Starting phenix.real_space_refine on Sun Feb 18 14:56:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wad_32382/02_2024/7wad_32382_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wad_32382/02_2024/7wad_32382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wad_32382/02_2024/7wad_32382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wad_32382/02_2024/7wad_32382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wad_32382/02_2024/7wad_32382_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wad_32382/02_2024/7wad_32382_updated.pdb" } resolution = 2.96 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= -0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 4 5.21 5 S 80 5.16 5 C 14000 2.51 5 N 3884 2.21 5 O 4276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D GLU 575": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22268 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "B" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "C" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "D" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 11.93, per 1000 atoms: 0.54 Number of scatterers: 22268 At special positions: 0 Unit cell: (146.08, 139.92, 104.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 24 15.00 Mg 4 11.99 O 4276 8.00 N 3884 7.00 C 14000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.86 Conformation dependent library (CDL) restraints added in 4.2 seconds 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5208 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 24 sheets defined 37.0% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.04 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 119 through 139 removed outlier: 3.844A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.723A pdb=" N ALA A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 243 through 253 removed outlier: 4.233A pdb=" N GLN A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 291 Processing helix chain 'A' and resid 336 through 344 removed outlier: 4.631A pdb=" N GLU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 410 through 423 Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.969A pdb=" N VAL A 461 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 499 through 512 removed outlier: 3.676A pdb=" N GLN A 512 " --> pdb=" O HIS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.595A pdb=" N HIS A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 595 through 607 removed outlier: 4.064A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 628 removed outlier: 3.629A pdb=" N MET A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 691 through 707 removed outlier: 3.579A pdb=" N ALA A 695 " --> pdb=" O PRO A 691 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 719 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 66 through 72 Processing helix chain 'B' and resid 77 through 91 Processing helix chain 'B' and resid 119 through 139 removed outlier: 3.884A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 160 Processing helix chain 'B' and resid 165 through 176 removed outlier: 3.734A pdb=" N ALA B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 220 through 229 Processing helix chain 'B' and resid 243 through 253 removed outlier: 4.269A pdb=" N GLN B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 291 Processing helix chain 'B' and resid 336 through 344 removed outlier: 4.629A pdb=" N GLU B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 410 through 423 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.674A pdb=" N GLN B 512 " --> pdb=" O HIS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.582A pdb=" N HIS B 544 " --> pdb=" O PRO B 540 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 546 " --> pdb=" O SER B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 595 through 607 removed outlier: 4.058A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 628 removed outlier: 3.633A pdb=" N MET B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA B 628 " --> pdb=" O VAL B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 683 through 685 No H-bonds generated for 'chain 'B' and resid 683 through 685' Processing helix chain 'B' and resid 691 through 707 removed outlier: 3.576A pdb=" N ALA B 695 " --> pdb=" O PRO B 691 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 719 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 66 through 72 Processing helix chain 'C' and resid 77 through 91 Processing helix chain 'C' and resid 119 through 139 removed outlier: 3.833A pdb=" N VAL C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 Processing helix chain 'C' and resid 165 through 176 removed outlier: 3.715A pdb=" N ALA C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 220 through 229 Processing helix chain 'C' and resid 243 through 253 removed outlier: 4.234A pdb=" N GLN C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASP C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 291 Processing helix chain 'C' and resid 336 through 344 removed outlier: 4.632A pdb=" N GLU C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 410 through 423 Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 499 through 512 removed outlier: 3.677A pdb=" N GLN C 512 " --> pdb=" O HIS C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 547 removed outlier: 3.567A pdb=" N HIS C 544 " --> pdb=" O PRO C 540 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE C 546 " --> pdb=" O SER C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 567 Processing helix chain 'C' and resid 595 through 607 removed outlier: 4.065A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 628 removed outlier: 3.647A pdb=" N MET C 627 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA C 628 " --> pdb=" O VAL C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 652 Processing helix chain 'C' and resid 683 through 685 No H-bonds generated for 'chain 'C' and resid 683 through 685' Processing helix chain 'C' and resid 691 through 707 removed outlier: 3.590A pdb=" N ALA C 695 " --> pdb=" O PRO C 691 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 704 " --> pdb=" O ALA C 700 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 719 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 66 through 72 Processing helix chain 'D' and resid 77 through 91 Processing helix chain 'D' and resid 119 through 139 removed outlier: 3.814A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 160 Processing helix chain 'D' and resid 165 through 176 removed outlier: 3.741A pdb=" N ALA D 169 " --> pdb=" O PRO D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 220 through 229 Processing helix chain 'D' and resid 243 through 253 removed outlier: 4.240A pdb=" N GLN D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU D 251 " --> pdb=" O GLN D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 291 Processing helix chain 'D' and resid 336 through 344 removed outlier: 4.625A pdb=" N GLU D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 372 Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 410 through 423 Processing helix chain 'D' and resid 457 through 459 No H-bonds generated for 'chain 'D' and resid 457 through 459' Processing helix chain 'D' and resid 471 through 479 Processing helix chain 'D' and resid 499 through 512 removed outlier: 3.674A pdb=" N GLN D 512 " --> pdb=" O HIS D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 547 removed outlier: 3.571A pdb=" N HIS D 544 " --> pdb=" O PRO D 540 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE D 546 " --> pdb=" O SER D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 567 Processing helix chain 'D' and resid 595 through 607 removed outlier: 4.061A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 628 removed outlier: 3.623A pdb=" N MET D 627 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA D 628 " --> pdb=" O VAL D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 652 Processing helix chain 'D' and resid 683 through 685 No H-bonds generated for 'chain 'D' and resid 683 through 685' Processing helix chain 'D' and resid 691 through 707 removed outlier: 3.589A pdb=" N ALA D 695 " --> pdb=" O PRO D 691 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN D 707 " --> pdb=" O ALA D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 719 Processing sheet with id= A, first strand: chain 'A' and resid 99 through 103 removed outlier: 3.877A pdb=" N LYS A 5 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASP A 28 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE A 3 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= C, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= D, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.906A pdb=" N LEU A 311 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A 320 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG A 309 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU A 322 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ASP A 307 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 434 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 450 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 433 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 327 through 329 Processing sheet with id= F, first strand: chain 'A' and resid 673 through 677 removed outlier: 6.559A pdb=" N ILE A 665 " --> pdb=" O ILE A 676 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER A 639 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 618 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE A 527 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 99 through 103 removed outlier: 3.795A pdb=" N LYS B 5 " --> pdb=" O ARG B 26 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASP B 28 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE B 3 " --> pdb=" O ASP B 28 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= I, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= J, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.900A pdb=" N LEU B 311 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 320 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG B 309 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU B 322 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP B 307 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 434 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU B 450 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 433 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE B 448 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 327 through 329 Processing sheet with id= L, first strand: chain 'B' and resid 673 through 677 removed outlier: 6.604A pdb=" N ILE B 665 " --> pdb=" O ILE B 676 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER B 639 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN B 618 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE B 527 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 99 through 103 removed outlier: 3.857A pdb=" N LYS C 5 " --> pdb=" O ARG C 26 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP C 28 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE C 3 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= O, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= P, first strand: chain 'C' and resid 400 through 403 removed outlier: 6.914A pdb=" N LEU C 311 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL C 320 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG C 309 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU C 322 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP C 307 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 434 " --> pdb=" O LYS C 306 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU C 450 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 433 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE C 448 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 327 through 329 Processing sheet with id= R, first strand: chain 'C' and resid 673 through 677 removed outlier: 6.604A pdb=" N ILE C 665 " --> pdb=" O ILE C 676 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N SER C 639 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN C 618 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE C 527 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU C 531 " --> pdb=" O ILE C 527 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 99 through 103 removed outlier: 3.887A pdb=" N LYS D 5 " --> pdb=" O ARG D 26 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP D 28 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE D 3 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= U, first strand: chain 'D' and resid 237 through 240 Processing sheet with id= V, first strand: chain 'D' and resid 400 through 403 removed outlier: 6.900A pdb=" N LEU D 311 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL D 320 " --> pdb=" O ARG D 309 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG D 309 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU D 322 " --> pdb=" O ASP D 307 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP D 307 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 434 " --> pdb=" O LYS D 306 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU D 450 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE D 448 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 327 through 329 Processing sheet with id= X, first strand: chain 'D' and resid 673 through 677 removed outlier: 6.611A pdb=" N ILE D 665 " --> pdb=" O ILE D 676 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N ALA D 658 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR D 637 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N TYR D 660 " --> pdb=" O TYR D 637 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N SER D 639 " --> pdb=" O TYR D 660 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN D 618 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE D 527 " --> pdb=" O LEU D 531 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU D 531 " --> pdb=" O ILE D 527 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2499 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.00 Time building geometry restraints manager: 9.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 7591 1.37 - 1.51: 7151 1.51 - 1.66: 7770 1.66 - 1.80: 109 1.80 - 1.95: 19 Bond restraints: 22640 Sorted by residual: bond pdb=" CA GLY A 518 " pdb=" C GLY A 518 " ideal model delta sigma weight residual 1.520 1.509 0.011 7.30e-03 1.88e+04 2.24e+00 bond pdb=" CA GLY C 518 " pdb=" C GLY C 518 " ideal model delta sigma weight residual 1.520 1.509 0.011 7.30e-03 1.88e+04 2.11e+00 bond pdb=" CA GLY D 518 " pdb=" C GLY D 518 " ideal model delta sigma weight residual 1.520 1.510 0.010 7.30e-03 1.88e+04 2.03e+00 bond pdb=" CA GLY B 518 " pdb=" C GLY B 518 " ideal model delta sigma weight residual 1.520 1.510 0.010 7.30e-03 1.88e+04 1.89e+00 bond pdb=" C PRO A 455 " pdb=" N GLY A 456 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 1.86e+00 ... (remaining 22635 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.82: 679 106.82 - 113.61: 12962 113.61 - 120.39: 8318 120.39 - 127.17: 8562 127.17 - 133.96: 239 Bond angle restraints: 30760 Sorted by residual: angle pdb=" N GLY B 655 " pdb=" CA GLY B 655 " pdb=" C GLY B 655 " ideal model delta sigma weight residual 110.20 114.98 -4.78 1.32e+00 5.74e-01 1.31e+01 angle pdb=" N GLY C 655 " pdb=" CA GLY C 655 " pdb=" C GLY C 655 " ideal model delta sigma weight residual 110.20 114.96 -4.76 1.32e+00 5.74e-01 1.30e+01 angle pdb=" N GLY D 655 " pdb=" CA GLY D 655 " pdb=" C GLY D 655 " ideal model delta sigma weight residual 110.20 114.96 -4.76 1.32e+00 5.74e-01 1.30e+01 angle pdb=" N GLY A 655 " pdb=" CA GLY A 655 " pdb=" C GLY A 655 " ideal model delta sigma weight residual 110.20 114.93 -4.73 1.32e+00 5.74e-01 1.28e+01 angle pdb=" N THR C 204 " pdb=" CA THR C 204 " pdb=" C THR C 204 " ideal model delta sigma weight residual 114.56 110.78 3.78 1.27e+00 6.20e-01 8.84e+00 ... (remaining 30755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.56: 13135 27.56 - 55.13: 426 55.13 - 82.69: 66 82.69 - 110.25: 13 110.25 - 137.82: 4 Dihedral angle restraints: 13644 sinusoidal: 5460 harmonic: 8184 Sorted by residual: dihedral pdb=" O1A AGS B1003 " pdb=" O3A AGS B1003 " pdb=" PA AGS B1003 " pdb=" PB AGS B1003 " ideal model delta sinusoidal sigma weight residual 292.27 154.45 137.82 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" O1A AGS A1003 " pdb=" O3A AGS A1003 " pdb=" PA AGS A1003 " pdb=" PB AGS A1003 " ideal model delta sinusoidal sigma weight residual 292.27 157.95 134.32 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" O1A AGS C1003 " pdb=" O3A AGS C1003 " pdb=" PA AGS C1003 " pdb=" PB AGS C1003 " ideal model delta sinusoidal sigma weight residual 292.27 158.03 134.24 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 13641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2235 0.035 - 0.070: 958 0.070 - 0.105: 272 0.105 - 0.140: 146 0.140 - 0.175: 5 Chirality restraints: 3616 Sorted by residual: chirality pdb=" CB ILE D 40 " pdb=" CA ILE D 40 " pdb=" CG1 ILE D 40 " pdb=" CG2 ILE D 40 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA ILE D 260 " pdb=" N ILE D 260 " pdb=" C ILE D 260 " pdb=" CB ILE D 260 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA ILE B 260 " pdb=" N ILE B 260 " pdb=" C ILE B 260 " pdb=" CB ILE B 260 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 3613 not shown) Planarity restraints: 3920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 60 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 61 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 60 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO D 61 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 61 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 61 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 60 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 61 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " 0.026 5.00e-02 4.00e+02 ... (remaining 3917 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 149 2.57 - 3.16: 17692 3.16 - 3.74: 33036 3.74 - 4.32: 45678 4.32 - 4.90: 78120 Nonbonded interactions: 174675 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb=" O2B AGS A1003 " model vdw 1.992 2.170 nonbonded pdb="MG MG B1001 " pdb=" O2B AGS B1003 " model vdw 1.993 2.170 nonbonded pdb="MG MG C1001 " pdb=" O2B AGS C1003 " model vdw 1.994 2.170 nonbonded pdb="MG MG D1001 " pdb=" O2B AGS D1003 " model vdw 1.995 2.170 nonbonded pdb="MG MG A1001 " pdb=" O3G AGS A1003 " model vdw 2.081 2.170 ... (remaining 174670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.100 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 61.160 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 0.024 22640 Z= 0.206 Angle : 0.577 7.570 30760 Z= 0.338 Chirality : 0.045 0.175 3616 Planarity : 0.004 0.045 3920 Dihedral : 13.991 137.817 8436 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 2884 helix: 1.38 (0.16), residues: 1048 sheet: 0.20 (0.23), residues: 512 loop : -1.27 (0.15), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 15 HIS 0.003 0.001 HIS C 79 PHE 0.024 0.001 PHE D 43 TYR 0.009 0.001 TYR A 33 ARG 0.002 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8337 (tp30) cc_final: 0.8109 (tp30) REVERT: A 33 TYR cc_start: 0.8039 (p90) cc_final: 0.7819 (p90) REVERT: A 150 ASP cc_start: 0.6921 (m-30) cc_final: 0.6619 (m-30) REVERT: A 160 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8358 (tm-30) REVERT: A 173 GLU cc_start: 0.8298 (tp30) cc_final: 0.8021 (mm-30) REVERT: A 300 GLU cc_start: 0.7793 (mp0) cc_final: 0.7299 (mp0) REVERT: B 30 GLU cc_start: 0.8623 (tp30) cc_final: 0.8343 (tp30) REVERT: B 33 TYR cc_start: 0.8096 (p90) cc_final: 0.7799 (p90) REVERT: B 150 ASP cc_start: 0.6737 (m-30) cc_final: 0.6368 (m-30) REVERT: B 160 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8470 (tm-30) REVERT: B 173 GLU cc_start: 0.8327 (tp30) cc_final: 0.8033 (mm-30) REVERT: B 300 GLU cc_start: 0.7475 (mp0) cc_final: 0.7189 (mp0) REVERT: C 33 TYR cc_start: 0.8187 (p90) cc_final: 0.7928 (p90) REVERT: C 89 GLN cc_start: 0.8007 (tt0) cc_final: 0.7623 (tt0) REVERT: C 150 ASP cc_start: 0.6929 (m-30) cc_final: 0.6635 (m-30) REVERT: C 173 GLU cc_start: 0.8308 (tp30) cc_final: 0.8030 (mm-30) REVERT: C 236 ARG cc_start: 0.6387 (ptm160) cc_final: 0.5870 (ptm160) REVERT: C 300 GLU cc_start: 0.7823 (mp0) cc_final: 0.7346 (mp0) REVERT: D 30 GLU cc_start: 0.8508 (tp30) cc_final: 0.8287 (tp30) REVERT: D 150 ASP cc_start: 0.6822 (m-30) cc_final: 0.6482 (m-30) REVERT: D 173 GLU cc_start: 0.8309 (tp30) cc_final: 0.8031 (mm-30) REVERT: D 236 ARG cc_start: 0.6814 (ttp-170) cc_final: 0.6539 (ptm160) REVERT: D 300 GLU cc_start: 0.7465 (mp0) cc_final: 0.7196 (mp0) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 1.5257 time to fit residues: 384.2287 Evaluate side-chains 180 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 22640 Z= 0.494 Angle : 0.616 7.443 30760 Z= 0.325 Chirality : 0.049 0.175 3616 Planarity : 0.004 0.046 3920 Dihedral : 9.160 136.353 3284 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.15 % Allowed : 7.79 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 2884 helix: 1.16 (0.16), residues: 1068 sheet: 0.06 (0.23), residues: 524 loop : -1.30 (0.15), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 15 HIS 0.006 0.001 HIS B 18 PHE 0.016 0.002 PHE B 457 TYR 0.011 0.001 TYR D 519 ARG 0.010 0.001 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8514 (tp30) cc_final: 0.8245 (tp30) REVERT: A 33 TYR cc_start: 0.8206 (p90) cc_final: 0.8003 (p90) REVERT: A 150 ASP cc_start: 0.6987 (m-30) cc_final: 0.6668 (m-30) REVERT: A 160 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8358 (tm-30) REVERT: A 300 GLU cc_start: 0.7851 (mp0) cc_final: 0.7406 (mp0) REVERT: B 1 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8058 (mmt) REVERT: B 30 GLU cc_start: 0.8711 (tp30) cc_final: 0.8416 (tp30) REVERT: B 33 TYR cc_start: 0.8193 (p90) cc_final: 0.7920 (p90) REVERT: B 150 ASP cc_start: 0.6914 (m-30) cc_final: 0.6552 (m-30) REVERT: B 160 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8389 (tm-30) REVERT: B 300 GLU cc_start: 0.7488 (mp0) cc_final: 0.7259 (mp0) REVERT: C 33 TYR cc_start: 0.8309 (p90) cc_final: 0.8090 (p90) REVERT: C 150 ASP cc_start: 0.6981 (m-30) cc_final: 0.6664 (m-30) REVERT: C 236 ARG cc_start: 0.6663 (ptm160) cc_final: 0.6208 (ptm160) REVERT: C 300 GLU cc_start: 0.7857 (mp0) cc_final: 0.7440 (mp0) REVERT: D 30 GLU cc_start: 0.8633 (tp30) cc_final: 0.8338 (tp30) REVERT: D 150 ASP cc_start: 0.6909 (m-30) cc_final: 0.6594 (m-30) REVERT: D 236 ARG cc_start: 0.6820 (ttp-170) cc_final: 0.6279 (ptm160) REVERT: D 300 GLU cc_start: 0.7517 (mp0) cc_final: 0.7305 (mp0) outliers start: 27 outliers final: 13 residues processed: 194 average time/residue: 1.4671 time to fit residues: 324.4315 Evaluate side-chains 184 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 157 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.3980 chunk 81 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 chunk 178 optimal weight: 0.0020 chunk 72 optimal weight: 20.0000 chunk 262 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22640 Z= 0.131 Angle : 0.485 8.018 30760 Z= 0.254 Chirality : 0.045 0.163 3616 Planarity : 0.004 0.045 3920 Dihedral : 8.644 131.707 3284 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.24 % Allowed : 10.65 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 2884 helix: 1.50 (0.16), residues: 1068 sheet: 0.17 (0.23), residues: 512 loop : -1.13 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 15 HIS 0.003 0.001 HIS A 18 PHE 0.010 0.001 PHE D 43 TYR 0.010 0.001 TYR A 519 ARG 0.010 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8389 (tp30) cc_final: 0.8159 (tp30) REVERT: A 150 ASP cc_start: 0.6946 (m-30) cc_final: 0.6658 (m-30) REVERT: A 160 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8362 (tm-30) REVERT: A 168 GLU cc_start: 0.7923 (tp30) cc_final: 0.7529 (tp30) REVERT: A 236 ARG cc_start: 0.6529 (ptm160) cc_final: 0.6262 (ptm160) REVERT: A 300 GLU cc_start: 0.7792 (mp0) cc_final: 0.7373 (mp0) REVERT: A 526 TYR cc_start: 0.8251 (m-80) cc_final: 0.8025 (m-80) REVERT: B 30 GLU cc_start: 0.8635 (tp30) cc_final: 0.8354 (tp30) REVERT: B 33 TYR cc_start: 0.8088 (p90) cc_final: 0.7848 (p90) REVERT: B 150 ASP cc_start: 0.6853 (m-30) cc_final: 0.6521 (m-30) REVERT: B 151 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7409 (mm) REVERT: B 160 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8407 (tm-30) REVERT: C 33 TYR cc_start: 0.8213 (p90) cc_final: 0.7976 (p90) REVERT: C 150 ASP cc_start: 0.6975 (m-30) cc_final: 0.6686 (m-30) REVERT: C 160 GLN cc_start: 0.8689 (tt0) cc_final: 0.8483 (tm-30) REVERT: C 168 GLU cc_start: 0.7926 (tp30) cc_final: 0.7527 (tp30) REVERT: C 300 GLU cc_start: 0.7824 (mp0) cc_final: 0.7433 (mp0) REVERT: C 526 TYR cc_start: 0.8262 (m-80) cc_final: 0.8026 (m-80) REVERT: D 168 GLU cc_start: 0.7916 (tp30) cc_final: 0.7515 (tp30) REVERT: D 236 ARG cc_start: 0.6779 (ttp-170) cc_final: 0.6395 (ptm160) outliers start: 29 outliers final: 11 residues processed: 204 average time/residue: 1.4463 time to fit residues: 335.5412 Evaluate side-chains 175 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 251 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 0.6980 chunk 196 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 chunk 278 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 249 optimal weight: 40.0000 chunk 75 optimal weight: 20.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22640 Z= 0.168 Angle : 0.476 8.143 30760 Z= 0.249 Chirality : 0.044 0.154 3616 Planarity : 0.003 0.043 3920 Dihedral : 8.436 131.421 3284 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.94 % Allowed : 12.69 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 2884 helix: 1.57 (0.16), residues: 1072 sheet: 0.29 (0.23), residues: 512 loop : -1.07 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 15 HIS 0.002 0.001 HIS D 18 PHE 0.009 0.001 PHE D 43 TYR 0.011 0.001 TYR A 33 ARG 0.008 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8358 (tp30) cc_final: 0.8155 (tp30) REVERT: A 150 ASP cc_start: 0.6974 (m-30) cc_final: 0.6679 (m-30) REVERT: A 160 GLN cc_start: 0.8664 (tp-100) cc_final: 0.8363 (tm-30) REVERT: A 168 GLU cc_start: 0.8029 (tp30) cc_final: 0.7575 (tp30) REVERT: A 300 GLU cc_start: 0.7775 (mp0) cc_final: 0.7362 (mp0) REVERT: B 26 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8244 (mtm180) REVERT: B 30 GLU cc_start: 0.8623 (tp30) cc_final: 0.8339 (tp30) REVERT: B 33 TYR cc_start: 0.8108 (p90) cc_final: 0.7838 (p90) REVERT: B 150 ASP cc_start: 0.6901 (m-30) cc_final: 0.6567 (m-30) REVERT: B 151 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7432 (mm) REVERT: B 160 GLN cc_start: 0.8681 (tp-100) cc_final: 0.8409 (tm-30) REVERT: B 168 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7675 (tp30) REVERT: B 300 GLU cc_start: 0.7254 (mp0) cc_final: 0.6995 (mp0) REVERT: C 33 TYR cc_start: 0.8212 (p90) cc_final: 0.7991 (p90) REVERT: C 160 GLN cc_start: 0.8694 (tt0) cc_final: 0.8481 (tm-30) REVERT: C 168 GLU cc_start: 0.8035 (tp30) cc_final: 0.7585 (tp30) REVERT: C 236 ARG cc_start: 0.6490 (ptm160) cc_final: 0.6287 (ptm160) REVERT: C 300 GLU cc_start: 0.7841 (mp0) cc_final: 0.7420 (mp0) REVERT: D 94 MET cc_start: 0.7695 (mtm) cc_final: 0.7417 (mtt) REVERT: D 168 GLU cc_start: 0.8018 (tp30) cc_final: 0.7559 (tp30) REVERT: D 236 ARG cc_start: 0.6744 (ttp-170) cc_final: 0.6289 (ptm160) REVERT: D 300 GLU cc_start: 0.7254 (mp0) cc_final: 0.7003 (mp0) outliers start: 22 outliers final: 13 residues processed: 176 average time/residue: 1.4380 time to fit residues: 287.6506 Evaluate side-chains 166 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 204 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22640 Z= 0.271 Angle : 0.491 7.957 30760 Z= 0.258 Chirality : 0.045 0.148 3616 Planarity : 0.003 0.044 3920 Dihedral : 8.351 131.648 3284 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.58 % Allowed : 13.07 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 2884 helix: 1.59 (0.16), residues: 1072 sheet: 0.25 (0.23), residues: 512 loop : -1.13 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 15 HIS 0.002 0.001 HIS D 650 PHE 0.009 0.001 PHE D 43 TYR 0.009 0.001 TYR B 519 ARG 0.011 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8379 (tp30) cc_final: 0.8159 (tp30) REVERT: A 160 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8360 (tm-30) REVERT: A 168 GLU cc_start: 0.8120 (tp30) cc_final: 0.7660 (tp30) REVERT: A 300 GLU cc_start: 0.7764 (mp0) cc_final: 0.7310 (mp0) REVERT: B 26 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8177 (mtm180) REVERT: B 30 GLU cc_start: 0.8685 (tp30) cc_final: 0.8399 (tp30) REVERT: B 33 TYR cc_start: 0.8116 (p90) cc_final: 0.7845 (p90) REVERT: B 102 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.7642 (ttp-110) REVERT: B 150 ASP cc_start: 0.6872 (m-30) cc_final: 0.6514 (m-30) REVERT: B 160 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8396 (tm-30) REVERT: B 168 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7774 (tp30) REVERT: B 300 GLU cc_start: 0.7300 (mp0) cc_final: 0.7003 (mp0) REVERT: C 33 TYR cc_start: 0.8212 (p90) cc_final: 0.7995 (p90) REVERT: C 160 GLN cc_start: 0.8688 (tt0) cc_final: 0.8469 (tm-30) REVERT: C 168 GLU cc_start: 0.8124 (tp30) cc_final: 0.7667 (tp30) REVERT: C 300 GLU cc_start: 0.7811 (mp0) cc_final: 0.7349 (mp0) REVERT: D 26 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8508 (mtm180) REVERT: D 94 MET cc_start: 0.7830 (mtm) cc_final: 0.7621 (mtt) REVERT: D 168 GLU cc_start: 0.8128 (tp30) cc_final: 0.7675 (tp30) REVERT: D 236 ARG cc_start: 0.6734 (ttp-170) cc_final: 0.6346 (ptm160) REVERT: D 300 GLU cc_start: 0.7296 (mp0) cc_final: 0.6980 (mp0) outliers start: 37 outliers final: 21 residues processed: 188 average time/residue: 1.4483 time to fit residues: 308.8765 Evaluate side-chains 179 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 251 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 68 optimal weight: 0.0970 chunk 278 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 146 optimal weight: 20.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22640 Z= 0.133 Angle : 0.458 8.367 30760 Z= 0.238 Chirality : 0.044 0.148 3616 Planarity : 0.003 0.048 3920 Dihedral : 8.032 129.027 3284 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.89 % Allowed : 14.44 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 2884 helix: 1.70 (0.16), residues: 1076 sheet: 0.24 (0.23), residues: 504 loop : -0.93 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 15 HIS 0.003 0.000 HIS B 18 PHE 0.008 0.001 PHE A 43 TYR 0.009 0.001 TYR A 519 ARG 0.012 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8369 (tp30) cc_final: 0.8150 (tp30) REVERT: A 160 GLN cc_start: 0.8645 (tp-100) cc_final: 0.8352 (tm-30) REVERT: A 168 GLU cc_start: 0.8052 (tp30) cc_final: 0.7589 (tp30) REVERT: A 300 GLU cc_start: 0.7773 (mp0) cc_final: 0.7299 (mp0) REVERT: B 26 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8230 (mtm180) REVERT: B 30 GLU cc_start: 0.8620 (tp30) cc_final: 0.8336 (tp30) REVERT: B 33 TYR cc_start: 0.8114 (p90) cc_final: 0.7844 (p90) REVERT: B 102 ARG cc_start: 0.7894 (mtp-110) cc_final: 0.7642 (ttp-110) REVERT: B 150 ASP cc_start: 0.6876 (m-30) cc_final: 0.6539 (m-30) REVERT: B 160 GLN cc_start: 0.8676 (tp-100) cc_final: 0.8419 (tm-30) REVERT: B 168 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7677 (tp30) REVERT: B 300 GLU cc_start: 0.7246 (mp0) cc_final: 0.6924 (mp0) REVERT: C 33 TYR cc_start: 0.8191 (p90) cc_final: 0.7954 (p90) REVERT: C 160 GLN cc_start: 0.8688 (tt0) cc_final: 0.8461 (tm-30) REVERT: C 168 GLU cc_start: 0.8054 (tp30) cc_final: 0.7593 (tp30) REVERT: C 236 ARG cc_start: 0.6578 (ptm160) cc_final: 0.6221 (ptm160) REVERT: C 300 GLU cc_start: 0.7835 (mp0) cc_final: 0.7344 (mp0) REVERT: D 168 GLU cc_start: 0.8057 (tp30) cc_final: 0.7593 (tp30) REVERT: D 236 ARG cc_start: 0.6711 (ttp-170) cc_final: 0.6423 (ptm160) REVERT: D 300 GLU cc_start: 0.7276 (mp0) cc_final: 0.6944 (mp0) outliers start: 21 outliers final: 11 residues processed: 182 average time/residue: 1.4290 time to fit residues: 295.8896 Evaluate side-chains 169 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 251 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 277 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 208 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN C 208 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 22640 Z= 0.518 Angle : 0.592 8.496 30760 Z= 0.310 Chirality : 0.048 0.168 3616 Planarity : 0.004 0.044 3920 Dihedral : 8.284 133.054 3284 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.62 % Allowed : 14.82 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 2884 helix: 1.50 (0.16), residues: 1076 sheet: 0.19 (0.23), residues: 520 loop : -1.25 (0.15), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 15 HIS 0.003 0.001 HIS C 713 PHE 0.013 0.002 PHE B 192 TYR 0.013 0.001 TYR D 116 ARG 0.008 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 161 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8478 (tp30) cc_final: 0.8210 (tp30) REVERT: A 160 GLN cc_start: 0.8673 (tp-100) cc_final: 0.8342 (tm-30) REVERT: A 168 GLU cc_start: 0.8272 (tp30) cc_final: 0.7832 (tp30) REVERT: A 300 GLU cc_start: 0.7854 (mp0) cc_final: 0.7400 (mp0) REVERT: B 26 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8218 (mtm180) REVERT: B 30 GLU cc_start: 0.8745 (tp30) cc_final: 0.8417 (tp30) REVERT: B 33 TYR cc_start: 0.8172 (p90) cc_final: 0.7913 (p90) REVERT: B 102 ARG cc_start: 0.7958 (mtp-110) cc_final: 0.7745 (ttp-110) REVERT: B 150 ASP cc_start: 0.6897 (m-30) cc_final: 0.6554 (m-30) REVERT: B 151 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7627 (mm) REVERT: B 160 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8373 (tm-30) REVERT: B 168 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7866 (tp30) REVERT: B 300 GLU cc_start: 0.7257 (mp0) cc_final: 0.6933 (mp0) REVERT: C 33 TYR cc_start: 0.8273 (p90) cc_final: 0.8065 (p90) REVERT: C 160 GLN cc_start: 0.8711 (tt0) cc_final: 0.8464 (tm-30) REVERT: C 168 GLU cc_start: 0.8274 (tp30) cc_final: 0.7834 (tp30) REVERT: C 300 GLU cc_start: 0.7881 (mp0) cc_final: 0.7401 (mp0) REVERT: D 26 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8455 (mtm180) REVERT: D 160 GLN cc_start: 0.8664 (tt0) cc_final: 0.8464 (tm-30) REVERT: D 168 GLU cc_start: 0.8303 (tp30) cc_final: 0.7859 (tp30) REVERT: D 300 GLU cc_start: 0.7329 (mp0) cc_final: 0.6983 (mp0) outliers start: 38 outliers final: 23 residues processed: 192 average time/residue: 1.4531 time to fit residues: 316.4139 Evaluate side-chains 188 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 251 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 20.0000 chunk 110 optimal weight: 30.0000 chunk 165 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 355 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22640 Z= 0.319 Angle : 0.521 8.723 30760 Z= 0.274 Chirality : 0.046 0.168 3616 Planarity : 0.004 0.056 3920 Dihedral : 8.136 132.500 3284 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.45 % Allowed : 15.84 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2884 helix: 1.56 (0.16), residues: 1068 sheet: 0.23 (0.23), residues: 512 loop : -1.23 (0.15), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 15 HIS 0.006 0.001 HIS A 460 PHE 0.015 0.001 PHE A 457 TYR 0.011 0.001 TYR D 116 ARG 0.015 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8486 (tp30) cc_final: 0.8235 (tp30) REVERT: A 160 GLN cc_start: 0.8693 (tp-100) cc_final: 0.8352 (tm-30) REVERT: A 168 GLU cc_start: 0.8236 (tp30) cc_final: 0.7786 (tp30) REVERT: A 300 GLU cc_start: 0.7827 (mp0) cc_final: 0.7381 (mp0) REVERT: B 26 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8187 (mtm180) REVERT: B 30 GLU cc_start: 0.8733 (tp30) cc_final: 0.8434 (tp30) REVERT: B 33 TYR cc_start: 0.8147 (p90) cc_final: 0.7880 (p90) REVERT: B 102 ARG cc_start: 0.7940 (mtp-110) cc_final: 0.7724 (ttp-110) REVERT: B 160 GLN cc_start: 0.8693 (tp-100) cc_final: 0.8381 (tm-30) REVERT: B 168 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7794 (tp30) REVERT: B 300 GLU cc_start: 0.7208 (mp0) cc_final: 0.6973 (mp0) REVERT: C 160 GLN cc_start: 0.8712 (tt0) cc_final: 0.8471 (tm-30) REVERT: C 168 GLU cc_start: 0.8242 (tp30) cc_final: 0.7795 (tp30) REVERT: C 300 GLU cc_start: 0.7890 (mp0) cc_final: 0.7397 (mp0) REVERT: D 26 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8399 (mtm180) REVERT: D 160 GLN cc_start: 0.8682 (tt0) cc_final: 0.8450 (tm-30) REVERT: D 168 GLU cc_start: 0.8246 (tp30) cc_final: 0.7799 (tp30) REVERT: D 300 GLU cc_start: 0.7279 (mp0) cc_final: 0.6921 (mp0) outliers start: 34 outliers final: 25 residues processed: 182 average time/residue: 1.4400 time to fit residues: 297.7079 Evaluate side-chains 181 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 251 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 242 optimal weight: 50.0000 chunk 258 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 244 optimal weight: 20.0000 chunk 257 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22640 Z= 0.247 Angle : 0.494 8.640 30760 Z= 0.259 Chirality : 0.045 0.166 3616 Planarity : 0.003 0.043 3920 Dihedral : 7.926 132.084 3284 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.41 % Allowed : 16.10 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 2884 helix: 1.67 (0.16), residues: 1064 sheet: 0.24 (0.23), residues: 508 loop : -1.18 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 15 HIS 0.003 0.001 HIS B 18 PHE 0.012 0.001 PHE B 43 TYR 0.011 0.001 TYR A 519 ARG 0.009 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8485 (tp30) cc_final: 0.8236 (tp30) REVERT: A 160 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8354 (tm-30) REVERT: A 168 GLU cc_start: 0.8218 (tp30) cc_final: 0.7758 (tp30) REVERT: A 300 GLU cc_start: 0.7824 (mp0) cc_final: 0.7293 (mp0) REVERT: B 18 HIS cc_start: 0.8688 (p-80) cc_final: 0.8391 (p-80) REVERT: B 26 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8168 (mtm180) REVERT: B 30 GLU cc_start: 0.8732 (tp30) cc_final: 0.8456 (tp30) REVERT: B 33 TYR cc_start: 0.8173 (p90) cc_final: 0.7901 (p90) REVERT: B 102 ARG cc_start: 0.7918 (mtp-110) cc_final: 0.7713 (ttp-110) REVERT: B 160 GLN cc_start: 0.8693 (tp-100) cc_final: 0.8378 (tm-30) REVERT: B 168 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7776 (tp30) REVERT: B 300 GLU cc_start: 0.7195 (mp0) cc_final: 0.6954 (mp0) REVERT: C 160 GLN cc_start: 0.8709 (tt0) cc_final: 0.8470 (tm-30) REVERT: C 168 GLU cc_start: 0.8225 (tp30) cc_final: 0.7767 (tp30) REVERT: C 300 GLU cc_start: 0.7872 (mp0) cc_final: 0.7377 (mp0) REVERT: D 26 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8397 (mtm180) REVERT: D 160 GLN cc_start: 0.8697 (tt0) cc_final: 0.8463 (tm-30) REVERT: D 168 GLU cc_start: 0.8228 (tp30) cc_final: 0.7771 (tp30) REVERT: D 236 ARG cc_start: 0.6735 (ttp-170) cc_final: 0.6137 (ptm160) REVERT: D 300 GLU cc_start: 0.7267 (mp0) cc_final: 0.6983 (mp0) outliers start: 33 outliers final: 25 residues processed: 185 average time/residue: 1.3812 time to fit residues: 290.9247 Evaluate side-chains 184 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 251 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 chunk 190 optimal weight: 0.0170 chunk 286 optimal weight: 0.9990 chunk 264 optimal weight: 0.5980 chunk 228 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22640 Z= 0.123 Angle : 0.471 8.818 30760 Z= 0.243 Chirality : 0.043 0.156 3616 Planarity : 0.003 0.042 3920 Dihedral : 7.488 128.462 3284 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.94 % Allowed : 16.74 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2884 helix: 1.76 (0.16), residues: 1076 sheet: 0.42 (0.23), residues: 508 loop : -0.99 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 15 HIS 0.003 0.000 HIS B 18 PHE 0.010 0.001 PHE B 43 TYR 0.009 0.001 TYR D 660 ARG 0.017 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8388 (tp30) cc_final: 0.8161 (tp30) REVERT: A 160 GLN cc_start: 0.8677 (tp-100) cc_final: 0.8360 (tm-30) REVERT: A 168 GLU cc_start: 0.8106 (tp30) cc_final: 0.7617 (tp30) REVERT: A 300 GLU cc_start: 0.7752 (mp0) cc_final: 0.7232 (mp0) REVERT: B 18 HIS cc_start: 0.8630 (p-80) cc_final: 0.8359 (p-80) REVERT: B 26 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8175 (mtm180) REVERT: B 30 GLU cc_start: 0.8645 (tp30) cc_final: 0.8371 (tp30) REVERT: B 33 TYR cc_start: 0.8180 (p90) cc_final: 0.7871 (p90) REVERT: B 160 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8381 (tm-30) REVERT: B 168 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7686 (tp30) REVERT: B 300 GLU cc_start: 0.7145 (mp0) cc_final: 0.6893 (mp0) REVERT: C 160 GLN cc_start: 0.8704 (tt0) cc_final: 0.8460 (tm-30) REVERT: C 168 GLU cc_start: 0.8115 (tp30) cc_final: 0.7627 (tp30) REVERT: C 300 GLU cc_start: 0.7830 (mp0) cc_final: 0.7262 (mp0) REVERT: D 33 TYR cc_start: 0.7987 (p90) cc_final: 0.7548 (p90) REVERT: D 160 GLN cc_start: 0.8663 (tt0) cc_final: 0.8441 (tm-30) REVERT: D 168 GLU cc_start: 0.8122 (tp30) cc_final: 0.7633 (tp30) REVERT: D 236 ARG cc_start: 0.6733 (ttp-170) cc_final: 0.6335 (ptm160) REVERT: D 300 GLU cc_start: 0.7240 (mp0) cc_final: 0.6875 (mp0) outliers start: 22 outliers final: 16 residues processed: 185 average time/residue: 1.4006 time to fit residues: 295.1513 Evaluate side-chains 176 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 84 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 234 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN ** D 89 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 = 0.3984 r_free = 0.3984 target = 0.153287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.092407 restraints weight = 36301.235| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.50 r_work: 0.2895 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22640 Z= 0.306 Angle : 0.509 8.749 30760 Z= 0.266 Chirality : 0.045 0.168 3616 Planarity : 0.004 0.042 3920 Dihedral : 7.602 130.670 3284 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.06 % Allowed : 16.87 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 2884 helix: 1.71 (0.16), residues: 1080 sheet: 0.40 (0.23), residues: 508 loop : -1.12 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 15 HIS 0.003 0.001 HIS B 18 PHE 0.012 0.001 PHE B 43 TYR 0.018 0.001 TYR A 33 ARG 0.010 0.000 ARG C 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6025.66 seconds wall clock time: 108 minutes 47.22 seconds (6527.22 seconds total)