pdb=" O ALA Y 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 896 through 900' Processing helix chain 'Y' and resid 914 through 925 removed outlier: 3.686A pdb=" N ILE Y 918 " --> pdb=" O ALA Y 914 " (cutoff:3.500A) Processing helix chain 'Y' and resid 926 through 930 Processing helix chain 'Y' and resid 944 through 949 removed outlier: 3.754A pdb=" N SER Y 949 " --> pdb=" O ALA Y 946 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1137 through 1146 Processing helix chain 'Y' and resid 1216 through 1225 Processing helix chain 'Y' and resid 1225 through 1245 removed outlier: 3.978A pdb=" N VAL Y1229 " --> pdb=" O GLY Y1225 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR Y1230 " --> pdb=" O VAL Y1226 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN Y1244 " --> pdb=" O VAL Y1240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1249 through 1261 removed outlier: 4.357A pdb=" N ILE Y1253 " --> pdb=" O ASN Y1249 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1281 through 1295 removed outlier: 3.594A pdb=" N ASN Y1295 " --> pdb=" O GLU Y1291 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1308 through 1313 removed outlier: 3.631A pdb=" N SER Y1313 " --> pdb=" O ILE Y1309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1319 through 1325 removed outlier: 3.619A pdb=" N PHE Y1325 " --> pdb=" O SER Y1321 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1327 through 1338 removed outlier: 3.738A pdb=" N VAL Y1331 " --> pdb=" O GLU Y1327 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1347 through 1354 Processing helix chain 'Y' and resid 1362 through 1373 removed outlier: 3.580A pdb=" N ARG Y1372 " --> pdb=" O ASP Y1368 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG Y1373 " --> pdb=" O ARG Y1369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'f' and resid 49 through 57 removed outlier: 3.855A pdb=" N LEU f 113 " --> pdb=" O TYR f 80 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS f 100 " --> pdb=" O LEU f 114 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL f 116 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER f 98 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU f 118 " --> pdb=" O THR f 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR f 96 " --> pdb=" O GLU f 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'f' and resid 228 through 231 removed outlier: 7.677A pdb=" N VAL f 228 " --> pdb=" O LEU f 207 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE f 209 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER f 230 " --> pdb=" O ILE f 209 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE f 261 " --> pdb=" O VAL f 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'f' and resid 228 through 231 removed outlier: 7.677A pdb=" N VAL f 228 " --> pdb=" O LEU f 207 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE f 209 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER f 230 " --> pdb=" O ILE f 209 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE f 261 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY f 174 " --> pdb=" O ALA f 317 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA f 319 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE f 176 " --> pdb=" O ALA f 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'f' and resid 284 through 285 removed outlier: 3.933A pdb=" N VAL f 289 " --> pdb=" O LEU f 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 49 through 57 removed outlier: 3.856A pdb=" N LEU a 113 " --> pdb=" O TYR a 80 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LYS a 100 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL a 116 " --> pdb=" O SER a 98 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER a 98 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU a 118 " --> pdb=" O THR a 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR a 96 " --> pdb=" O GLU a 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 228 through 231 removed outlier: 7.677A pdb=" N VAL a 228 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE a 209 " --> pdb=" O VAL a 228 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER a 230 " --> pdb=" O ILE a 209 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE a 261 " --> pdb=" O VAL a 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 228 through 231 removed outlier: 7.677A pdb=" N VAL a 228 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE a 209 " --> pdb=" O VAL a 228 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER a 230 " --> pdb=" O ILE a 209 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE a 261 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY a 174 " --> pdb=" O ALA a 317 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA a 319 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE a 176 " --> pdb=" O ALA a 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 284 through 285 removed outlier: 3.932A pdb=" N VAL a 289 " --> pdb=" O LEU a 285 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 49 through 57 removed outlier: 3.855A pdb=" N LEU b 113 " --> pdb=" O TYR b 80 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS b 100 " --> pdb=" O LEU b 114 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL b 116 " --> pdb=" O SER b 98 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER b 98 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU b 118 " --> pdb=" O THR b 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR b 96 " --> pdb=" O GLU b 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 228 through 231 removed outlier: 7.677A pdb=" N VAL b 228 " --> pdb=" O LEU b 207 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE b 209 " --> pdb=" O VAL b 228 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER b 230 " --> pdb=" O ILE b 209 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE b 261 " --> pdb=" O VAL b 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 228 through 231 removed outlier: 7.677A pdb=" N VAL b 228 " --> pdb=" O LEU b 207 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE b 209 " --> pdb=" O VAL b 228 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER b 230 " --> pdb=" O ILE b 209 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE b 261 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY b 174 " --> pdb=" O ALA b 317 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA b 319 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE b 176 " --> pdb=" O ALA b 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 284 through 285 removed outlier: 3.933A pdb=" N VAL b 289 " --> pdb=" O LEU b 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 49 through 57 removed outlier: 3.855A pdb=" N LEU c 113 " --> pdb=" O TYR c 80 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LYS c 100 " --> pdb=" O LEU c 114 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL c 116 " --> pdb=" O SER c 98 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N SER c 98 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU c 118 " --> pdb=" O THR c 96 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR c 96 " --> pdb=" O GLU c 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 228 through 231 removed outlier: 7.677A pdb=" N VAL c 228 " --> pdb=" O LEU c 207 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE c 209 " --> pdb=" O VAL c 228 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER c 230 " --> pdb=" O ILE c 209 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE c 261 " --> pdb=" O VAL c 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 228 through 231 removed outlier: 7.677A pdb=" N VAL c 228 " --> pdb=" O LEU c 207 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE c 209 " --> pdb=" O VAL c 228 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER c 230 " --> pdb=" O ILE c 209 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE c 261 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY c 174 " --> pdb=" O ALA c 317 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA c 319 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE c 176 " --> pdb=" O ALA c 319 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 284 through 285 removed outlier: 3.933A pdb=" N VAL c 289 " --> pdb=" O LEU c 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 49 through 57 removed outlier: 3.855A pdb=" N LEU d 113 " --> pdb=" O TYR d 80 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LYS d 100 " --> pdb=" O LEU d 114 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL d 116 " --> pdb=" O SER d 98 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N SER d 98 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU d 118 " --> pdb=" O THR d 96 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR d 96 " --> pdb=" O GLU d 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 228 through 231 removed outlier: 7.676A pdb=" N VAL d 228 " --> pdb=" O LEU d 207 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE d 209 " --> pdb=" O VAL d 228 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER d 230 " --> pdb=" O ILE d 209 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE d 261 " --> pdb=" O VAL d 203 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 228 through 231 removed outlier: 7.676A pdb=" N VAL d 228 " --> pdb=" O LEU d 207 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE d 209 " --> pdb=" O VAL d 228 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER d 230 " --> pdb=" O ILE d 209 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE d 261 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY d 174 " --> pdb=" O ALA d 317 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA d 319 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE d 176 " --> pdb=" O ALA d 319 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'd' and resid 284 through 285 removed outlier: 3.933A pdb=" N VAL d 289 " --> pdb=" O LEU d 285 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 49 through 57 removed outlier: 3.856A pdb=" N LEU e 113 " --> pdb=" O TYR e 80 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS e 100 " --> pdb=" O LEU e 114 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL e 116 " --> pdb=" O SER e 98 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N SER e 98 " --> pdb=" O VAL e 116 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU e 118 " --> pdb=" O THR e 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR e 96 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 228 through 231 removed outlier: 7.678A pdb=" N VAL e 228 " --> pdb=" O LEU e 207 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE e 209 " --> pdb=" O VAL e 228 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER e 230 " --> pdb=" O ILE e 209 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE e 261 " --> pdb=" O VAL e 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 228 through 231 removed outlier: 7.678A pdb=" N VAL e 228 " --> pdb=" O LEU e 207 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE e 209 " --> pdb=" O VAL e 228 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER e 230 " --> pdb=" O ILE e 209 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE e 261 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY e 174 " --> pdb=" O ALA e 317 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA e 319 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE e 176 " --> pdb=" O ALA e 319 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 284 through 285 removed outlier: 3.933A pdb=" N VAL e 289 " --> pdb=" O LEU e 285 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 137 through 138 removed outlier: 3.638A pdb=" N GLY A 181 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N PHE A 196 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 141 through 144 removed outlier: 6.379A pdb=" N SER A 151 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 221 through 229 removed outlier: 6.712A pdb=" N ALA A 237 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA A 226 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS A 235 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG A 228 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG A 233 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 234 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL A 274 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A 236 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 297 through 299 Processing sheet with id=AD2, first strand: chain 'U' and resid 12 through 13 removed outlier: 3.687A pdb=" N GLU U 29 " --> pdb=" O ARG U 12 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP U 199 " --> pdb=" O PRO U 30 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'U' and resid 52 through 53 removed outlier: 3.584A pdb=" N GLY U 53 " --> pdb=" O GLY U 149 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 115 through 116 removed outlier: 4.439A pdb=" N THR U 101 " --> pdb=" O THR U 116 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU U 58 " --> pdb=" O LYS U 145 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN U 147 " --> pdb=" O VAL U 56 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL U 56 " --> pdb=" O GLN U 147 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 90 through 92 Processing sheet with id=AD6, first strand: chain 'U' and resid 108 through 111 Processing sheet with id=AD7, first strand: chain 'V' and resid 16 through 17 Processing sheet with id=AD8, first strand: chain 'V' and resid 97 through 101 removed outlier: 6.175A pdb=" N GLN V 147 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL V 56 " --> pdb=" O GLN V 147 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL V 59 " --> pdb=" O LEU V 171 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 90 through 92 Processing sheet with id=AE1, first strand: chain 'V' and resid 104 through 105 removed outlier: 4.071A pdb=" N LYS V 104 " --> pdb=" O ILE V 140 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE V 140 " --> pdb=" O LYS V 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'V' and resid 110 through 111 Processing sheet with id=AE3, first strand: chain 'V' and resid 152 through 153 removed outlier: 3.728A pdb=" N ALA V 175 " --> pdb=" O VAL V 153 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 59 through 60 removed outlier: 6.858A pdb=" N LYS X 99 " --> pdb=" O VAL X 71 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR X 73 " --> pdb=" O ARG X 97 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG X 97 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU X 75 " --> pdb=" O PRO X 95 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ALA X 94 " --> pdb=" O GLU X 126 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU X 126 " --> pdb=" O ALA X 94 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU X 96 " --> pdb=" O MET X 124 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 136 through 137 Processing sheet with id=AE6, first strand: chain 'X' and resid 451 through 454 Processing sheet with id=AE7, first strand: chain 'X' and resid 154 through 160 removed outlier: 6.257A pdb=" N TYR X 172 " --> pdb=" O PHE X 188 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE X 188 " --> pdb=" O TYR X 172 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 228 through 231 Processing sheet with id=AE9, first strand: chain 'X' and resid 239 through 240 removed outlier: 3.749A pdb=" N MET X 239 " --> pdb=" O ILE X 285 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE X 285 " --> pdb=" O MET X 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'X' and resid 255 through 257 removed outlier: 6.241A pdb=" N ALA X 257 " --> pdb=" O VAL X 261 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL X 261 " --> pdb=" O ALA X 257 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 301 through 302 removed outlier: 7.799A pdb=" N TYR X 301 " --> pdb=" O ILE X 310 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE X 310 " --> pdb=" O TYR X 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'X' and resid 580 through 581 removed outlier: 3.558A pdb=" N LYS X 593 " --> pdb=" O GLU X 602 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLU X 602 " --> pdb=" O LYS X 593 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 580 through 581 Processing sheet with id=AF5, first strand: chain 'X' and resid 616 through 617 removed outlier: 3.516A pdb=" N ILE X 616 " --> pdb=" O ARG X 637 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 623 through 624 Processing sheet with id=AF7, first strand: chain 'X' and resid 716 through 717 removed outlier: 6.580A pdb=" N ALA X 716 " --> pdb=" O LEU X 783 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 722 through 727 removed outlier: 6.626A pdb=" N VAL X 733 " --> pdb=" O GLN X 725 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL X 727 " --> pdb=" O ARG X 731 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ARG X 731 " --> pdb=" O VAL X 727 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'X' and resid 757 through 758 removed outlier: 3.705A pdb=" N THR X 757 " --> pdb=" O ILE X 765 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE X 765 " --> pdb=" O THR X 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'X' and resid 798 through 804 removed outlier: 8.667A pdb=" N ILE X1096 " --> pdb=" O ASN X 799 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG X 801 " --> pdb=" O ILE X1096 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU X1098 " --> pdb=" O ARG X 801 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA X 803 " --> pdb=" O LEU X1098 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU X 817 " --> pdb=" O VAL X1097 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE X 816 " --> pdb=" O SER X1077 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE X1079 " --> pdb=" O ILE X 816 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL X 818 " --> pdb=" O ILE X1079 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'X' and resid 830 through 841 removed outlier: 6.353A pdb=" N THR X 830 " --> pdb=" O LYS X1057 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS X1057 " --> pdb=" O THR X 830 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS X 832 " --> pdb=" O ALA X1055 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA X1055 " --> pdb=" O HIS X 832 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN X 834 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR X1053 " --> pdb=" O GLN X 834 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU X 836 " --> pdb=" O LYS X1051 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS X1051 " --> pdb=" O LEU X 836 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N CYS X 838 " --> pdb=" O ILE X1049 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE X1049 " --> pdb=" O CYS X 838 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER X 840 " --> pdb=" O LEU X1047 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP X 930 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA X1055 " --> pdb=" O VAL X 928 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL X 928 " --> pdb=" O ALA X1055 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LYS X1057 " --> pdb=" O GLY X 926 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY X 926 " --> pdb=" O LYS X1057 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 1087 through 1088 removed outlier: 4.511A pdb=" N LEU X1212 " --> pdb=" O PHE X1221 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 1244 through 1246 Processing sheet with id=AG5, first strand: chain 'X' and resid 1244 through 1246 removed outlier: 7.971A pdb=" N ILE Y 447 " --> pdb=" O ARG Y 352 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL Y 354 " --> pdb=" O ILE Y 447 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU Y 449 " --> pdb=" O VAL Y 354 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR Y 356 " --> pdb=" O LEU Y 449 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 1268 through 1269 removed outlier: 3.842A pdb=" N GLN X1268 " --> pdb=" O VAL Y 347 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 1335 through 1339 removed outlier: 3.627A pdb=" N ILE Y 20 " --> pdb=" O ASP Y1342 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP Y1342 " --> pdb=" O ILE Y 20 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 34 through 37 removed outlier: 7.100A pdb=" N HIS Y 104 " --> pdb=" O PHE Y 35 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU Y 37 " --> pdb=" O HIS Y 104 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLU Y 106 " --> pdb=" O GLU Y 37 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR Y 240 " --> pdb=" O LEU Y 107 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N SER Y 109 " --> pdb=" O ILE Y 238 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N ILE Y 238 " --> pdb=" O SER Y 109 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.071A pdb=" N ASP Y 177 " --> pdb=" O ILE Y 147 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 253 through 254 Processing sheet with id=AH2, first strand: chain 'Y' and resid 526 through 527 Processing sheet with id=AH3, first strand: chain 'Y' and resid 809 through 811 Processing sheet with id=AH4, first strand: chain 'Y' and resid 819 through 822 Processing sheet with id=AH5, first strand: chain 'Y' and resid 991 through 996 removed outlier: 4.166A pdb=" N GLU Y 993 " --> pdb=" O LEU Y 984 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 965 through 967 Processing sheet with id=AH7, first strand: chain 'Y' and resid 1033 through 1034 removed outlier: 3.502A pdb=" N GLY Y1033 " --> pdb=" O ILE Y1115 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Y' and resid 1046 through 1049 removed outlier: 3.834A pdb=" N GLN Y1049 " --> pdb=" O SER Y1058 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER Y1058 " --> pdb=" O GLN Y1049 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Y' and resid 1077 through 1079 Processing sheet with id=AI1, first strand: chain 'Y' and resid 1162 through 1164 removed outlier: 3.617A pdb=" N LEU Y1175 " --> pdb=" O GLU Y1188 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU Y1188 " --> pdb=" O LEU Y1175 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 1264 through 1266 2186 hydrogen bonds defined for protein. 6186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 25.12 Time building geometry restraints manager: 12.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17069 1.34 - 1.46: 6841 1.46 - 1.58: 27981 1.58 - 1.70: 182 1.70 - 1.81: 409 Bond restraints: 52482 Sorted by residual: bond pdb=" C4' U R 24 " pdb=" O4' U R 24 " ideal model delta sigma weight residual 1.454 1.814 -0.360 1.50e-02 4.44e+03 5.78e+02 bond pdb=" F2 BEF b1002 " pdb="BE BEF b1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF a1002 " pdb="BE BEF a1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF e1002 " pdb="BE BEF e1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" F2 BEF c 504 " pdb="BE BEF c 504 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 52477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 70971 3.53 - 7.06: 223 7.06 - 10.59: 17 10.59 - 14.12: 6 14.12 - 17.65: 1 Bond angle restraints: 71218 Sorted by residual: angle pdb=" C4' U R 24 " pdb=" O4' U R 24 " pdb=" C1' U R 24 " ideal model delta sigma weight residual 109.70 92.05 17.65 1.00e+00 1.00e+00 3.11e+02 angle pdb=" C5' U R 24 " pdb=" C4' U R 24 " pdb=" O4' U R 24 " ideal model delta sigma weight residual 109.10 97.00 12.10 1.50e+00 4.44e-01 6.50e+01 angle pdb=" F2 BEF c 503 " pdb="BE BEF c 503 " pdb=" F3 BEF c 503 " ideal model delta sigma weight residual 119.96 107.09 12.87 3.00e+00 1.11e-01 1.84e+01 angle pdb=" F2 BEF b1002 " pdb="BE BEF b1002 " pdb=" F3 BEF b1002 " ideal model delta sigma weight residual 119.96 107.18 12.78 3.00e+00 1.11e-01 1.82e+01 angle pdb=" F2 BEF c 504 " pdb="BE BEF c 504 " pdb=" F3 BEF c 504 " ideal model delta sigma weight residual 119.96 107.28 12.68 3.00e+00 1.11e-01 1.79e+01 ... (remaining 71213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.04: 31154 34.04 - 68.08: 1020 68.08 - 102.12: 84 102.12 - 136.16: 3 136.16 - 170.20: 5 Dihedral angle restraints: 32266 sinusoidal: 14068 harmonic: 18198 Sorted by residual: dihedral pdb=" O1B ADP c 501 " pdb=" O3A ADP c 501 " pdb=" PB ADP c 501 " pdb=" PA ADP c 501 " ideal model delta sinusoidal sigma weight residual 300.00 154.63 145.37 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP b1000 " pdb=" O3A ADP b1000 " pdb=" PB ADP b1000 " pdb=" PA ADP b1000 " ideal model delta sinusoidal sigma weight residual 300.00 161.68 138.32 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" O2A ADP b1000 " pdb=" O3A ADP b1000 " pdb=" PA ADP b1000 " pdb=" PB ADP b1000 " ideal model delta sinusoidal sigma weight residual -60.00 59.31 -119.31 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 32263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 8150 0.208 - 0.415: 0 0.415 - 0.623: 0 0.623 - 0.831: 0 0.831 - 1.039: 1 Chirality restraints: 8151 Sorted by residual: chirality pdb=" C4' U R 24 " pdb=" C5' U R 24 " pdb=" O4' U R 24 " pdb=" C3' U R 24 " both_signs ideal model delta sigma weight residual False -2.50 -3.54 1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" C1' C R 21 " pdb=" O4' C R 21 " pdb=" C2' C R 21 " pdb=" N1 C R 21 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA ILE A 97 " pdb=" N ILE A 97 " pdb=" C ILE A 97 " pdb=" CB ILE A 97 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 8148 not shown) Planarity restraints: 9004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C R 21 " 0.033 2.00e-02 2.50e+03 1.72e-02 6.67e+00 pdb=" N1 C R 21 " -0.037 2.00e-02 2.50e+03 pdb=" C2 C R 21 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C R 21 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C R 21 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C R 21 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C R 21 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C R 21 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C R 21 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG L 19 " -0.012 2.00e-02 2.50e+03 1.34e-02 5.35e+00 pdb=" N9 DG L 19 " 0.006 2.00e-02 2.50e+03 pdb=" C8 DG L 19 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DG L 19 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG L 19 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG L 19 " 0.031 2.00e-02 2.50e+03 pdb=" O6 DG L 19 " -0.031 2.00e-02 2.50e+03 pdb=" N1 DG L 19 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG L 19 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG L 19 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG L 19 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG L 19 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP a 233 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" CG ASP a 233 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP a 233 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP a 233 " -0.012 2.00e-02 2.50e+03 ... (remaining 9001 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 525 2.54 - 3.13: 40325 3.13 - 3.72: 83620 3.72 - 4.31: 111551 4.31 - 4.90: 178898 Nonbonded interactions: 414919 Sorted by model distance: nonbonded pdb=" F3 BEF c 504 " pdb="MG MG d1001 " model vdw 1.950 2.120 nonbonded pdb=" O3B ADP c 501 " pdb="MG MG c 502 " model vdw 1.978 2.170 nonbonded pdb=" OG1 THR d 185 " pdb="MG MG d1001 " model vdw 1.983 2.170 nonbonded pdb=" O1B ADP a1000 " pdb="MG MG a1001 " model vdw 2.006 2.170 nonbonded pdb="MG MG c 502 " pdb=" O HOH c 603 " model vdw 2.014 2.170 ... (remaining 414914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and resid 1 through 417) selection = (chain 'b' and resid 1 through 417) selection = (chain 'c' and resid 1 through 417) selection = (chain 'd' and resid 1 through 417) selection = (chain 'e' and resid 1 through 417) selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.090 Extract box with map and model: 1.600 Check model and map are aligned: 0.310 Set scattering table: 0.390 Process input model: 114.690 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.003 0.360 52482 Z= 0.200 Angle : 0.603 17.649 71218 Z= 0.336 Chirality : 0.042 1.039 8151 Planarity : 0.003 0.045 9004 Dihedral : 15.845 170.196 20520 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.78 % Allowed : 6.27 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -2.77 (0.09), residues: 6306 helix: -1.07 (0.10), residues: 2350 sheet: -1.42 (0.16), residues: 790 loop : -2.59 (0.09), residues: 3166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP f 381 HIS 0.005 0.001 HIS Y1366 PHE 0.027 0.001 PHE Y 227 TYR 0.007 0.001 TYR Y 631 ARG 0.007 0.000 ARG b 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 377 time to evaluate : 4.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.6072 (mmm) cc_final: 0.5436 (mtt) REVERT: f 98 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8255 (p) REVERT: f 207 LEU cc_start: 0.8413 (tp) cc_final: 0.7876 (tt) REVERT: f 210 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8524 (m-30) REVERT: f 343 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9192 (mt) REVERT: a 210 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7441 (t0) REVERT: a 245 MET cc_start: 0.8271 (tpp) cc_final: 0.7901 (tpt) REVERT: a 281 SER cc_start: 0.6506 (OUTLIER) cc_final: 0.6251 (p) REVERT: b 59 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: b 245 MET cc_start: 0.7767 (tpp) cc_final: 0.7476 (tpp) REVERT: b 281 SER cc_start: 0.7051 (OUTLIER) cc_final: 0.6846 (p) REVERT: d 59 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7926 (pm20) REVERT: d 230 SER cc_start: 0.7681 (OUTLIER) cc_final: 0.7376 (p) REVERT: d 245 MET cc_start: 0.7711 (tpp) cc_final: 0.6821 (tpp) REVERT: d 281 SER cc_start: 0.7340 (OUTLIER) cc_final: 0.7030 (p) REVERT: e 281 SER cc_start: 0.4919 (OUTLIER) cc_final: 0.4551 (p) REVERT: e 380 MET cc_start: 0.8972 (mtp) cc_final: 0.8674 (mtp) REVERT: U 86 LYS cc_start: 0.8366 (ttmt) cc_final: 0.7424 (ttpp) REVERT: U 137 ASN cc_start: 0.7891 (p0) cc_final: 0.7496 (p0) REVERT: W 30 MET cc_start: 0.8311 (mmt) cc_final: 0.7970 (mmt) REVERT: X 842 ASP cc_start: 0.7570 (t0) cc_final: 0.7349 (t0) REVERT: Y 697 MET cc_start: 0.8159 (tmm) cc_final: 0.7711 (tmm) REVERT: Y 698 MET cc_start: 0.8193 (tpp) cc_final: 0.7890 (tpp) REVERT: Y 1040 MET cc_start: 0.7014 (ttm) cc_final: 0.6722 (ttt) outliers start: 204 outliers final: 46 residues processed: 563 average time/residue: 0.5253 time to fit residues: 492.4312 Evaluate side-chains 319 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 262 time to evaluate : 4.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 98 SER Chi-restraints excluded: chain f residue 166 SER Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 210 ASP Chi-restraints excluded: chain f residue 281 SER Chi-restraints excluded: chain f residue 329 GLU Chi-restraints excluded: chain f residue 343 LEU Chi-restraints excluded: chain f residue 346 SER Chi-restraints excluded: chain f residue 369 GLU Chi-restraints excluded: chain f residue 373 THR Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain a residue 71 SER Chi-restraints excluded: chain a residue 166 SER Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 210 ASP Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 281 SER Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 369 GLU Chi-restraints excluded: chain b residue 16 THR Chi-restraints excluded: chain b residue 32 GLN Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 166 SER Chi-restraints excluded: chain b residue 281 SER Chi-restraints excluded: chain b residue 323 THR Chi-restraints excluded: chain b residue 346 SER Chi-restraints excluded: chain b residue 369 GLU Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 228 VAL Chi-restraints excluded: chain c residue 277 VAL Chi-restraints excluded: chain c residue 281 SER Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 369 GLU Chi-restraints excluded: chain c residue 373 THR Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 59 GLN Chi-restraints excluded: chain d residue 166 SER Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 230 SER Chi-restraints excluded: chain d residue 265 ASP Chi-restraints excluded: chain d residue 277 VAL Chi-restraints excluded: chain d residue 281 SER Chi-restraints excluded: chain d residue 323 THR Chi-restraints excluded: chain d residue 329 GLU Chi-restraints excluded: chain d residue 369 GLU Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain e residue 166 SER Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 281 SER Chi-restraints excluded: chain e residue 323 THR Chi-restraints excluded: chain e residue 329 GLU Chi-restraints excluded: chain e residue 346 SER Chi-restraints excluded: chain e residue 369 GLU Chi-restraints excluded: chain e residue 373 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 534 optimal weight: 3.9990 chunk 479 optimal weight: 2.9990 chunk 266 optimal weight: 30.0000 chunk 163 optimal weight: 2.9990 chunk 323 optimal weight: 20.0000 chunk 256 optimal weight: 9.9990 chunk 496 optimal weight: 5.9990 chunk 191 optimal weight: 0.0570 chunk 301 optimal weight: 0.7980 chunk 369 optimal weight: 1.9990 chunk 574 optimal weight: 30.0000 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 142 ASN ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 275 ASN ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 275 ASN b 190 ASN b 275 ASN c 42 HIS c 190 ASN c 275 ASN d 42 HIS d 190 ASN d 275 ASN e 42 HIS e 142 ASN e 190 ASN ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN A 41 GLN A 321 ASN U 132 HIS V 37 HIS X 41 GLN X 343 HIS ** X 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 628 HIS X 808 ASN X1008 GLN X1010 GLN X1013 GLN X1017 GLN X1236 ASN X1237 HIS X1257 GLN X1268 GLN Y 274 ASN Y 365 GLN Y 488 ASN Y 489 ASN Y 702 GLN Y 861 ASN Y1114 GLN Y1244 GLN ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1367 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 52482 Z= 0.176 Angle : 0.589 10.792 71218 Z= 0.297 Chirality : 0.042 0.178 8151 Planarity : 0.004 0.072 9004 Dihedral : 12.574 173.066 8095 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.24 % Allowed : 11.50 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -1.72 (0.10), residues: 6306 helix: 0.04 (0.10), residues: 2453 sheet: -1.14 (0.17), residues: 779 loop : -2.17 (0.10), residues: 3074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 997 HIS 0.004 0.001 HIS X1023 PHE 0.017 0.001 PHE X 195 TYR 0.029 0.001 TYR c 274 ARG 0.017 0.000 ARG V 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 270 time to evaluate : 4.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.5973 (mmm) cc_final: 0.5247 (mtt) REVERT: f 147 MET cc_start: 0.8695 (tpp) cc_final: 0.8357 (tpt) REVERT: f 207 LEU cc_start: 0.8372 (tp) cc_final: 0.8054 (tp) REVERT: f 341 MET cc_start: 0.8141 (tmm) cc_final: 0.7678 (tmm) REVERT: f 343 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9240 (mt) REVERT: f 390 MET cc_start: 0.7324 (ptp) cc_final: 0.6842 (ptt) REVERT: f 416 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.9111 (mmm) REVERT: a 147 MET cc_start: 0.8529 (tpp) cc_final: 0.8120 (tpp) REVERT: a 219 MET cc_start: 0.8530 (tpp) cc_final: 0.8320 (mmm) REVERT: a 396 MET cc_start: 0.8602 (mmm) cc_final: 0.8349 (mmm) REVERT: b 219 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7876 (mmm) REVERT: b 369 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: b 390 MET cc_start: 0.7129 (ptp) cc_final: 0.6369 (ptp) REVERT: b 416 MET cc_start: 0.8330 (ptt) cc_final: 0.8026 (ptt) REVERT: c 241 GLN cc_start: 0.7102 (tm-30) cc_final: 0.5394 (tm-30) REVERT: d 21 MET cc_start: 0.8459 (mmm) cc_final: 0.6206 (ptt) REVERT: d 245 MET cc_start: 0.7437 (tpp) cc_final: 0.7166 (tpp) REVERT: d 416 MET cc_start: 0.7560 (ptt) cc_final: 0.7092 (ptt) REVERT: e 1 MET cc_start: 0.5780 (ptm) cc_final: 0.5216 (ppp) REVERT: e 341 MET cc_start: 0.8720 (tmm) cc_final: 0.8474 (tmm) REVERT: e 380 MET cc_start: 0.9107 (mtp) cc_final: 0.8830 (mtp) REVERT: U 137 ASN cc_start: 0.7889 (p0) cc_final: 0.7532 (p0) REVERT: W 36 ASP cc_start: 0.8284 (p0) cc_final: 0.8017 (p0) REVERT: X 741 MET cc_start: 0.8053 (tpp) cc_final: 0.7850 (tpp) REVERT: X 842 ASP cc_start: 0.7540 (t0) cc_final: 0.7219 (t0) REVERT: Y 1040 MET cc_start: 0.7118 (ttm) cc_final: 0.6823 (ttt) outliers start: 67 outliers final: 26 residues processed: 329 average time/residue: 0.5096 time to fit residues: 284.4837 Evaluate side-chains 273 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 243 time to evaluate : 4.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 142 ASN Chi-restraints excluded: chain f residue 286 THR Chi-restraints excluded: chain f residue 326 LYS Chi-restraints excluded: chain f residue 343 LEU Chi-restraints excluded: chain f residue 373 THR Chi-restraints excluded: chain f residue 416 MET Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 230 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 346 SER Chi-restraints excluded: chain b residue 219 MET Chi-restraints excluded: chain b residue 286 THR Chi-restraints excluded: chain b residue 323 THR Chi-restraints excluded: chain b residue 369 GLU Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 228 VAL Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 330 VAL Chi-restraints excluded: chain c residue 346 SER Chi-restraints excluded: chain c residue 373 THR Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 323 THR Chi-restraints excluded: chain e residue 323 THR Chi-restraints excluded: chain e residue 346 SER Chi-restraints excluded: chain e residue 416 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 319 optimal weight: 4.9990 chunk 178 optimal weight: 20.0000 chunk 478 optimal weight: 10.0000 chunk 391 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 575 optimal weight: 10.0000 chunk 622 optimal weight: 9.9990 chunk 512 optimal weight: 0.0970 chunk 571 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 461 optimal weight: 7.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 42 HIS f 90 ASN f 190 ASN ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 344 HIS a 90 ASN a 142 ASN ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN b 42 HIS b 142 ASN ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 42 HIS c 142 ASN ** c 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 344 HIS d 142 ASN ** e 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 GLN A 303 HIS V 147 GLN X 517 GLN X 658 GLN X 832 HIS X1157 GLN X1209 GLN X1288 GLN Y 320 ASN Y 477 GLN Y 545 HIS ** Y 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 817 HIS ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 52482 Z= 0.267 Angle : 0.633 13.224 71218 Z= 0.322 Chirality : 0.042 0.186 8151 Planarity : 0.004 0.058 9004 Dihedral : 12.200 178.487 8027 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.50 % Allowed : 14.66 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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 (0.10), residues: 6306 helix: 0.46 (0.11), residues: 2497 sheet: -0.91 (0.17), residues: 802 loop : -1.80 (0.11), residues: 3007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y1020 HIS 0.007 0.001 HIS Y 104 PHE 0.024 0.002 PHE X 828 TYR 0.026 0.002 TYR c 274 ARG 0.007 0.001 ARG W 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 242 time to evaluate : 4.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.5977 (mmm) cc_final: 0.5216 (mtt) REVERT: f 147 MET cc_start: 0.8919 (tpp) cc_final: 0.8465 (tpt) REVERT: f 186 MET cc_start: 0.9254 (ppp) cc_final: 0.8903 (pmm) REVERT: f 207 LEU cc_start: 0.8425 (tp) cc_final: 0.8182 (tp) REVERT: f 390 MET cc_start: 0.7623 (ptp) cc_final: 0.7162 (ptt) REVERT: f 405 MET cc_start: 0.8734 (ptt) cc_final: 0.8020 (ppp) REVERT: f 416 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8929 (mmm) REVERT: a 147 MET cc_start: 0.8785 (tpp) cc_final: 0.8146 (tpp) REVERT: a 326 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8491 (ptmm) REVERT: a 405 MET cc_start: 0.8649 (ptp) cc_final: 0.8425 (ptp) REVERT: a 415 MET cc_start: 0.9024 (tmm) cc_final: 0.8651 (tmm) REVERT: b 147 MET cc_start: 0.8849 (tpp) cc_final: 0.8570 (tpp) REVERT: b 219 MET cc_start: 0.8170 (mpp) cc_final: 0.7955 (tpp) REVERT: b 285 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8070 (pp) REVERT: b 390 MET cc_start: 0.7332 (ptp) cc_final: 0.6685 (ptp) REVERT: b 416 MET cc_start: 0.8449 (ptt) cc_final: 0.8152 (ptt) REVERT: c 21 MET cc_start: 0.7131 (mtp) cc_final: 0.6538 (ptm) REVERT: c 241 GLN cc_start: 0.7480 (tm-30) cc_final: 0.6591 (tm-30) REVERT: c 245 MET cc_start: 0.6901 (mmm) cc_final: 0.6372 (mmm) REVERT: c 390 MET cc_start: 0.6993 (ptp) cc_final: 0.6757 (ptp) REVERT: d 147 MET cc_start: 0.8276 (mmm) cc_final: 0.7974 (mmm) REVERT: e 1 MET cc_start: 0.5645 (ptm) cc_final: 0.5424 (ppp) REVERT: e 380 MET cc_start: 0.9176 (mtp) cc_final: 0.8792 (mtp) REVERT: e 416 MET cc_start: 0.6996 (ptt) cc_final: 0.6592 (ppp) REVERT: A 338 VAL cc_start: 0.2998 (OUTLIER) cc_final: 0.2742 (m) REVERT: A 389 MET cc_start: -0.1287 (mmm) cc_final: -0.1571 (mmm) REVERT: V 277 TYR cc_start: 0.8293 (m-80) cc_final: 0.8078 (m-80) REVERT: X 403 MET cc_start: 0.7990 (tmm) cc_final: 0.7722 (tmm) REVERT: X 741 MET cc_start: 0.8230 (tpp) cc_final: 0.8024 (tpp) REVERT: X 1085 MET cc_start: 0.8962 (mmm) cc_final: 0.8630 (mmm) outliers start: 81 outliers final: 30 residues processed: 312 average time/residue: 0.4790 time to fit residues: 258.6936 Evaluate side-chains 264 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 230 time to evaluate : 4.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 228 VAL Chi-restraints excluded: chain f residue 416 MET Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 142 ASN Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 230 SER Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 286 THR Chi-restraints excluded: chain b residue 323 THR Chi-restraints excluded: chain b residue 330 VAL Chi-restraints excluded: chain b residue 346 SER Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 330 VAL Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 294 LEU Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 346 SER Chi-restraints excluded: chain e residue 373 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 231 PHE Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain Y residue 242 LEU Chi-restraints excluded: chain Y residue 363 LEU Chi-restraints excluded: chain Y residue 704 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 568 optimal weight: 6.9990 chunk 432 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 386 optimal weight: 7.9990 chunk 577 optimal weight: 9.9990 chunk 611 optimal weight: 7.9990 chunk 301 optimal weight: 0.0670 chunk 547 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 142 ASN ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS b 142 ASN ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 42 HIS ** c 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 GLN X 165 HIS X 658 GLN Y 274 ASN Y 792 ASN ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 52482 Z= 0.203 Angle : 0.581 10.988 71218 Z= 0.293 Chirality : 0.041 0.193 8151 Planarity : 0.004 0.057 9004 Dihedral : 12.016 175.882 8015 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.43 % Allowed : 15.90 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -0.84 (0.10), residues: 6306 helix: 0.72 (0.11), residues: 2481 sheet: -0.81 (0.17), residues: 803 loop : -1.58 (0.11), residues: 3022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 997 HIS 0.008 0.001 HIS c 42 PHE 0.037 0.001 PHE c 412 TYR 0.024 0.001 TYR c 274 ARG 0.005 0.000 ARG f 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 226 time to evaluate : 4.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.5908 (mmm) cc_final: 0.5267 (mtt) REVERT: f 207 LEU cc_start: 0.8449 (tp) cc_final: 0.8169 (tp) REVERT: f 380 MET cc_start: 0.8859 (ptp) cc_final: 0.8471 (ptp) REVERT: f 390 MET cc_start: 0.7751 (ptp) cc_final: 0.7289 (ptt) REVERT: f 405 MET cc_start: 0.8735 (ptt) cc_final: 0.8351 (ppp) REVERT: f 416 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8965 (mmm) REVERT: a 147 MET cc_start: 0.8876 (tpp) cc_final: 0.8261 (tpp) REVERT: a 326 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8403 (ptmm) REVERT: a 415 MET cc_start: 0.9058 (tmm) cc_final: 0.8733 (tmm) REVERT: a 416 MET cc_start: 0.9105 (mmm) cc_final: 0.8880 (mmm) REVERT: b 147 MET cc_start: 0.8885 (tpp) cc_final: 0.8571 (tpp) REVERT: b 219 MET cc_start: 0.8318 (mpp) cc_final: 0.8038 (mmm) REVERT: b 285 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8147 (pp) REVERT: b 390 MET cc_start: 0.7544 (ptp) cc_final: 0.7238 (ptp) REVERT: b 416 MET cc_start: 0.8455 (ptt) cc_final: 0.8254 (ptt) REVERT: c 21 MET cc_start: 0.6960 (mtp) cc_final: 0.6182 (ptp) REVERT: c 241 GLN cc_start: 0.7400 (tm-30) cc_final: 0.6381 (tm-30) REVERT: c 245 MET cc_start: 0.6745 (mmm) cc_final: 0.6055 (mmm) REVERT: c 390 MET cc_start: 0.7028 (ptp) cc_final: 0.6731 (ptp) REVERT: d 21 MET cc_start: 0.8597 (mmm) cc_final: 0.6497 (ptt) REVERT: d 147 MET cc_start: 0.8475 (mmm) cc_final: 0.8216 (mmm) REVERT: d 314 THR cc_start: 0.9555 (OUTLIER) cc_final: 0.9265 (m) REVERT: e 186 MET cc_start: 0.8468 (pmm) cc_final: 0.8130 (pmm) REVERT: e 380 MET cc_start: 0.9186 (mtp) cc_final: 0.8854 (mtp) REVERT: e 416 MET cc_start: 0.6893 (ptt) cc_final: 0.6491 (ppp) REVERT: W 30 MET cc_start: 0.9043 (mmt) cc_final: 0.8817 (tpp) REVERT: X 1085 MET cc_start: 0.8957 (mmm) cc_final: 0.8740 (mmm) REVERT: Y 1040 MET cc_start: 0.6839 (ttt) cc_final: 0.6571 (ttt) outliers start: 77 outliers final: 37 residues processed: 294 average time/residue: 0.5195 time to fit residues: 265.9910 Evaluate side-chains 262 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 221 time to evaluate : 4.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 228 VAL Chi-restraints excluded: chain f residue 322 ASP Chi-restraints excluded: chain f residue 416 MET Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 142 ASN Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 230 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 314 THR Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 286 THR Chi-restraints excluded: chain b residue 323 THR Chi-restraints excluded: chain b residue 346 SER Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 184 LYS Chi-restraints excluded: chain c residue 295 HIS Chi-restraints excluded: chain c residue 330 VAL Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 208 LEU Chi-restraints excluded: chain d residue 314 THR Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 314 THR Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain X residue 111 GLU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 429 MET Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 931 VAL Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 974 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 509 optimal weight: 5.9990 chunk 347 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 455 optimal weight: 4.9990 chunk 252 optimal weight: 9.9990 chunk 522 optimal weight: 7.9990 chunk 422 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 312 optimal weight: 2.9990 chunk 549 optimal weight: 3.9990 chunk 154 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 142 ASN ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 142 ASN ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 126 ASN e 344 HIS ** V 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X1009 ASN X1061 GLN ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 52482 Z= 0.228 Angle : 0.603 12.173 71218 Z= 0.302 Chirality : 0.041 0.210 8151 Planarity : 0.004 0.062 9004 Dihedral : 12.013 177.806 8013 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.65 % Allowed : 16.53 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.11), residues: 6306 helix: 0.80 (0.11), residues: 2474 sheet: -0.79 (0.17), residues: 802 loop : -1.40 (0.11), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y1020 HIS 0.006 0.001 HIS X 165 PHE 0.043 0.001 PHE c 412 TYR 0.026 0.001 TYR c 274 ARG 0.010 0.000 ARG f 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 221 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 1 MET cc_start: 0.5656 (mtm) cc_final: 0.5376 (pmm) REVERT: f 21 MET cc_start: 0.6005 (mmm) cc_final: 0.5157 (mtt) REVERT: f 147 MET cc_start: 0.8884 (tpp) cc_final: 0.8334 (tpp) REVERT: f 186 MET cc_start: 0.9248 (ppp) cc_final: 0.8815 (pmm) REVERT: f 390 MET cc_start: 0.7948 (ptp) cc_final: 0.7519 (ptt) REVERT: f 405 MET cc_start: 0.8763 (ptt) cc_final: 0.8331 (ppp) REVERT: f 416 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.8908 (mmm) REVERT: a 147 MET cc_start: 0.9037 (tpp) cc_final: 0.8172 (tpp) REVERT: a 219 MET cc_start: 0.8516 (mmt) cc_final: 0.8010 (mmm) REVERT: a 326 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8479 (ptmm) REVERT: a 396 MET cc_start: 0.8475 (mmm) cc_final: 0.7997 (mmm) REVERT: a 405 MET cc_start: 0.8656 (ptp) cc_final: 0.8364 (ppp) REVERT: a 415 MET cc_start: 0.9043 (tmm) cc_final: 0.8489 (tmm) REVERT: b 21 MET cc_start: 0.7154 (tmm) cc_final: 0.6899 (tmm) REVERT: b 142 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7700 (m-40) REVERT: b 147 MET cc_start: 0.8919 (tpp) cc_final: 0.8680 (tpp) REVERT: b 219 MET cc_start: 0.8337 (mpp) cc_final: 0.8131 (tpp) REVERT: c 21 MET cc_start: 0.7166 (mtp) cc_final: 0.6303 (ptm) REVERT: c 241 GLN cc_start: 0.7506 (tm-30) cc_final: 0.6573 (tm-30) REVERT: c 245 MET cc_start: 0.6762 (mmm) cc_final: 0.6263 (mmm) REVERT: c 390 MET cc_start: 0.7030 (ptp) cc_final: 0.6691 (ptp) REVERT: c 405 MET cc_start: 0.9135 (ppp) cc_final: 0.8855 (ppp) REVERT: d 21 MET cc_start: 0.8641 (mmm) cc_final: 0.6511 (ptt) REVERT: d 147 MET cc_start: 0.8618 (mmm) cc_final: 0.8331 (mmm) REVERT: d 245 MET cc_start: 0.7949 (tpp) cc_final: 0.7566 (mmt) REVERT: d 314 THR cc_start: 0.9586 (OUTLIER) cc_final: 0.9355 (m) REVERT: e 380 MET cc_start: 0.9234 (mtp) cc_final: 0.8893 (mtp) REVERT: e 416 MET cc_start: 0.6462 (ptt) cc_final: 0.6076 (ppp) REVERT: W 30 MET cc_start: 0.9046 (mmt) cc_final: 0.8813 (tpp) REVERT: W 36 ASP cc_start: 0.7884 (p0) cc_final: 0.7634 (p0) REVERT: X 1085 MET cc_start: 0.9040 (mmm) cc_final: 0.8809 (mmm) REVERT: Y 130 MET cc_start: 0.8390 (ppp) cc_final: 0.7798 (ppp) REVERT: Y 151 MET cc_start: 0.8709 (ppp) cc_final: 0.8387 (pmm) outliers start: 89 outliers final: 52 residues processed: 303 average time/residue: 0.4917 time to fit residues: 261.3942 Evaluate side-chains 274 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 218 time to evaluate : 4.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 181 LYS Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 322 ASP Chi-restraints excluded: chain f residue 416 MET Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 142 ASN Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 230 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 314 THR Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 323 THR Chi-restraints excluded: chain b residue 346 SER Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 184 LYS Chi-restraints excluded: chain c residue 295 HIS Chi-restraints excluded: chain c residue 314 THR Chi-restraints excluded: chain c residue 326 LYS Chi-restraints excluded: chain c residue 330 VAL Chi-restraints excluded: chain d residue 126 ASN Chi-restraints excluded: chain d residue 142 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 294 LEU Chi-restraints excluded: chain d residue 314 THR Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain e residue 96 THR Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 294 LEU Chi-restraints excluded: chain e residue 295 HIS Chi-restraints excluded: chain e residue 314 THR Chi-restraints excluded: chain e residue 322 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 231 PHE Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 111 GLU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 884 VAL Chi-restraints excluded: chain X residue 931 VAL Chi-restraints excluded: chain X residue 933 VAL Chi-restraints excluded: chain X residue 1227 VAL Chi-restraints excluded: chain X residue 1287 LEU Chi-restraints excluded: chain Y residue 146 VAL Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 903 LEU Chi-restraints excluded: chain Y residue 974 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 205 optimal weight: 10.0000 chunk 551 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 359 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 612 optimal weight: 3.9990 chunk 508 optimal weight: 0.4980 chunk 283 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 202 optimal weight: 0.7980 chunk 321 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 42 HIS ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 142 ASN ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS b 172 GLN ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 126 ASN e 172 GLN U 93 GLN ** V 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 147 GLN ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1366 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 52482 Z= 0.150 Angle : 0.585 12.316 71218 Z= 0.288 Chirality : 0.041 0.221 8151 Planarity : 0.003 0.062 9004 Dihedral : 11.854 177.612 8013 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.43 % Allowed : 17.44 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -0.53 (0.11), residues: 6306 helix: 0.87 (0.11), residues: 2486 sheet: -0.65 (0.17), residues: 795 loop : -1.31 (0.11), residues: 3025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 381 HIS 0.004 0.001 HIS X 165 PHE 0.020 0.001 PHE b 412 TYR 0.026 0.001 TYR c 274 ARG 0.007 0.000 ARG f 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 223 time to evaluate : 4.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 1 MET cc_start: 0.5672 (mtm) cc_final: 0.5458 (pmm) REVERT: f 21 MET cc_start: 0.6054 (mmm) cc_final: 0.5195 (mtt) REVERT: f 147 MET cc_start: 0.8913 (tpp) cc_final: 0.8461 (tpp) REVERT: f 390 MET cc_start: 0.8024 (ptp) cc_final: 0.7589 (ptt) REVERT: f 405 MET cc_start: 0.8732 (ptt) cc_final: 0.8401 (ppp) REVERT: f 416 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8903 (mmm) REVERT: a 219 MET cc_start: 0.8547 (mmt) cc_final: 0.8102 (mmm) REVERT: a 326 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8555 (ptmm) REVERT: a 405 MET cc_start: 0.8622 (ptp) cc_final: 0.8350 (ppp) REVERT: a 415 MET cc_start: 0.8943 (tmm) cc_final: 0.8692 (tmm) REVERT: b 21 MET cc_start: 0.7039 (tmm) cc_final: 0.6818 (tmm) REVERT: b 219 MET cc_start: 0.8314 (mpp) cc_final: 0.8003 (mmm) REVERT: b 390 MET cc_start: 0.7285 (ptp) cc_final: 0.6583 (ptp) REVERT: c 21 MET cc_start: 0.7188 (mtp) cc_final: 0.6432 (ptp) REVERT: c 241 GLN cc_start: 0.7344 (tm-30) cc_final: 0.6641 (tm-30) REVERT: c 245 MET cc_start: 0.6649 (mmm) cc_final: 0.6196 (mmm) REVERT: c 390 MET cc_start: 0.6951 (ptp) cc_final: 0.6683 (ptp) REVERT: d 21 MET cc_start: 0.8543 (mmm) cc_final: 0.6439 (ptt) REVERT: d 147 MET cc_start: 0.8588 (mmm) cc_final: 0.8354 (mmm) REVERT: d 245 MET cc_start: 0.7892 (tpp) cc_final: 0.7504 (mmt) REVERT: d 314 THR cc_start: 0.9510 (OUTLIER) cc_final: 0.9252 (m) REVERT: d 396 MET cc_start: 0.7349 (tpt) cc_final: 0.7114 (tpp) REVERT: e 186 MET cc_start: 0.8345 (pmm) cc_final: 0.8066 (pmm) REVERT: e 380 MET cc_start: 0.9218 (mtp) cc_final: 0.8906 (mtp) REVERT: A 167 MET cc_start: 0.4505 (ptp) cc_final: 0.4223 (ptp) REVERT: W 30 MET cc_start: 0.9080 (mmt) cc_final: 0.8857 (mmt) REVERT: X 403 MET cc_start: 0.7883 (tmm) cc_final: 0.7616 (tmm) REVERT: Y 151 MET cc_start: 0.8817 (ppp) cc_final: 0.8420 (pmm) REVERT: Y 180 MET cc_start: 0.4541 (tpt) cc_final: 0.4319 (tpt) REVERT: Y 704 GLU cc_start: 0.5691 (OUTLIER) cc_final: 0.5232 (pm20) REVERT: Y 822 MET cc_start: 0.6489 (tpp) cc_final: 0.6237 (tpp) outliers start: 77 outliers final: 40 residues processed: 293 average time/residue: 0.5021 time to fit residues: 258.4915 Evaluate side-chains 261 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 217 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 181 LYS Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 416 MET Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 142 ASN Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 230 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 314 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain b residue 346 SER Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 295 HIS Chi-restraints excluded: chain c residue 314 THR Chi-restraints excluded: chain c residue 326 LYS Chi-restraints excluded: chain d residue 142 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 314 THR Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain e residue 96 THR Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 314 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain X residue 111 GLU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 515 MET Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 933 VAL Chi-restraints excluded: chain Y residue 146 VAL Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 484 MET Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 777 HIS Chi-restraints excluded: chain Y residue 903 LEU Chi-restraints excluded: chain Y residue 974 VAL Chi-restraints excluded: chain Y residue 1261 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 590 optimal weight: 20.0000 chunk 69 optimal weight: 0.0270 chunk 348 optimal weight: 10.0000 chunk 447 optimal weight: 3.9990 chunk 346 optimal weight: 7.9990 chunk 515 optimal weight: 8.9990 chunk 341 optimal weight: 7.9990 chunk 610 optimal weight: 20.0000 chunk 381 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 281 optimal weight: 10.0000 overall best weight: 5.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 ASN c 42 HIS d 42 HIS d 172 GLN d 344 HIS ** V 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 147 GLN V 276 HIS X 604 HIS ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 488 ASN ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 52482 Z= 0.307 Angle : 0.688 14.166 71218 Z= 0.344 Chirality : 0.043 0.349 8151 Planarity : 0.004 0.060 9004 Dihedral : 12.059 175.630 8011 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.50 % Allowed : 18.11 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.11), residues: 6306 helix: 0.76 (0.11), residues: 2486 sheet: -0.65 (0.17), residues: 811 loop : -1.33 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP f 381 HIS 0.007 0.001 HIS X 165 PHE 0.021 0.002 PHE Y1037 TYR 0.026 0.002 TYR U 177 ARG 0.011 0.001 ARG a 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 218 time to evaluate : 4.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.6036 (mmm) cc_final: 0.5149 (mtt) REVERT: f 405 MET cc_start: 0.8849 (ptt) cc_final: 0.8431 (ppp) REVERT: f 416 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8821 (mmm) REVERT: a 1 MET cc_start: 0.7449 (ppp) cc_final: 0.7042 (ppp) REVERT: a 147 MET cc_start: 0.8854 (tpt) cc_final: 0.7795 (tpp) REVERT: a 219 MET cc_start: 0.8673 (mmt) cc_final: 0.8204 (mmm) REVERT: a 396 MET cc_start: 0.8512 (mmm) cc_final: 0.7904 (mmm) REVERT: a 405 MET cc_start: 0.8703 (ptp) cc_final: 0.8391 (ppp) REVERT: a 415 MET cc_start: 0.9000 (tmm) cc_final: 0.8675 (tmm) REVERT: b 147 MET cc_start: 0.8334 (tpp) cc_final: 0.6934 (tpp) REVERT: b 219 MET cc_start: 0.8481 (mpp) cc_final: 0.8241 (tpp) REVERT: c 245 MET cc_start: 0.6802 (mmm) cc_final: 0.6421 (mmm) REVERT: c 390 MET cc_start: 0.7021 (ptp) cc_final: 0.6678 (ptp) REVERT: d 21 MET cc_start: 0.8656 (mmm) cc_final: 0.6565 (ptt) REVERT: d 147 MET cc_start: 0.8687 (mmm) cc_final: 0.8369 (mmm) REVERT: d 245 MET cc_start: 0.8006 (tpp) cc_final: 0.7623 (mmt) REVERT: d 396 MET cc_start: 0.7586 (tpt) cc_final: 0.7101 (tpp) REVERT: e 186 MET cc_start: 0.8556 (pmm) cc_final: 0.8232 (pmm) REVERT: e 380 MET cc_start: 0.9238 (mtp) cc_final: 0.8908 (mtp) REVERT: e 396 MET cc_start: 0.8081 (tpt) cc_final: 0.7876 (tpt) REVERT: e 416 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.5908 (ppp) REVERT: A 167 MET cc_start: 0.4941 (ptp) cc_final: 0.4728 (ptp) REVERT: W 30 MET cc_start: 0.9017 (mmt) cc_final: 0.8730 (mmt) REVERT: X 124 MET cc_start: 0.8656 (ppp) cc_final: 0.8406 (ppp) REVERT: X 403 MET cc_start: 0.8089 (tmm) cc_final: 0.7795 (tmm) REVERT: Y 151 MET cc_start: 0.8763 (ppp) cc_final: 0.8273 (pmm) REVERT: Y 180 MET cc_start: 0.5148 (tpt) cc_final: 0.4795 (tpt) REVERT: Y 466 MET cc_start: 0.7338 (tmm) cc_final: 0.7007 (tmm) outliers start: 81 outliers final: 56 residues processed: 289 average time/residue: 0.5110 time to fit residues: 260.4757 Evaluate side-chains 272 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 214 time to evaluate : 4.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 181 LYS Chi-restraints excluded: chain f residue 199 HIS Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 228 VAL Chi-restraints excluded: chain f residue 322 ASP Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 416 MET Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 142 ASN Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 230 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 314 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain b residue 346 SER Chi-restraints excluded: chain b residue 393 ILE Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 184 LYS Chi-restraints excluded: chain c residue 295 HIS Chi-restraints excluded: chain c residue 314 THR Chi-restraints excluded: chain c residue 326 LYS Chi-restraints excluded: chain d residue 142 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 314 THR Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain e residue 96 THR Chi-restraints excluded: chain e residue 206 VAL Chi-restraints excluded: chain e residue 294 LEU Chi-restraints excluded: chain e residue 295 HIS Chi-restraints excluded: chain e residue 314 THR Chi-restraints excluded: chain e residue 416 MET Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 231 PHE Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 111 GLU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 515 MET Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 782 VAL Chi-restraints excluded: chain X residue 877 VAL Chi-restraints excluded: chain X residue 884 VAL Chi-restraints excluded: chain X residue 931 VAL Chi-restraints excluded: chain X residue 933 VAL Chi-restraints excluded: chain Y residue 146 VAL Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 484 MET Chi-restraints excluded: chain Y residue 639 VAL Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 825 VAL Chi-restraints excluded: chain Y residue 903 LEU Chi-restraints excluded: chain Y residue 974 VAL Chi-restraints excluded: chain Y residue 1298 VAL Chi-restraints excluded: chain Y residue 1351 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 377 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 364 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 387 optimal weight: 0.0030 chunk 415 optimal weight: 4.9990 chunk 301 optimal weight: 9.9990 chunk 56 optimal weight: 0.1980 chunk 479 optimal weight: 1.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 25 ASN a 190 ASN ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 HIS V 147 GLN X 952 GLN X1288 GLN ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 52482 Z= 0.157 Angle : 0.634 14.709 71218 Z= 0.310 Chirality : 0.042 0.256 8151 Planarity : 0.003 0.061 9004 Dihedral : 11.869 175.566 8011 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.06 % Allowed : 18.94 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 6306 helix: 0.85 (0.11), residues: 2502 sheet: -0.53 (0.18), residues: 795 loop : -1.23 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 580 HIS 0.006 0.001 HIS V 276 PHE 0.014 0.001 PHE c 412 TYR 0.037 0.001 TYR V 277 ARG 0.017 0.000 ARG Y 535 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 225 time to evaluate : 4.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.6057 (mmm) cc_final: 0.5359 (mtt) REVERT: f 147 MET cc_start: 0.8661 (tpp) cc_final: 0.8363 (tpp) REVERT: f 405 MET cc_start: 0.8756 (ptt) cc_final: 0.8441 (ppp) REVERT: f 416 MET cc_start: 0.9316 (tpp) cc_final: 0.8847 (mmm) REVERT: a 1 MET cc_start: 0.7471 (ppp) cc_final: 0.7073 (ppp) REVERT: a 147 MET cc_start: 0.8809 (tpt) cc_final: 0.7843 (tpp) REVERT: a 219 MET cc_start: 0.8565 (mmt) cc_final: 0.8158 (mmm) REVERT: a 326 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8480 (ptmm) REVERT: a 396 MET cc_start: 0.8516 (mmm) cc_final: 0.7970 (mmm) REVERT: a 405 MET cc_start: 0.8703 (ptp) cc_final: 0.8408 (ppp) REVERT: a 415 MET cc_start: 0.8974 (tmm) cc_final: 0.8563 (tmm) REVERT: b 29 MET cc_start: 0.6819 (mpp) cc_final: 0.5890 (pmm) REVERT: b 147 MET cc_start: 0.8523 (tpp) cc_final: 0.7149 (tpp) REVERT: b 219 MET cc_start: 0.8319 (mpp) cc_final: 0.7979 (mmm) REVERT: c 21 MET cc_start: 0.7444 (mtp) cc_final: 0.6703 (ptm) REVERT: c 390 MET cc_start: 0.6919 (ptp) cc_final: 0.6632 (ptp) REVERT: d 21 MET cc_start: 0.8448 (mmm) cc_final: 0.6357 (ptt) REVERT: d 245 MET cc_start: 0.7931 (tpp) cc_final: 0.7540 (mmt) REVERT: d 314 THR cc_start: 0.9520 (OUTLIER) cc_final: 0.9292 (m) REVERT: d 396 MET cc_start: 0.7273 (tpt) cc_final: 0.6889 (tpp) REVERT: e 21 MET cc_start: 0.7544 (tmm) cc_final: 0.7297 (ppp) REVERT: e 186 MET cc_start: 0.8508 (pmm) cc_final: 0.8142 (pmm) REVERT: e 380 MET cc_start: 0.9217 (mtp) cc_final: 0.8924 (mtp) REVERT: e 393 ILE cc_start: 0.9612 (OUTLIER) cc_final: 0.9398 (tp) REVERT: W 30 MET cc_start: 0.8990 (mmt) cc_final: 0.8725 (mmt) REVERT: X 403 MET cc_start: 0.7974 (tmm) cc_final: 0.7713 (tmm) REVERT: Y 130 MET cc_start: 0.8313 (ppp) cc_final: 0.7674 (ppp) REVERT: Y 151 MET cc_start: 0.8790 (ppp) cc_final: 0.8321 (pmm) REVERT: Y 180 MET cc_start: 0.4512 (tpt) cc_final: 0.4185 (tpt) REVERT: Y 604 MET cc_start: 0.7802 (mmm) cc_final: 0.7258 (tpp) REVERT: Y 704 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5323 (pm20) outliers start: 57 outliers final: 43 residues processed: 276 average time/residue: 0.5007 time to fit residues: 242.7774 Evaluate side-chains 266 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 219 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 181 LYS Chi-restraints excluded: chain f residue 199 HIS Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 294 LEU Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 230 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 314 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 346 SER Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 295 HIS Chi-restraints excluded: chain c residue 314 THR Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 314 THR Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain e residue 96 THR Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 206 VAL Chi-restraints excluded: chain e residue 294 LEU Chi-restraints excluded: chain e residue 295 HIS Chi-restraints excluded: chain e residue 322 ASP Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 231 PHE Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 515 MET Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 727 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 931 VAL Chi-restraints excluded: chain X residue 933 VAL Chi-restraints excluded: chain Y residue 146 VAL Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 777 HIS Chi-restraints excluded: chain Y residue 790 THR Chi-restraints excluded: chain Y residue 825 VAL Chi-restraints excluded: chain Y residue 903 LEU Chi-restraints excluded: chain Y residue 974 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 554 optimal weight: 0.0980 chunk 584 optimal weight: 0.9980 chunk 533 optimal weight: 10.0000 chunk 568 optimal weight: 6.9990 chunk 342 optimal weight: 30.0000 chunk 247 optimal weight: 0.9980 chunk 446 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 513 optimal weight: 8.9990 chunk 537 optimal weight: 2.9990 chunk 566 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 172 GLN ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 147 GLN ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 667 GLN ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 52482 Z= 0.175 Angle : 0.647 14.820 71218 Z= 0.316 Chirality : 0.042 0.274 8151 Planarity : 0.003 0.059 9004 Dihedral : 11.826 172.563 8011 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.98 % Allowed : 19.29 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -0.39 (0.11), residues: 6306 helix: 0.90 (0.11), residues: 2497 sheet: -0.52 (0.18), residues: 802 loop : -1.16 (0.12), residues: 3007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 381 HIS 0.004 0.001 HIS Y 450 PHE 0.021 0.001 PHE c 412 TYR 0.020 0.001 TYR e 72 ARG 0.011 0.000 ARG Y 535 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 219 time to evaluate : 4.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.6090 (mmm) cc_final: 0.5186 (mtt) REVERT: f 147 MET cc_start: 0.8790 (tpp) cc_final: 0.8296 (tpp) REVERT: f 405 MET cc_start: 0.8768 (ptt) cc_final: 0.8438 (ppp) REVERT: f 416 MET cc_start: 0.9323 (tpp) cc_final: 0.8811 (mmm) REVERT: a 1 MET cc_start: 0.7602 (ppp) cc_final: 0.6954 (ppp) REVERT: a 147 MET cc_start: 0.8772 (tpt) cc_final: 0.7784 (tpp) REVERT: a 219 MET cc_start: 0.8622 (mmt) cc_final: 0.8219 (mmm) REVERT: a 326 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8519 (ptmm) REVERT: a 396 MET cc_start: 0.8530 (mmm) cc_final: 0.8024 (mmm) REVERT: a 405 MET cc_start: 0.8662 (ptp) cc_final: 0.8361 (ppp) REVERT: a 415 MET cc_start: 0.8986 (tmm) cc_final: 0.8581 (tmm) REVERT: b 29 MET cc_start: 0.6843 (mpp) cc_final: 0.6065 (pmm) REVERT: b 147 MET cc_start: 0.8563 (tpp) cc_final: 0.7254 (tpp) REVERT: b 219 MET cc_start: 0.8349 (mpp) cc_final: 0.8105 (tpp) REVERT: c 21 MET cc_start: 0.7293 (mtp) cc_final: 0.6507 (ptm) REVERT: c 205 MET cc_start: 0.7527 (mmm) cc_final: 0.7046 (mmt) REVERT: c 390 MET cc_start: 0.6907 (ptp) cc_final: 0.6627 (ptp) REVERT: d 21 MET cc_start: 0.8514 (mmm) cc_final: 0.6511 (ptt) REVERT: d 245 MET cc_start: 0.7932 (tpp) cc_final: 0.7528 (mmt) REVERT: d 396 MET cc_start: 0.7351 (tpt) cc_final: 0.6949 (tpp) REVERT: e 186 MET cc_start: 0.8525 (pmm) cc_final: 0.8148 (pmm) REVERT: e 380 MET cc_start: 0.9232 (mtp) cc_final: 0.8937 (mtp) REVERT: W 30 MET cc_start: 0.8939 (mmt) cc_final: 0.8653 (mmt) REVERT: X 403 MET cc_start: 0.7930 (tmm) cc_final: 0.7643 (tmm) REVERT: X 429 MET cc_start: 0.8079 (mpp) cc_final: 0.7870 (mpp) REVERT: Y 151 MET cc_start: 0.8761 (ppp) cc_final: 0.8547 (pmm) REVERT: Y 180 MET cc_start: 0.4560 (tpt) cc_final: 0.4223 (tpt) REVERT: Y 704 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5438 (pm20) REVERT: Y 743 MET cc_start: 0.7940 (tmm) cc_final: 0.6755 (tmm) REVERT: Y 822 MET cc_start: 0.6528 (tpt) cc_final: 0.6294 (tpt) REVERT: Y 975 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8870 (tp) outliers start: 53 outliers final: 46 residues processed: 268 average time/residue: 0.5021 time to fit residues: 235.5345 Evaluate side-chains 264 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 215 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 181 LYS Chi-restraints excluded: chain f residue 199 HIS Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 294 LEU Chi-restraints excluded: chain f residue 322 ASP Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 230 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 314 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain b residue 346 SER Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 295 HIS Chi-restraints excluded: chain c residue 314 THR Chi-restraints excluded: chain d residue 142 ASN Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain e residue 96 THR Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 206 VAL Chi-restraints excluded: chain e residue 294 LEU Chi-restraints excluded: chain e residue 295 HIS Chi-restraints excluded: chain e residue 322 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 231 PHE Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 515 MET Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 727 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 782 VAL Chi-restraints excluded: chain X residue 931 VAL Chi-restraints excluded: chain X residue 933 VAL Chi-restraints excluded: chain X residue 1056 VAL Chi-restraints excluded: chain Y residue 146 VAL Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 639 VAL Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 710 ASP Chi-restraints excluded: chain Y residue 790 THR Chi-restraints excluded: chain Y residue 825 VAL Chi-restraints excluded: chain Y residue 903 LEU Chi-restraints excluded: chain Y residue 974 VAL Chi-restraints excluded: chain Y residue 975 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 373 optimal weight: 7.9990 chunk 601 optimal weight: 7.9990 chunk 366 optimal weight: 9.9990 chunk 285 optimal weight: 30.0000 chunk 417 optimal weight: 10.0000 chunk 630 optimal weight: 10.0000 chunk 580 optimal weight: 9.9990 chunk 502 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 387 optimal weight: 40.0000 chunk 307 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 172 GLN ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 190 ASN ** V 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 75 GLN ** X 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 52482 Z= 0.374 Angle : 0.781 15.678 71218 Z= 0.391 Chirality : 0.044 0.306 8151 Planarity : 0.004 0.056 9004 Dihedral : 12.217 155.008 8011 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.22 % Allowed : 19.17 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.11), residues: 6306 helix: 0.59 (0.11), residues: 2500 sheet: -0.61 (0.18), residues: 806 loop : -1.27 (0.11), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y1020 HIS 0.008 0.002 HIS X 165 PHE 0.020 0.002 PHE c 412 TYR 0.030 0.002 TYR U 177 ARG 0.019 0.001 ARG X 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 213 time to evaluate : 4.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.5729 (mmm) cc_final: 0.5159 (mtt) REVERT: f 147 MET cc_start: 0.8811 (tpp) cc_final: 0.8420 (tpp) REVERT: f 405 MET cc_start: 0.8933 (ptt) cc_final: 0.8694 (ppp) REVERT: f 416 MET cc_start: 0.9392 (tpp) cc_final: 0.8857 (mmm) REVERT: a 1 MET cc_start: 0.8019 (ppp) cc_final: 0.7450 (ppp) REVERT: a 147 MET cc_start: 0.8827 (tpt) cc_final: 0.7814 (tpp) REVERT: a 219 MET cc_start: 0.8765 (mmt) cc_final: 0.8318 (mmm) REVERT: a 396 MET cc_start: 0.8489 (mmm) cc_final: 0.7864 (mmm) REVERT: a 405 MET cc_start: 0.8748 (ptp) cc_final: 0.8347 (ppp) REVERT: a 415 MET cc_start: 0.9025 (tmm) cc_final: 0.8678 (tmm) REVERT: b 147 MET cc_start: 0.8648 (tpp) cc_final: 0.7229 (tpp) REVERT: b 326 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8902 (pttm) REVERT: c 21 MET cc_start: 0.7331 (mtp) cc_final: 0.6439 (mtm) REVERT: c 390 MET cc_start: 0.7151 (ptp) cc_final: 0.6808 (ptp) REVERT: d 21 MET cc_start: 0.8710 (mmm) cc_final: 0.6668 (ptt) REVERT: d 245 MET cc_start: 0.8071 (tpp) cc_final: 0.7649 (mmt) REVERT: d 396 MET cc_start: 0.7560 (tpt) cc_final: 0.7096 (tpp) REVERT: e 186 MET cc_start: 0.8691 (pmm) cc_final: 0.8324 (pmm) REVERT: e 380 MET cc_start: 0.9290 (mtp) cc_final: 0.8984 (mtp) REVERT: W 30 MET cc_start: 0.8968 (mmt) cc_final: 0.8649 (mmt) REVERT: X 403 MET cc_start: 0.8150 (tmm) cc_final: 0.7846 (tmm) REVERT: Y 130 MET cc_start: 0.8571 (ppp) cc_final: 0.7929 (ppp) REVERT: Y 151 MET cc_start: 0.8789 (ppp) cc_final: 0.8443 (pmm) REVERT: Y 180 MET cc_start: 0.5316 (tpt) cc_final: 0.4910 (tpt) REVERT: Y 604 MET cc_start: 0.7782 (mmm) cc_final: 0.7298 (tpp) REVERT: Y 704 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.6031 (pm20) REVERT: Y 743 MET cc_start: 0.8156 (tmm) cc_final: 0.7030 (tmm) REVERT: Y 822 MET cc_start: 0.6620 (tpt) cc_final: 0.6414 (tpt) outliers start: 66 outliers final: 55 residues processed: 272 average time/residue: 0.4923 time to fit residues: 235.4623 Evaluate side-chains 268 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 211 time to evaluate : 4.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 181 LYS Chi-restraints excluded: chain f residue 199 HIS Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 294 LEU Chi-restraints excluded: chain f residue 322 ASP Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 230 SER Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 314 THR Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain b residue 21 MET Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 346 SER Chi-restraints excluded: chain b residue 411 ASP Chi-restraints excluded: chain c residue 295 HIS Chi-restraints excluded: chain c residue 314 THR Chi-restraints excluded: chain d residue 142 ASN Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain d residue 373 THR Chi-restraints excluded: chain e residue 96 THR Chi-restraints excluded: chain e residue 203 VAL Chi-restraints excluded: chain e residue 206 VAL Chi-restraints excluded: chain e residue 294 LEU Chi-restraints excluded: chain e residue 295 HIS Chi-restraints excluded: chain e residue 322 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain V residue 160 HIS Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 231 PHE Chi-restraints excluded: chain V residue 318 LEU Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 165 HIS Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 515 MET Chi-restraints excluded: chain X residue 563 THR Chi-restraints excluded: chain X residue 663 VAL Chi-restraints excluded: chain X residue 727 VAL Chi-restraints excluded: chain X residue 765 ILE Chi-restraints excluded: chain X residue 782 VAL Chi-restraints excluded: chain X residue 877 VAL Chi-restraints excluded: chain X residue 931 VAL Chi-restraints excluded: chain X residue 933 VAL Chi-restraints excluded: chain X residue 1056 VAL Chi-restraints excluded: chain Y residue 146 VAL Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 639 VAL Chi-restraints excluded: chain Y residue 704 GLU Chi-restraints excluded: chain Y residue 710 ASP Chi-restraints excluded: chain Y residue 790 THR Chi-restraints excluded: chain Y residue 825 VAL Chi-restraints excluded: chain Y residue 903 LEU Chi-restraints excluded: chain Y residue 974 VAL Chi-restraints excluded: chain Y residue 1351 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 398 optimal weight: 3.9990 chunk 534 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 463 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 502 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 516 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 142 ASN ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.038924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.025029 restraints weight = 627041.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.025636 restraints weight = 362967.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.025841 restraints weight = 255105.528| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 52482 Z= 0.211 Angle : 0.691 15.663 71218 Z= 0.339 Chirality : 0.043 0.310 8151 Planarity : 0.004 0.059 9004 Dihedral : 12.080 149.519 8011 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.15 % Allowed : 19.24 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.12 % 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: -0.53 (0.11), residues: 6306 helix: 0.71 (0.11), residues: 2501 sheet: -0.56 (0.18), residues: 797 loop : -1.19 (0.12), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 381 HIS 0.006 0.001 HIS X 165 PHE 0.012 0.001 PHE f 398 TYR 0.023 0.001 TYR U 177 ARG 0.009 0.000 ARG a 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7548.48 seconds wall clock time: 134 minutes 18.84 seconds (8058.84 seconds total)