Starting phenix.real_space_refine on Thu Feb 15 17:24:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io7_35610/02_2024/8io7_35610_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io7_35610/02_2024/8io7_35610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io7_35610/02_2024/8io7_35610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io7_35610/02_2024/8io7_35610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io7_35610/02_2024/8io7_35610_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io7_35610/02_2024/8io7_35610_updated.pdb" } resolution = 2.62 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= 0.004 sd= 0.047 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 4 5.49 5 Mg 2 5.21 5 S 40 5.16 5 C 8166 2.51 5 N 2194 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 43": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A ARG 748": "NH1" <-> "NH2" Residue "A ARG 754": "NH1" <-> "NH2" Residue "A GLU 783": "OE1" <-> "OE2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B ARG 383": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B GLU 685": "OE1" <-> "OE2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "B ARG 748": "NH1" <-> "NH2" Residue "B ARG 754": "NH1" <-> "NH2" Residue "B GLU 783": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12876 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "B" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.35, per 1000 atoms: 0.57 Number of scatterers: 12876 At special positions: 0 Unit cell: (103.75, 103.75, 115.37, 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 40 16.00 P 4 15.00 Mg 2 11.99 O 2470 8.00 N 2194 7.00 C 8166 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: 5.57 Conformation dependent library (CDL) restraints added in 2.3 seconds 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 6 sheets defined 43.6% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 68 through 85 Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 182 through 186 removed outlier: 3.684A pdb=" N GLU A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 186' Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.503A pdb=" N THR A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER A 196 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LYS A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEU A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 227 No H-bonds generated for 'chain 'A' and resid 224 through 227' Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.614A pdb=" N MET A 240 " --> pdb=" O PHE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 283 removed outlier: 3.513A pdb=" N GLN A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 331 through 344 removed outlier: 4.182A pdb=" N TYR A 344 " --> pdb=" O TRP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 349 No H-bonds generated for 'chain 'A' and resid 346 through 349' Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 379 through 382 No H-bonds generated for 'chain 'A' and resid 379 through 382' Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.893A pdb=" N TYR A 402 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 425 removed outlier: 4.094A pdb=" N LEU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 503 through 525 removed outlier: 3.863A pdb=" N HIS A 506 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N SER A 510 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 512 " --> pdb=" O ASP A 509 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 520 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 521 " --> pdb=" O TRP A 518 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 523 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 524 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A 525 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 558 through 565 removed outlier: 3.924A pdb=" N ASN A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 593 Processing helix chain 'A' and resid 614 through 623 removed outlier: 3.710A pdb=" N LYS A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 removed outlier: 3.700A pdb=" N LEU A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 680 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 726 through 728 No H-bonds generated for 'chain 'A' and resid 726 through 728' Processing helix chain 'A' and resid 743 through 749 Processing helix chain 'A' and resid 754 through 766 removed outlier: 3.698A pdb=" N ILE A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 791 removed outlier: 3.625A pdb=" N ASP A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 799 No H-bonds generated for 'chain 'A' and resid 796 through 799' Processing helix chain 'B' and resid 19 through 41 Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 68 through 85 Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 160 through 168 Processing helix chain 'B' and resid 182 through 186 removed outlier: 3.685A pdb=" N GLU B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 186' Processing helix chain 'B' and resid 188 through 199 removed outlier: 3.504A pdb=" N THR B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASN B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYS B 198 " --> pdb=" O TRP B 194 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 227 No H-bonds generated for 'chain 'B' and resid 224 through 227' Processing helix chain 'B' and resid 230 through 240 removed outlier: 3.614A pdb=" N MET B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 283 removed outlier: 3.512A pdb=" N GLN B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 331 through 344 removed outlier: 4.183A pdb=" N TYR B 344 " --> pdb=" O TRP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 349 No H-bonds generated for 'chain 'B' and resid 346 through 349' Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 379 through 382 No H-bonds generated for 'chain 'B' and resid 379 through 382' Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.894A pdb=" N TYR B 402 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 425 removed outlier: 4.093A pdb=" N LEU B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 479 through 491 Processing helix chain 'B' and resid 503 through 525 removed outlier: 3.862A pdb=" N HIS B 506 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N SER B 510 " --> pdb=" O VAL B 507 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 512 " --> pdb=" O ASP B 509 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU B 520 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 521 " --> pdb=" O TRP B 518 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 523 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 524 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU B 525 " --> pdb=" O THR B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 558 through 565 removed outlier: 3.925A pdb=" N ASN B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 593 Processing helix chain 'B' and resid 614 through 623 removed outlier: 3.709A pdb=" N LYS B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 665 removed outlier: 3.699A pdb=" N LEU B 665 " --> pdb=" O LYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 680 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 726 through 728 No H-bonds generated for 'chain 'B' and resid 726 through 728' Processing helix chain 'B' and resid 743 through 749 Processing helix chain 'B' and resid 754 through 763 Processing helix chain 'B' and resid 771 through 791 removed outlier: 3.626A pdb=" N ASP B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 799 No H-bonds generated for 'chain 'B' and resid 796 through 799' Processing sheet with id= A, first strand: chain 'A' and resid 175 through 181 removed outlier: 6.587A pdb=" N ILE A 207 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA A 178 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU A 209 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL A 180 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 211 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N LEU A 212 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A 294 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A 214 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE A 296 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 473 through 475 removed outlier: 8.766A pdb=" N VAL A 474 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 432 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N HIS A 495 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N PHE A 433 " --> pdb=" O HIS A 495 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 497 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN A 536 " --> pdb=" O TRP A 498 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER A 500 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A 538 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 625 through 627 removed outlier: 6.651A pdb=" N VAL A 642 " --> pdb=" O LYS A 670 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL A 672 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU A 644 " --> pdb=" O VAL A 672 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL A 674 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 646 " --> pdb=" O VAL A 674 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 175 through 181 removed outlier: 6.587A pdb=" N ILE B 207 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ALA B 178 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 209 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL B 180 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 211 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N LEU B 212 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU B 294 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 214 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE B 296 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 473 through 475 removed outlier: 8.766A pdb=" N VAL B 474 " --> pdb=" O PHE B 430 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE B 432 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N HIS B 495 " --> pdb=" O ARG B 431 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N PHE B 433 " --> pdb=" O HIS B 495 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE B 497 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN B 536 " --> pdb=" O TRP B 498 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER B 500 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 538 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 625 through 627 removed outlier: 6.650A pdb=" N VAL B 642 " --> pdb=" O LYS B 670 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL B 672 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 644 " --> pdb=" O VAL B 672 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL B 674 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1152 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: 3.63 Time building geometry restraints manager: 5.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2222 1.29 - 1.42: 3573 1.42 - 1.55: 7355 1.55 - 1.68: 10 1.68 - 1.81: 70 Bond restraints: 13230 Sorted by residual: bond pdb=" C GLY B 155 " pdb=" O GLY B 155 " ideal model delta sigma weight residual 1.234 1.160 0.073 1.21e-02 6.83e+03 3.67e+01 bond pdb=" C GLY A 155 " pdb=" O GLY A 155 " ideal model delta sigma weight residual 1.235 1.158 0.077 1.35e-02 5.49e+03 3.26e+01 bond pdb=" O1A TPP A 900 " pdb=" PA TPP A 900 " ideal model delta sigma weight residual 1.479 1.519 -0.040 1.00e-02 1.00e+04 1.61e+01 bond pdb=" CA GLY B 155 " pdb=" C GLY B 155 " ideal model delta sigma weight residual 1.516 1.474 0.042 1.09e-02 8.42e+03 1.47e+01 bond pdb=" C GLY A 154 " pdb=" O GLY A 154 " ideal model delta sigma weight residual 1.238 1.184 0.054 1.42e-02 4.96e+03 1.46e+01 ... (remaining 13225 not shown) Histogram of bond angle deviations from ideal: 91.21 - 100.88: 29 100.88 - 110.56: 3965 110.56 - 120.23: 8397 120.23 - 129.90: 5461 129.90 - 139.58: 148 Bond angle restraints: 18000 Sorted by residual: angle pdb=" O2B TPP A 900 " pdb=" PB TPP A 900 " pdb=" O3A TPP A 900 " ideal model delta sigma weight residual 104.26 110.74 -6.48 1.33e+00 5.64e-01 2.37e+01 angle pdb=" N GLY B 155 " pdb=" CA GLY B 155 " pdb=" C GLY B 155 " ideal model delta sigma weight residual 112.50 107.53 4.97 1.16e+00 7.43e-01 1.83e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 109.40 116.30 -6.90 1.63e+00 3.76e-01 1.79e+01 angle pdb=" N LEU A 157 " pdb=" CA LEU A 157 " pdb=" C LEU A 157 " ideal model delta sigma weight residual 109.40 115.96 -6.56 1.63e+00 3.76e-01 1.62e+01 angle pdb=" O1B TPP A 900 " pdb=" PB TPP A 900 " pdb=" O3A TPP A 900 " ideal model delta sigma weight residual 111.16 104.20 6.96 1.82e+00 3.03e-01 1.47e+01 ... (remaining 17995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 7084 17.68 - 35.37: 517 35.37 - 53.05: 99 53.05 - 70.73: 20 70.73 - 88.42: 16 Dihedral angle restraints: 7736 sinusoidal: 3080 harmonic: 4656 Sorted by residual: dihedral pdb=" CA PHE B 143 " pdb=" C PHE B 143 " pdb=" N ALA B 144 " pdb=" CA ALA B 144 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA PHE A 143 " pdb=" C PHE A 143 " pdb=" N ALA A 144 " pdb=" CA ALA A 144 " ideal model delta harmonic sigma weight residual -180.00 -160.55 -19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLY B 301 " pdb=" C GLY B 301 " pdb=" N TRP B 302 " pdb=" CA TRP B 302 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 7733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1640 0.064 - 0.129: 236 0.129 - 0.193: 10 0.193 - 0.257: 0 0.257 - 0.322: 2 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CA LEU A 157 " pdb=" N LEU A 157 " pdb=" C LEU A 157 " pdb=" CB LEU A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA LEU B 157 " pdb=" N LEU B 157 " pdb=" C LEU B 157 " pdb=" CB LEU B 157 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CG LEU B 157 " pdb=" CB LEU B 157 " pdb=" CD1 LEU B 157 " pdb=" CD2 LEU B 157 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 1885 not shown) Planarity restraints: 2364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 156 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" CD GLU B 156 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 156 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 156 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 156 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" CD GLU A 156 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU A 156 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 156 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 558 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C VAL B 558 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL B 558 " 0.010 2.00e-02 2.50e+03 pdb=" N THR B 559 " 0.009 2.00e-02 2.50e+03 ... (remaining 2361 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 112 2.55 - 3.14: 10620 3.14 - 3.72: 21116 3.72 - 4.31: 31194 4.31 - 4.90: 51311 Nonbonded interactions: 114353 Sorted by model distance: nonbonded pdb=" O2B TPP A 900 " pdb="MG MG A 901 " model vdw 1.959 2.170 nonbonded pdb=" O1B TPP B 900 " pdb="MG MG B 901 " model vdw 1.961 2.170 nonbonded pdb=" OD1 ASN B 215 " pdb="MG MG B 901 " model vdw 2.014 2.170 nonbonded pdb=" OD1 ASN A 215 " pdb="MG MG A 901 " model vdw 2.015 2.170 nonbonded pdb=" O2A TPP B 900 " pdb="MG MG B 901 " model vdw 2.055 2.170 ... (remaining 114348 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 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: 0.010 Extract box with map and model: 12.180 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 36.880 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 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 : 0.005 0.077 13230 Z= 0.372 Angle : 0.657 8.217 18000 Z= 0.393 Chirality : 0.045 0.322 1888 Planarity : 0.004 0.037 2364 Dihedral : 13.561 88.417 4756 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.55 (0.20), residues: 1608 helix: 1.13 (0.20), residues: 648 sheet: -0.09 (0.38), residues: 198 loop : -0.06 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 302 HIS 0.010 0.001 HIS A 320 PHE 0.010 0.001 PHE A 296 TYR 0.009 0.001 TYR B 165 ARG 0.004 0.000 ARG B 717 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.663 Fit side-chains REVERT: A 261 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7463 (mtt-85) REVERT: A 751 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.8113 (mtp180) REVERT: B 243 GLU cc_start: 0.8106 (tp30) cc_final: 0.7755 (tp30) REVERT: B 509 ASP cc_start: 0.8503 (m-30) cc_final: 0.8248 (m-30) REVERT: B 688 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7562 (mt-10) outliers start: 0 outliers final: 1 residues processed: 126 average time/residue: 1.4974 time to fit residues: 205.0191 Evaluate side-chains 78 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 382 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13230 Z= 0.255 Angle : 0.505 6.112 18000 Z= 0.269 Chirality : 0.042 0.137 1888 Planarity : 0.004 0.040 2364 Dihedral : 4.820 39.915 1756 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.04 % Allowed : 6.15 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1608 helix: 1.23 (0.20), residues: 662 sheet: -0.31 (0.37), residues: 214 loop : 0.09 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 302 HIS 0.008 0.001 HIS B 320 PHE 0.017 0.001 PHE B 504 TYR 0.010 0.001 TYR A 744 ARG 0.008 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 1.631 Fit side-chains REVERT: A 265 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: A 560 SER cc_start: 0.9436 (OUTLIER) cc_final: 0.9174 (p) REVERT: A 751 ARG cc_start: 0.8440 (mtm-85) cc_final: 0.8149 (mtp180) REVERT: B 243 GLU cc_start: 0.8107 (tp30) cc_final: 0.7767 (tp30) REVERT: B 509 ASP cc_start: 0.8521 (m-30) cc_final: 0.8204 (m-30) REVERT: B 535 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7612 (ttp) outliers start: 14 outliers final: 5 residues processed: 95 average time/residue: 1.3566 time to fit residues: 141.2937 Evaluate side-chains 81 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 768 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 GLN ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 13230 Z= 0.459 Angle : 0.576 8.459 18000 Z= 0.302 Chirality : 0.046 0.138 1888 Planarity : 0.004 0.044 2364 Dihedral : 4.912 39.238 1754 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.93 % Allowed : 7.93 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.53 (0.21), residues: 1608 helix: 1.08 (0.20), residues: 662 sheet: -0.27 (0.38), residues: 208 loop : -0.00 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 302 HIS 0.009 0.001 HIS B 320 PHE 0.015 0.002 PHE A 504 TYR 0.012 0.002 TYR B 135 ARG 0.008 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 75 time to evaluate : 1.453 Fit side-chains REVERT: A 265 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: A 555 ASP cc_start: 0.8296 (t0) cc_final: 0.8077 (t0) REVERT: B 243 GLU cc_start: 0.8133 (tp30) cc_final: 0.7824 (tp30) REVERT: B 273 GLU cc_start: 0.7641 (tp30) cc_final: 0.7432 (tp30) REVERT: B 555 ASP cc_start: 0.7867 (t0) cc_final: 0.7464 (t0) REVERT: B 618 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7275 (mtt180) outliers start: 26 outliers final: 11 residues processed: 95 average time/residue: 1.2663 time to fit residues: 132.7822 Evaluate side-chains 87 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 618 ARG Chi-restraints excluded: chain B residue 768 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 714 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13230 Z= 0.167 Angle : 0.465 6.292 18000 Z= 0.246 Chirality : 0.041 0.128 1888 Planarity : 0.004 0.042 2364 Dihedral : 4.655 38.858 1754 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.19 % Allowed : 9.48 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.79 (0.21), residues: 1608 helix: 1.31 (0.20), residues: 660 sheet: -0.32 (0.38), residues: 216 loop : 0.21 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 302 HIS 0.006 0.001 HIS A 714 PHE 0.008 0.001 PHE B 504 TYR 0.010 0.001 TYR A 744 ARG 0.009 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: A 265 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: A 555 ASP cc_start: 0.8226 (t0) cc_final: 0.8013 (t0) REVERT: B 243 GLU cc_start: 0.8119 (tp30) cc_final: 0.7799 (tp30) REVERT: B 273 GLU cc_start: 0.7539 (tp30) cc_final: 0.7264 (tp30) REVERT: B 487 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7843 (mt-10) REVERT: B 555 ASP cc_start: 0.7848 (t0) cc_final: 0.7507 (t0) outliers start: 16 outliers final: 8 residues processed: 102 average time/residue: 1.2413 time to fit residues: 139.8441 Evaluate side-chains 87 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 768 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 506 HIS ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13230 Z= 0.324 Angle : 0.500 8.043 18000 Z= 0.264 Chirality : 0.043 0.131 1888 Planarity : 0.004 0.044 2364 Dihedral : 4.659 38.991 1754 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.63 % Allowed : 9.26 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.76 (0.21), residues: 1608 helix: 1.28 (0.20), residues: 660 sheet: -0.21 (0.38), residues: 210 loop : 0.14 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 302 HIS 0.005 0.001 HIS B 320 PHE 0.012 0.001 PHE B 504 TYR 0.020 0.001 TYR A 165 ARG 0.008 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 1.765 Fit side-chains revert: symmetry clash REVERT: A 265 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: B 243 GLU cc_start: 0.8133 (tp30) cc_final: 0.7809 (tp30) REVERT: B 273 GLU cc_start: 0.7603 (tp30) cc_final: 0.7255 (tp30) REVERT: B 555 ASP cc_start: 0.7826 (t0) cc_final: 0.7498 (t0) REVERT: B 618 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7109 (mtm180) outliers start: 22 outliers final: 13 residues processed: 105 average time/residue: 1.3405 time to fit residues: 154.5081 Evaluate side-chains 95 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 618 ARG Chi-restraints excluded: chain B residue 714 HIS Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 768 ASP Chi-restraints excluded: chain B residue 775 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.0370 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 154 optimal weight: 0.0980 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 HIS B 39 GLN ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 714 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.103 13230 Z= 0.166 Angle : 0.490 12.570 18000 Z= 0.257 Chirality : 0.041 0.257 1888 Planarity : 0.004 0.042 2364 Dihedral : 4.510 39.095 1754 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.63 % Allowed : 10.07 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.21), residues: 1608 helix: 1.39 (0.20), residues: 664 sheet: -0.13 (0.38), residues: 228 loop : 0.23 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 65 HIS 0.026 0.001 HIS B 714 PHE 0.009 0.001 PHE A 263 TYR 0.015 0.001 TYR B 165 ARG 0.011 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.574 Fit side-chains revert: symmetry clash REVERT: A 265 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: B 243 GLU cc_start: 0.8110 (tp30) cc_final: 0.7812 (tp30) REVERT: B 475 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8109 (mm-30) REVERT: B 555 ASP cc_start: 0.7765 (t0) cc_final: 0.7494 (t0) outliers start: 22 outliers final: 10 residues processed: 115 average time/residue: 1.2444 time to fit residues: 157.9855 Evaluate side-chains 94 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 768 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 HIS B 77 HIS B 384 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13230 Z= 0.248 Angle : 0.482 8.309 18000 Z= 0.249 Chirality : 0.041 0.128 1888 Planarity : 0.004 0.046 2364 Dihedral : 4.447 38.929 1754 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.63 % Allowed : 10.52 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.92 (0.21), residues: 1608 helix: 1.44 (0.20), residues: 660 sheet: -0.09 (0.38), residues: 228 loop : 0.20 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 454 HIS 0.004 0.001 HIS B 714 PHE 0.011 0.001 PHE B 73 TYR 0.014 0.001 TYR A 489 ARG 0.008 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: A 265 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: B 243 GLU cc_start: 0.8145 (tp30) cc_final: 0.7834 (tp30) REVERT: B 475 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8008 (mm-30) REVERT: B 555 ASP cc_start: 0.7785 (t0) cc_final: 0.7462 (t0) outliers start: 22 outliers final: 11 residues processed: 102 average time/residue: 1.3256 time to fit residues: 150.1163 Evaluate side-chains 95 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 768 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 8.9990 chunk 61 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 105 optimal weight: 0.2980 chunk 76 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 HIS B 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13230 Z= 0.180 Angle : 0.470 8.696 18000 Z= 0.244 Chirality : 0.040 0.125 1888 Planarity : 0.004 0.051 2364 Dihedral : 4.353 38.795 1754 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.33 % Allowed : 11.19 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.94 (0.21), residues: 1608 helix: 1.42 (0.20), residues: 664 sheet: -0.01 (0.38), residues: 228 loop : 0.21 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 194 HIS 0.004 0.001 HIS A 77 PHE 0.012 0.001 PHE B 73 TYR 0.012 0.001 TYR A 165 ARG 0.010 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 1.562 Fit side-chains revert: symmetry clash REVERT: A 265 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: B 243 GLU cc_start: 0.8121 (tp30) cc_final: 0.7821 (tp30) REVERT: B 475 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7977 (mm-30) REVERT: B 555 ASP cc_start: 0.7728 (t0) cc_final: 0.7380 (t0) outliers start: 18 outliers final: 9 residues processed: 106 average time/residue: 1.2096 time to fit residues: 141.8563 Evaluate side-chains 93 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 768 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 0.0060 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 HIS B 384 ASN B 714 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13230 Z= 0.260 Angle : 0.502 9.421 18000 Z= 0.260 Chirality : 0.041 0.128 1888 Planarity : 0.004 0.053 2364 Dihedral : 4.404 38.694 1754 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.56 % Allowed : 11.63 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.92 (0.21), residues: 1608 helix: 1.43 (0.20), residues: 662 sheet: 0.09 (0.39), residues: 222 loop : 0.14 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 302 HIS 0.005 0.001 HIS A 320 PHE 0.011 0.001 PHE B 73 TYR 0.013 0.001 TYR A 165 ARG 0.009 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 265 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7655 (mm-30) REVERT: B 243 GLU cc_start: 0.8105 (tp30) cc_final: 0.7829 (tp30) REVERT: B 555 ASP cc_start: 0.7713 (t0) cc_final: 0.7372 (t0) outliers start: 21 outliers final: 9 residues processed: 104 average time/residue: 1.1818 time to fit residues: 136.1753 Evaluate side-chains 92 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 768 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 0.0770 chunk 105 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 HIS B 384 ASN B 714 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13230 Z= 0.197 Angle : 0.491 9.479 18000 Z= 0.253 Chirality : 0.041 0.125 1888 Planarity : 0.004 0.051 2364 Dihedral : 4.340 38.735 1754 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.33 % Allowed : 12.07 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.97 (0.21), residues: 1608 helix: 1.46 (0.20), residues: 662 sheet: 0.10 (0.39), residues: 222 loop : 0.17 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 194 HIS 0.004 0.001 HIS A 77 PHE 0.011 0.001 PHE B 73 TYR 0.011 0.001 TYR A 165 ARG 0.010 0.000 ARG B 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 1.628 Fit side-chains revert: symmetry clash REVERT: A 265 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: B 243 GLU cc_start: 0.8132 (tp30) cc_final: 0.7830 (tp30) REVERT: B 555 ASP cc_start: 0.7653 (t0) cc_final: 0.7338 (t0) outliers start: 18 outliers final: 8 residues processed: 104 average time/residue: 1.1857 time to fit residues: 136.7162 Evaluate side-chains 98 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 768 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 53 optimal weight: 0.0070 chunk 130 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 HIS B 384 ASN B 714 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.086108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.072908 restraints weight = 25784.299| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.68 r_work: 0.2924 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13230 Z= 0.149 Angle : 0.473 9.558 18000 Z= 0.243 Chirality : 0.040 0.124 1888 Planarity : 0.004 0.046 2364 Dihedral : 4.204 38.783 1754 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.33 % Allowed : 11.93 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1608 helix: 1.52 (0.20), residues: 664 sheet: 0.05 (0.38), residues: 228 loop : 0.24 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 498 HIS 0.005 0.000 HIS A 77 PHE 0.011 0.001 PHE B 73 TYR 0.011 0.001 TYR B 501 ARG 0.010 0.000 ARG A 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3671.18 seconds wall clock time: 67 minutes 15.91 seconds (4035.91 seconds total)