Starting phenix.real_space_refine on Tue Mar 19 08:05:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whw_21678/03_2024/6whw_21678_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whw_21678/03_2024/6whw_21678.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whw_21678/03_2024/6whw_21678_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whw_21678/03_2024/6whw_21678_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whw_21678/03_2024/6whw_21678_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whw_21678/03_2024/6whw_21678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whw_21678/03_2024/6whw_21678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whw_21678/03_2024/6whw_21678_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whw_21678/03_2024/6whw_21678_updated.pdb" } resolution = 4.09 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= -0.019 sd= 0.707 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 2 5.49 5 S 142 5.16 5 Cl 4 4.86 5 C 15166 2.51 5 N 3862 2.21 5 O 4464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A ARG 822": "NH1" <-> "NH2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B GLU 804": "OE1" <-> "OE2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C GLU 683": "OE1" <-> "OE2" Residue "C ARG 822": "NH1" <-> "NH2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D GLU 804": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23640 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5920 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 32, 'TRANS': 762} Chain breaks: 4 Unresolved non-hydrogen bonds: 372 Unresolved non-hydrogen angles: 439 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 244 Chain: "B" Number of atoms: 5860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5860 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 251 Chain: "C" Number of atoms: 5920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5920 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 32, 'TRANS': 762} Chain breaks: 4 Unresolved non-hydrogen bonds: 372 Unresolved non-hydrogen angles: 439 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 244 Chain: "D" Number of atoms: 5860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5860 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 251 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.56, per 1000 atoms: 0.49 Number of scatterers: 23640 At special positions: 0 Unit cell: (135.63, 149.33, 184.95, 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) Cl 4 17.00 S 142 16.00 P 2 15.00 O 4464 8.00 N 3862 7.00 C 15166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.04 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.07 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.04 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=1.99 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.04 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.04 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 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 Links applied NAG-ASN " NAG B 902 " - " ASN B 542 " " NAG D 902 " - " ASN D 542 " Time building additional restraints: 8.94 Conformation dependent library (CDL) restraints added in 4.3 seconds 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5900 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 34 sheets defined 36.7% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.76 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 removed outlier: 3.598A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 75 through 82 removed outlier: 4.141A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 126 through 129 removed outlier: 3.793A pdb=" N SER A 129 " --> pdb=" O SER A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 129' Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.846A pdb=" N SER A 148 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 removed outlier: 4.205A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 184 Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 247 through 256 removed outlier: 4.920A pdb=" N VAL A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 302 through 316 removed outlier: 3.653A pdb=" N GLY A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 521 through 527 Processing helix chain 'A' and resid 542 through 545 No H-bonds generated for 'chain 'A' and resid 542 through 545' Processing helix chain 'A' and resid 575 through 578 Proline residue: A 578 - end of helix No H-bonds generated for 'chain 'A' and resid 575 through 578' Processing helix chain 'A' and resid 581 through 603 removed outlier: 4.196A pdb=" N LEU A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 601 " --> pdb=" O MET A 597 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 634 Processing helix chain 'A' and resid 649 through 678 removed outlier: 3.793A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 694 No H-bonds generated for 'chain 'A' and resid 691 through 694' Processing helix chain 'A' and resid 709 through 715 Processing helix chain 'A' and resid 721 through 729 removed outlier: 5.105A pdb=" N LYS A 729 " --> pdb=" O ARG A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 742 removed outlier: 3.993A pdb=" N GLN A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 763 removed outlier: 4.449A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 760 " --> pdb=" O VAL A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 801 removed outlier: 4.034A pdb=" N LEU A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS A 801 " --> pdb=" O ILE A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 813 Processing helix chain 'A' and resid 834 through 858 removed outlier: 3.776A pdb=" N PHE A 838 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 852 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 854 " --> pdb=" O LEU A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 78 through 92 removed outlier: 4.151A pdb=" N ASP B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER B 90 " --> pdb=" O CYS B 86 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.872A pdb=" N LEU B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 163 Processing helix chain 'B' and resid 179 through 192 removed outlier: 3.804A pdb=" N THR B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.815A pdb=" N SER B 214 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 246 Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 289 through 310 removed outlier: 3.989A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 339 removed outlier: 4.414A pdb=" N TYR B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 338 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B 339 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 Processing helix chain 'B' and resid 499 through 502 No H-bonds generated for 'chain 'B' and resid 499 through 502' Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 549 through 551 No H-bonds generated for 'chain 'B' and resid 549 through 551' Processing helix chain 'B' and resid 556 through 579 removed outlier: 4.754A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 614 Processing helix chain 'B' and resid 628 through 651 removed outlier: 4.360A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 644 " --> pdb=" O VAL B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 672 No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'B' and resid 690 through 697 removed outlier: 3.982A pdb=" N ASN B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 695 " --> pdb=" O THR B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 709 removed outlier: 3.939A pdb=" N MET B 706 " --> pdb=" O MET B 702 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE B 709 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 721 removed outlier: 3.789A pdb=" N SER B 720 " --> pdb=" O ASP B 716 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 721 " --> pdb=" O ALA B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 740 removed outlier: 3.642A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 785 Processing helix chain 'B' and resid 788 through 796 Processing helix chain 'B' and resid 815 through 841 removed outlier: 5.380A pdb=" N GLY B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 50 removed outlier: 3.598A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 75 through 82 removed outlier: 4.140A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLU C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 126 through 129 removed outlier: 3.793A pdb=" N SER C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 129' Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.845A pdb=" N SER C 148 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 removed outlier: 4.206A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 184 Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 247 through 256 removed outlier: 4.920A pdb=" N VAL C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA C 255 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.654A pdb=" N GLY C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 346 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 479 through 491 Processing helix chain 'C' and resid 521 through 527 Processing helix chain 'C' and resid 542 through 545 No H-bonds generated for 'chain 'C' and resid 542 through 545' Processing helix chain 'C' and resid 575 through 578 Proline residue: C 578 - end of helix No H-bonds generated for 'chain 'C' and resid 575 through 578' Processing helix chain 'C' and resid 581 through 603 removed outlier: 4.196A pdb=" N LEU C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 601 " --> pdb=" O MET C 597 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG C 603 " --> pdb=" O TYR C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 634 Processing helix chain 'C' and resid 649 through 678 removed outlier: 3.794A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 678 " --> pdb=" O ALA C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 694 No H-bonds generated for 'chain 'C' and resid 691 through 694' Processing helix chain 'C' and resid 709 through 715 Processing helix chain 'C' and resid 721 through 729 removed outlier: 5.105A pdb=" N LYS C 729 " --> pdb=" O ARG C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 742 removed outlier: 3.994A pdb=" N GLN C 740 " --> pdb=" O ALA C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 763 removed outlier: 4.450A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU C 760 " --> pdb=" O VAL C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 801 removed outlier: 4.034A pdb=" N LEU C 798 " --> pdb=" O SER C 794 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS C 801 " --> pdb=" O ILE C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 813 Processing helix chain 'C' and resid 834 through 858 removed outlier: 3.776A pdb=" N PHE C 838 " --> pdb=" O ALA C 835 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE C 852 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE C 854 " --> pdb=" O LEU C 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 78 through 92 removed outlier: 4.152A pdb=" N ASP D 87 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER D 90 " --> pdb=" O CYS D 86 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.872A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 179 through 192 removed outlier: 3.804A pdb=" N THR D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.816A pdb=" N SER D 214 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 246 Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 289 through 310 removed outlier: 3.988A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA D 304 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 339 removed outlier: 4.414A pdb=" N TYR D 330 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR D 338 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D 339 " --> pdb=" O ASN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 Processing helix chain 'D' and resid 499 through 502 No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 549 through 551 No H-bonds generated for 'chain 'D' and resid 549 through 551' Processing helix chain 'D' and resid 556 through 579 removed outlier: 4.754A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 614 Processing helix chain 'D' and resid 628 through 651 removed outlier: 4.359A pdb=" N SER D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 644 " --> pdb=" O VAL D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 672 No H-bonds generated for 'chain 'D' and resid 669 through 672' Processing helix chain 'D' and resid 690 through 697 removed outlier: 3.982A pdb=" N ASN D 694 " --> pdb=" O SER D 690 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 695 " --> pdb=" O THR D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 709 removed outlier: 3.939A pdb=" N MET D 706 " --> pdb=" O MET D 702 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LYS D 708 " --> pdb=" O ALA D 704 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE D 709 " --> pdb=" O TYR D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 721 removed outlier: 3.789A pdb=" N SER D 720 " --> pdb=" O ASP D 716 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 721 " --> pdb=" O ALA D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 740 removed outlier: 3.641A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 785 Processing helix chain 'D' and resid 788 through 796 Processing helix chain 'D' and resid 815 through 841 removed outlier: 5.380A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 30 through 32 Processing sheet with id= B, first strand: chain 'A' and resid 215 through 217 removed outlier: 6.388A pdb=" N LEU A 165 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 375 through 377 Processing sheet with id= D, first strand: chain 'A' and resid 386 through 389 Processing sheet with id= E, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.495A pdb=" N THR A 494 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE A 421 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU A 496 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR A 423 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N HIS A 498 " --> pdb=" O THR A 423 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 430 through 433 removed outlier: 3.517A pdb=" N TYR A 477 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 455 " --> pdb=" O CYS A 476 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 548 through 550 Processing sheet with id= H, first strand: chain 'A' and resid 555 through 557 removed outlier: 4.347A pdb=" N LYS A 555 " --> pdb=" O PHE A 779 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN A 557 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 559 through 561 removed outlier: 3.526A pdb=" N TRP A 752 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 562 through 564 Processing sheet with id= K, first strand: chain 'B' and resid 40 through 42 removed outlier: 3.639A pdb=" N LEU B 124 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 99 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 202 through 204 removed outlier: 9.315A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE B 227 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL B 172 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 229 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR B 255 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU B 230 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 257 " --> pdb=" O LEU B 230 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 278 through 281 removed outlier: 3.525A pdb=" N LEU B 362 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 408 through 410 removed outlier: 3.587A pdb=" N THR B 410 " --> pdb=" O TYR B 479 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 417 through 420 Processing sheet with id= P, first strand: chain 'B' and resid 534 through 537 Processing sheet with id= Q, first strand: chain 'B' and resid 655 through 657 removed outlier: 3.928A pdb=" N GLN B 656 " --> pdb=" O VAL B 808 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 30 through 32 Processing sheet with id= S, first strand: chain 'C' and resid 215 through 217 removed outlier: 6.388A pdb=" N LEU C 165 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 243 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 375 through 377 Processing sheet with id= U, first strand: chain 'C' and resid 386 through 389 Processing sheet with id= V, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.495A pdb=" N THR C 494 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE C 421 " --> pdb=" O THR C 494 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU C 496 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR C 423 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N HIS C 498 " --> pdb=" O THR C 423 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'C' and resid 430 through 433 removed outlier: 3.517A pdb=" N TYR C 477 " --> pdb=" O TYR C 431 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 455 " --> pdb=" O CYS C 476 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 548 through 550 Processing sheet with id= Y, first strand: chain 'C' and resid 555 through 557 removed outlier: 4.347A pdb=" N LYS C 555 " --> pdb=" O PHE C 779 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN C 557 " --> pdb=" O SER C 777 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 559 through 561 removed outlier: 3.526A pdb=" N TRP C 752 " --> pdb=" O THR C 560 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 562 through 564 Processing sheet with id= AB, first strand: chain 'D' and resid 40 through 42 removed outlier: 3.639A pdb=" N LEU D 124 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE D 99 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 202 through 204 removed outlier: 9.316A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE D 227 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL D 172 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU D 229 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR D 255 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU D 230 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE D 257 " --> pdb=" O LEU D 230 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'D' and resid 278 through 281 removed outlier: 3.525A pdb=" N LEU D 362 " --> pdb=" O TRP D 379 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 408 through 410 removed outlier: 3.587A pdb=" N THR D 410 " --> pdb=" O TYR D 479 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 417 through 420 Processing sheet with id= AG, first strand: chain 'D' and resid 534 through 537 Processing sheet with id= AH, first strand: chain 'D' and resid 655 through 657 removed outlier: 3.928A pdb=" N GLN D 656 " --> pdb=" O VAL D 808 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 1854 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: 7.27 Time building geometry restraints manager: 9.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7616 1.34 - 1.47: 5948 1.47 - 1.59: 10332 1.59 - 1.71: 6 1.71 - 1.84: 242 Bond restraints: 24144 Sorted by residual: bond pdb=" C1 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.862 1.630 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C1 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.862 1.631 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C4 QGP B 901 " pdb=" O6 QGP B 901 " ideal model delta sigma weight residual 1.401 1.227 0.174 2.00e-02 2.50e+03 7.61e+01 bond pdb=" C4 QGP D 901 " pdb=" O6 QGP D 901 " ideal model delta sigma weight residual 1.401 1.227 0.174 2.00e-02 2.50e+03 7.54e+01 bond pdb=" C16 QGP B 901 " pdb=" C9 QGP B 901 " ideal model delta sigma weight residual 1.527 1.376 0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 24139 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.30: 461 105.30 - 112.73: 13221 112.73 - 120.15: 9134 120.15 - 127.57: 9855 127.57 - 134.99: 241 Bond angle restraints: 32912 Sorted by residual: angle pdb=" C THR B 76 " pdb=" N ASP B 77 " pdb=" CA ASP B 77 " ideal model delta sigma weight residual 123.56 134.99 -11.43 1.98e+00 2.55e-01 3.33e+01 angle pdb=" C THR D 76 " pdb=" N ASP D 77 " pdb=" CA ASP D 77 " ideal model delta sigma weight residual 123.56 134.99 -11.43 1.98e+00 2.55e-01 3.33e+01 angle pdb=" N GLY B 253 " pdb=" CA GLY B 253 " pdb=" C GLY B 253 " ideal model delta sigma weight residual 114.85 108.26 6.59 1.35e+00 5.49e-01 2.38e+01 angle pdb=" N GLY D 253 " pdb=" CA GLY D 253 " pdb=" C GLY D 253 " ideal model delta sigma weight residual 114.85 108.32 6.53 1.35e+00 5.49e-01 2.34e+01 angle pdb=" N VAL C 385 " pdb=" CA VAL C 385 " pdb=" C VAL C 385 " ideal model delta sigma weight residual 113.20 108.62 4.58 9.60e-01 1.09e+00 2.27e+01 ... (remaining 32907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 12760 17.45 - 34.90: 1260 34.90 - 52.36: 188 52.36 - 69.81: 30 69.81 - 87.26: 34 Dihedral angle restraints: 14272 sinusoidal: 5126 harmonic: 9146 Sorted by residual: dihedral pdb=" CB CYS D 86 " pdb=" SG CYS D 86 " pdb=" SG CYS D 321 " pdb=" CB CYS D 321 " ideal model delta sinusoidal sigma weight residual 93.00 10.42 82.58 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 321 " pdb=" CB CYS B 321 " ideal model delta sinusoidal sigma weight residual 93.00 10.43 82.57 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS C 765 " pdb=" SG CYS C 765 " pdb=" SG CYS C 819 " pdb=" CB CYS C 819 " ideal model delta sinusoidal sigma weight residual -86.00 -5.87 -80.13 1 1.00e+01 1.00e-02 7.95e+01 ... (remaining 14269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2314 0.039 - 0.078: 1109 0.078 - 0.116: 364 0.116 - 0.155: 63 0.155 - 0.194: 8 Chirality restraints: 3858 Sorted by residual: chirality pdb=" CB VAL B 258 " pdb=" CA VAL B 258 " pdb=" CG1 VAL B 258 " pdb=" CG2 VAL B 258 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CB VAL D 258 " pdb=" CA VAL D 258 " pdb=" CG1 VAL D 258 " pdb=" CG2 VAL D 258 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CA ASN B 622 " pdb=" N ASN B 622 " pdb=" C ASN B 622 " pdb=" CB ASN B 622 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 3855 not shown) Planarity restraints: 4184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 825 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.43e+00 pdb=" N PRO A 826 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 826 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 826 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 825 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.36e+00 pdb=" N PRO C 826 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 826 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 826 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 622 " 0.044 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO D 623 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 623 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 623 " 0.037 5.00e-02 4.00e+02 ... (remaining 4181 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 611 2.65 - 3.21: 24682 3.21 - 3.77: 34137 3.77 - 4.34: 45122 4.34 - 4.90: 72616 Nonbonded interactions: 177168 Sorted by model distance: nonbonded pdb=" O ASP D 113 " pdb=" OG SER D 116 " model vdw 2.086 2.440 nonbonded pdb=" O ASP B 113 " pdb=" OG SER B 116 " model vdw 2.086 2.440 nonbonded pdb=" O ASP B 306 " pdb=" OG SER B 309 " model vdw 2.110 2.440 nonbonded pdb=" O ASP D 306 " pdb=" OG SER D 309 " model vdw 2.111 2.440 nonbonded pdb=" O ASN B 694 " pdb=" ND2 ASN B 698 " model vdw 2.174 2.520 ... (remaining 177163 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 'C' } ncs_group { reference = chain 'B' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 4.930 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 60.070 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.009 0.232 24144 Z= 0.597 Angle : 0.863 11.431 32912 Z= 0.489 Chirality : 0.049 0.194 3858 Planarity : 0.005 0.068 4182 Dihedral : 14.468 87.258 8324 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.80 % Favored : 85.01 % Rotamer: Outliers : 0.74 % Allowed : 11.45 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -5.22 (0.12), residues: 3128 helix: -3.06 (0.11), residues: 1180 sheet: -3.94 (0.19), residues: 412 loop : -3.67 (0.13), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 632 HIS 0.006 0.001 HIS D 840 PHE 0.037 0.003 PHE C 113 TYR 0.029 0.002 TYR B 731 ARG 0.004 0.001 ARG C 822 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 324 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8099 (tpp) cc_final: 0.7765 (tpp) REVERT: A 125 MET cc_start: 0.8363 (mmt) cc_final: 0.8128 (mmm) REVERT: A 662 MET cc_start: 0.9146 (tmm) cc_final: 0.8901 (tmm) REVERT: A 806 MET cc_start: 0.8063 (mmt) cc_final: 0.7590 (mmt) REVERT: B 73 MET cc_start: 0.7487 (ttm) cc_final: 0.7126 (ttm) REVERT: B 201 GLU cc_start: 0.8061 (mp0) cc_final: 0.7772 (mp0) REVERT: B 307 MET cc_start: 0.6515 (ttp) cc_final: 0.6155 (ttp) REVERT: B 537 MET cc_start: 0.8214 (mmm) cc_final: 0.7865 (ttt) REVERT: B 654 MET cc_start: 0.8929 (mmt) cc_final: 0.8495 (mmm) REVERT: B 677 PHE cc_start: 0.8078 (t80) cc_final: 0.7552 (t80) REVERT: B 681 PHE cc_start: 0.6327 (m-10) cc_final: 0.5990 (m-80) REVERT: B 706 MET cc_start: 0.8954 (mtp) cc_final: 0.8559 (ttm) REVERT: B 824 MET cc_start: 0.5686 (mmt) cc_final: 0.5343 (mmm) REVERT: B 829 MET cc_start: 0.8285 (mtt) cc_final: 0.8051 (mtp) REVERT: C 125 MET cc_start: 0.8291 (mmt) cc_final: 0.7994 (mmm) REVERT: C 330 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7386 (m) REVERT: C 662 MET cc_start: 0.9250 (tmm) cc_final: 0.8832 (tmm) REVERT: C 680 ARG cc_start: 0.8138 (mtm110) cc_final: 0.7919 (mmt180) REVERT: D 73 MET cc_start: 0.7419 (ttm) cc_final: 0.7142 (ttm) REVERT: D 134 MET cc_start: 0.8438 (mtp) cc_final: 0.8176 (mtp) REVERT: D 508 MET cc_start: 0.8729 (mtt) cc_final: 0.8478 (mtp) REVERT: D 537 MET cc_start: 0.7918 (mmm) cc_final: 0.7637 (ttt) REVERT: D 631 MET cc_start: 0.8684 (tpp) cc_final: 0.8463 (tpp) REVERT: D 654 MET cc_start: 0.8894 (mmt) cc_final: 0.8520 (mmm) REVERT: D 677 PHE cc_start: 0.8168 (t80) cc_final: 0.7602 (t80) REVERT: D 681 PHE cc_start: 0.6429 (m-10) cc_final: 0.6100 (m-80) REVERT: D 706 MET cc_start: 0.8963 (mtp) cc_final: 0.8565 (ttm) REVERT: D 786 ASP cc_start: 0.8714 (m-30) cc_final: 0.8219 (m-30) REVERT: D 824 MET cc_start: 0.5543 (mmt) cc_final: 0.5343 (mmt) outliers start: 18 outliers final: 8 residues processed: 342 average time/residue: 0.3297 time to fit residues: 181.6961 Evaluate side-chains 268 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 259 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 40.0000 chunk 237 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 127 optimal weight: 0.0970 chunk 246 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 285 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 134 HIS A 171 HIS A 520 ASN A 592 HIS ** A 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN B 341 ASN B 357 GLN B 359 HIS B 437 GLN B 491 ASN B 703 HIS B 782 GLN B 817 ASN C 28 ASN C 134 HIS C 171 HIS C 520 ASN C 592 HIS C 763 GLN ** C 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 357 GLN D 359 HIS D 437 GLN D 703 HIS D 782 GLN D 817 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24144 Z= 0.287 Angle : 0.653 7.759 32912 Z= 0.350 Chirality : 0.046 0.228 3858 Planarity : 0.005 0.065 4182 Dihedral : 6.385 43.759 3374 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.37 % Favored : 90.51 % Rotamer: Outliers : 0.17 % Allowed : 6.07 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.65 (0.13), residues: 3128 helix: -1.44 (0.14), residues: 1188 sheet: -3.57 (0.21), residues: 386 loop : -2.93 (0.14), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 844 HIS 0.004 0.001 HIS B 703 PHE 0.023 0.002 PHE C 113 TYR 0.016 0.001 TYR C 253 ARG 0.002 0.000 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 323 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8232 (tpp) cc_final: 0.7988 (tpp) REVERT: A 125 MET cc_start: 0.8371 (mmt) cc_final: 0.8145 (mmm) REVERT: A 130 ASP cc_start: 0.8026 (m-30) cc_final: 0.7705 (m-30) REVERT: A 235 LEU cc_start: 0.8826 (mp) cc_final: 0.8619 (mp) REVERT: A 375 MET cc_start: 0.7427 (tpp) cc_final: 0.7101 (tpp) REVERT: A 662 MET cc_start: 0.9239 (tmm) cc_final: 0.8869 (tmm) REVERT: A 723 MET cc_start: 0.9060 (mtp) cc_final: 0.8649 (mtm) REVERT: A 774 PHE cc_start: 0.7853 (t80) cc_final: 0.7598 (t80) REVERT: B 73 MET cc_start: 0.7528 (ttm) cc_final: 0.7175 (ttm) REVERT: B 89 MET cc_start: 0.8206 (mtm) cc_final: 0.7853 (mtm) REVERT: B 94 ILE cc_start: 0.7052 (mm) cc_final: 0.6725 (mm) REVERT: B 132 MET cc_start: 0.6910 (mmp) cc_final: 0.6703 (mmm) REVERT: B 201 GLU cc_start: 0.8021 (mp0) cc_final: 0.7774 (mp0) REVERT: B 358 MET cc_start: 0.9012 (mmm) cc_final: 0.8791 (mmm) REVERT: B 641 ILE cc_start: 0.9511 (tt) cc_final: 0.9254 (tp) REVERT: B 654 MET cc_start: 0.8750 (mmt) cc_final: 0.8430 (mmm) REVERT: B 677 PHE cc_start: 0.8089 (t80) cc_final: 0.7492 (t80) REVERT: B 706 MET cc_start: 0.8935 (mtp) cc_final: 0.8644 (ttm) REVERT: B 824 MET cc_start: 0.5788 (mmt) cc_final: 0.5558 (mmt) REVERT: C 662 MET cc_start: 0.9279 (tmm) cc_final: 0.8842 (tmm) REVERT: C 723 MET cc_start: 0.8936 (mtp) cc_final: 0.8337 (mtm) REVERT: D 73 MET cc_start: 0.7625 (ttm) cc_final: 0.7251 (ttm) REVERT: D 508 MET cc_start: 0.8553 (mtt) cc_final: 0.8320 (mtt) REVERT: D 641 ILE cc_start: 0.9488 (tt) cc_final: 0.9247 (tp) REVERT: D 654 MET cc_start: 0.8794 (mmt) cc_final: 0.8466 (mmm) REVERT: D 677 PHE cc_start: 0.8196 (t80) cc_final: 0.7583 (t80) REVERT: D 706 MET cc_start: 0.8949 (mtp) cc_final: 0.8612 (ttm) REVERT: D 824 MET cc_start: 0.5453 (mmt) cc_final: 0.5122 (mmm) outliers start: 4 outliers final: 1 residues processed: 327 average time/residue: 0.3069 time to fit residues: 165.4229 Evaluate side-chains 261 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 285 optimal weight: 10.0000 chunk 308 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 283 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN A 801 HIS C 461 ASN C 801 HIS D 782 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24144 Z= 0.240 Angle : 0.594 8.383 32912 Z= 0.319 Chirality : 0.044 0.262 3858 Planarity : 0.005 0.058 4182 Dihedral : 5.888 44.468 3374 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.49 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.14), residues: 3128 helix: -0.70 (0.15), residues: 1182 sheet: -3.44 (0.21), residues: 442 loop : -2.50 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 607 HIS 0.003 0.001 HIS D 311 PHE 0.019 0.002 PHE C 775 TYR 0.012 0.001 TYR C 253 ARG 0.003 0.000 ARG C 776 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8327 (mmt) cc_final: 0.7998 (mmm) REVERT: A 130 ASP cc_start: 0.7970 (m-30) cc_final: 0.7626 (m-30) REVERT: A 235 LEU cc_start: 0.8825 (mp) cc_final: 0.8535 (mp) REVERT: A 375 MET cc_start: 0.7501 (tpp) cc_final: 0.7182 (tpp) REVERT: A 421 ILE cc_start: 0.8951 (mm) cc_final: 0.8699 (mm) REVERT: A 523 MET cc_start: 0.8045 (ttt) cc_final: 0.7843 (ttt) REVERT: A 662 MET cc_start: 0.9302 (tmm) cc_final: 0.8869 (tmm) REVERT: A 723 MET cc_start: 0.9016 (mtp) cc_final: 0.8609 (mtm) REVERT: B 73 MET cc_start: 0.7476 (ttm) cc_final: 0.7128 (ttm) REVERT: B 94 ILE cc_start: 0.7106 (mm) cc_final: 0.6790 (mm) REVERT: B 201 GLU cc_start: 0.7965 (mp0) cc_final: 0.7700 (mp0) REVERT: B 307 MET cc_start: 0.6172 (ttp) cc_final: 0.5361 (tmm) REVERT: B 641 ILE cc_start: 0.9478 (tt) cc_final: 0.9210 (tp) REVERT: B 706 MET cc_start: 0.8826 (mtp) cc_final: 0.8624 (ttm) REVERT: B 777 ASP cc_start: 0.8237 (m-30) cc_final: 0.7778 (m-30) REVERT: B 782 GLN cc_start: 0.8729 (tt0) cc_final: 0.8516 (tt0) REVERT: B 824 MET cc_start: 0.5708 (mmt) cc_final: 0.5461 (mmt) REVERT: C 235 LEU cc_start: 0.8893 (mp) cc_final: 0.8676 (mp) REVERT: C 662 MET cc_start: 0.9326 (tmm) cc_final: 0.8899 (tmm) REVERT: C 723 MET cc_start: 0.8881 (mtp) cc_final: 0.8373 (mtm) REVERT: C 774 PHE cc_start: 0.7586 (t80) cc_final: 0.7345 (t80) REVERT: D 73 MET cc_start: 0.7568 (ttm) cc_final: 0.7283 (ttm) REVERT: D 307 MET cc_start: 0.6062 (ttp) cc_final: 0.5607 (tpp) REVERT: D 641 ILE cc_start: 0.9481 (tt) cc_final: 0.9190 (tp) REVERT: D 706 MET cc_start: 0.8864 (mtp) cc_final: 0.8608 (ttm) REVERT: D 807 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7831 (mt-10) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.3033 time to fit residues: 170.8088 Evaluate side-chains 268 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 286 optimal weight: 7.9990 chunk 303 optimal weight: 0.9990 chunk 149 optimal weight: 0.3980 chunk 271 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 HIS ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 HIS C 801 HIS ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24144 Z= 0.288 Angle : 0.626 8.249 32912 Z= 0.333 Chirality : 0.045 0.258 3858 Planarity : 0.005 0.059 4182 Dihedral : 5.892 46.145 3374 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.65 % Favored : 90.22 % Rotamer: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.15), residues: 3128 helix: -0.55 (0.15), residues: 1188 sheet: -3.22 (0.21), residues: 436 loop : -2.31 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 632 HIS 0.007 0.001 HIS C 801 PHE 0.020 0.002 PHE C 775 TYR 0.013 0.001 TYR A 556 ARG 0.003 0.000 ARG C 776 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 322 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8845 (mp) cc_final: 0.8514 (mp) REVERT: A 662 MET cc_start: 0.9291 (tmm) cc_final: 0.8856 (tmm) REVERT: A 723 MET cc_start: 0.8911 (mtp) cc_final: 0.8397 (mtm) REVERT: B 73 MET cc_start: 0.7607 (ttm) cc_final: 0.7333 (ttm) REVERT: B 94 ILE cc_start: 0.7070 (mm) cc_final: 0.6760 (mm) REVERT: B 201 GLU cc_start: 0.8071 (mp0) cc_final: 0.7826 (mp0) REVERT: B 641 ILE cc_start: 0.9502 (tt) cc_final: 0.9190 (tp) REVERT: B 658 GLU cc_start: 0.7825 (mt-10) cc_final: 0.6637 (mt-10) REVERT: B 677 PHE cc_start: 0.8157 (t80) cc_final: 0.7623 (t80) REVERT: B 706 MET cc_start: 0.8835 (mtp) cc_final: 0.8593 (ttm) REVERT: B 732 ASP cc_start: 0.7530 (t0) cc_final: 0.7311 (t0) REVERT: B 782 GLN cc_start: 0.8769 (tt0) cc_final: 0.8552 (tt0) REVERT: B 824 MET cc_start: 0.5706 (mmt) cc_final: 0.5477 (mmt) REVERT: C 74 MET cc_start: 0.8308 (tpp) cc_final: 0.8052 (tpp) REVERT: C 235 LEU cc_start: 0.8746 (mp) cc_final: 0.8432 (mp) REVERT: C 491 MET cc_start: 0.7587 (mtt) cc_final: 0.7313 (mtt) REVERT: C 662 MET cc_start: 0.9312 (tmm) cc_final: 0.8852 (tmm) REVERT: C 686 THR cc_start: 0.8770 (p) cc_final: 0.8565 (t) REVERT: C 723 MET cc_start: 0.8879 (mtp) cc_final: 0.8377 (mtm) REVERT: C 834 MET cc_start: 0.9114 (mtp) cc_final: 0.8781 (mtp) REVERT: D 73 MET cc_start: 0.7495 (ttm) cc_final: 0.7204 (ttm) REVERT: D 132 MET cc_start: 0.7892 (mmm) cc_final: 0.7597 (tmm) REVERT: D 134 MET cc_start: 0.7743 (mtm) cc_final: 0.7469 (mtm) REVERT: D 641 ILE cc_start: 0.9516 (tt) cc_final: 0.9220 (tp) REVERT: D 824 MET cc_start: 0.5489 (mmt) cc_final: 0.5223 (mmm) outliers start: 2 outliers final: 0 residues processed: 324 average time/residue: 0.2954 time to fit residues: 161.6726 Evaluate side-chains 256 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 3.9990 chunk 172 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 225 optimal weight: 0.4980 chunk 125 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 154 optimal weight: 0.0570 chunk 272 optimal weight: 7.9990 chunk 76 optimal weight: 0.4980 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 782 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24144 Z= 0.179 Angle : 0.552 8.692 32912 Z= 0.296 Chirality : 0.043 0.279 3858 Planarity : 0.004 0.059 4182 Dihedral : 5.389 44.789 3374 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.67 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.15), residues: 3128 helix: -0.14 (0.16), residues: 1172 sheet: -2.83 (0.21), residues: 478 loop : -2.10 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 607 HIS 0.002 0.001 HIS B 127 PHE 0.019 0.001 PHE B 842 TYR 0.011 0.001 TYR D 282 ARG 0.002 0.000 ARG C 544 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8784 (mp) cc_final: 0.8438 (mp) REVERT: A 530 GLN cc_start: 0.8219 (tp-100) cc_final: 0.7939 (tp-100) REVERT: A 662 MET cc_start: 0.9361 (tmm) cc_final: 0.8935 (tmm) REVERT: A 834 MET cc_start: 0.9162 (mtp) cc_final: 0.8788 (mtp) REVERT: B 73 MET cc_start: 0.7528 (ttm) cc_final: 0.7252 (ttm) REVERT: B 94 ILE cc_start: 0.6977 (mm) cc_final: 0.6726 (mm) REVERT: B 201 GLU cc_start: 0.7939 (mp0) cc_final: 0.7709 (mp0) REVERT: B 307 MET cc_start: 0.6043 (ttp) cc_final: 0.5534 (tpp) REVERT: B 641 ILE cc_start: 0.9494 (tt) cc_final: 0.9242 (tp) REVERT: B 777 ASP cc_start: 0.8428 (m-30) cc_final: 0.8126 (m-30) REVERT: B 786 ASP cc_start: 0.8370 (m-30) cc_final: 0.8061 (m-30) REVERT: B 824 MET cc_start: 0.5752 (mmt) cc_final: 0.5475 (mmt) REVERT: C 235 LEU cc_start: 0.8628 (mp) cc_final: 0.8264 (mp) REVERT: C 585 LEU cc_start: 0.8736 (mm) cc_final: 0.8500 (mm) REVERT: C 662 MET cc_start: 0.9396 (tmm) cc_final: 0.8980 (tmm) REVERT: C 716 ARG cc_start: 0.7996 (ptm160) cc_final: 0.7739 (ttt180) REVERT: C 723 MET cc_start: 0.8838 (mtp) cc_final: 0.8543 (mtm) REVERT: C 834 MET cc_start: 0.9047 (mtp) cc_final: 0.8671 (mtp) REVERT: D 73 MET cc_start: 0.7555 (ttm) cc_final: 0.7242 (ttm) REVERT: D 307 MET cc_start: 0.6017 (ttp) cc_final: 0.5304 (tpp) REVERT: D 641 ILE cc_start: 0.9489 (tt) cc_final: 0.9222 (tp) REVERT: D 777 ASP cc_start: 0.8387 (m-30) cc_final: 0.8051 (m-30) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.2969 time to fit residues: 175.7752 Evaluate side-chains 274 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 0.7980 chunk 273 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 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 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 HIS D 127 HIS D 782 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24144 Z= 0.223 Angle : 0.577 9.768 32912 Z= 0.306 Chirality : 0.044 0.346 3858 Planarity : 0.004 0.057 4182 Dihedral : 5.399 45.744 3374 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.28 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.15), residues: 3128 helix: -0.12 (0.15), residues: 1180 sheet: -2.79 (0.23), residues: 450 loop : -1.99 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 632 HIS 0.008 0.001 HIS B 840 PHE 0.024 0.002 PHE C 113 TYR 0.009 0.001 TYR D 282 ARG 0.005 0.000 ARG C 776 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8714 (mp) cc_final: 0.8359 (mp) REVERT: A 491 MET cc_start: 0.6317 (mtt) cc_final: 0.6069 (mtt) REVERT: A 530 GLN cc_start: 0.8259 (tp-100) cc_final: 0.7973 (tp-100) REVERT: A 662 MET cc_start: 0.9319 (tmm) cc_final: 0.8869 (tmm) REVERT: A 834 MET cc_start: 0.9183 (mtp) cc_final: 0.8812 (mtp) REVERT: B 73 MET cc_start: 0.7460 (ttm) cc_final: 0.7198 (ttm) REVERT: B 201 GLU cc_start: 0.8043 (mp0) cc_final: 0.7833 (mp0) REVERT: B 307 MET cc_start: 0.6259 (ttp) cc_final: 0.5664 (tpp) REVERT: B 641 ILE cc_start: 0.9465 (tt) cc_final: 0.9209 (tp) REVERT: B 777 ASP cc_start: 0.8371 (m-30) cc_final: 0.8095 (m-30) REVERT: B 824 MET cc_start: 0.5761 (mmt) cc_final: 0.5521 (mmt) REVERT: C 235 LEU cc_start: 0.8592 (mp) cc_final: 0.8223 (mp) REVERT: C 585 LEU cc_start: 0.8724 (mm) cc_final: 0.8492 (mm) REVERT: C 662 MET cc_start: 0.9323 (tmm) cc_final: 0.8874 (tmm) REVERT: C 716 ARG cc_start: 0.7986 (ptm160) cc_final: 0.7620 (ttt-90) REVERT: C 723 MET cc_start: 0.8934 (mtp) cc_final: 0.8387 (mtm) REVERT: C 774 PHE cc_start: 0.7691 (t80) cc_final: 0.7397 (t80) REVERT: C 834 MET cc_start: 0.9123 (mtp) cc_final: 0.8676 (mtp) REVERT: D 73 MET cc_start: 0.7598 (ttm) cc_final: 0.7251 (ttm) REVERT: D 307 MET cc_start: 0.6122 (ttp) cc_final: 0.5320 (tpp) REVERT: D 641 ILE cc_start: 0.9463 (tt) cc_final: 0.9206 (tp) REVERT: D 732 ASP cc_start: 0.7360 (t0) cc_final: 0.7079 (t0) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.3022 time to fit residues: 171.9958 Evaluate side-chains 267 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 173 optimal weight: 0.3980 chunk 221 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 255 optimal weight: 0.4980 chunk 169 optimal weight: 0.7980 chunk 302 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 HIS D 782 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24144 Z= 0.211 Angle : 0.567 9.975 32912 Z= 0.300 Chirality : 0.044 0.359 3858 Planarity : 0.004 0.056 4182 Dihedral : 5.305 45.373 3374 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.74 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.15), residues: 3128 helix: -0.13 (0.15), residues: 1198 sheet: -2.62 (0.23), residues: 446 loop : -1.92 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 607 HIS 0.005 0.001 HIS B 840 PHE 0.024 0.002 PHE A 113 TYR 0.010 0.001 TYR D 282 ARG 0.003 0.000 ARG A 776 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8675 (mp) cc_final: 0.8309 (mp) REVERT: A 530 GLN cc_start: 0.8239 (tp-100) cc_final: 0.7929 (tp-100) REVERT: A 585 LEU cc_start: 0.8683 (mm) cc_final: 0.8474 (mm) REVERT: A 628 MET cc_start: 0.8443 (mmm) cc_final: 0.8179 (mmm) REVERT: A 662 MET cc_start: 0.9349 (tmm) cc_final: 0.8890 (tmm) REVERT: A 834 MET cc_start: 0.9188 (mtp) cc_final: 0.8856 (mtp) REVERT: B 73 MET cc_start: 0.7452 (ttm) cc_final: 0.7165 (ttm) REVERT: B 201 GLU cc_start: 0.8062 (mp0) cc_final: 0.7848 (mp0) REVERT: B 641 ILE cc_start: 0.9454 (tt) cc_final: 0.9175 (tp) REVERT: B 677 PHE cc_start: 0.7963 (t80) cc_final: 0.7730 (t80) REVERT: B 681 PHE cc_start: 0.6800 (m-10) cc_final: 0.6578 (m-80) REVERT: B 732 ASP cc_start: 0.7315 (t0) cc_final: 0.7010 (t0) REVERT: B 777 ASP cc_start: 0.8363 (m-30) cc_final: 0.8116 (m-30) REVERT: B 786 ASP cc_start: 0.8316 (m-30) cc_final: 0.8102 (m-30) REVERT: B 824 MET cc_start: 0.5763 (mmt) cc_final: 0.5500 (mmt) REVERT: C 235 LEU cc_start: 0.8632 (mp) cc_final: 0.8271 (mp) REVERT: C 491 MET cc_start: 0.6088 (mtt) cc_final: 0.5866 (mtt) REVERT: C 628 MET cc_start: 0.8453 (mmm) cc_final: 0.8178 (mmm) REVERT: C 662 MET cc_start: 0.9355 (tmm) cc_final: 0.8897 (tmm) REVERT: C 686 THR cc_start: 0.8863 (p) cc_final: 0.8633 (t) REVERT: C 716 ARG cc_start: 0.7976 (ptm160) cc_final: 0.7635 (ttt-90) REVERT: C 723 MET cc_start: 0.9003 (mtp) cc_final: 0.8385 (mtm) REVERT: C 774 PHE cc_start: 0.7766 (t80) cc_final: 0.7483 (t80) REVERT: C 834 MET cc_start: 0.9190 (mtp) cc_final: 0.8887 (mtp) REVERT: D 73 MET cc_start: 0.7619 (ttm) cc_final: 0.7280 (ttm) REVERT: D 307 MET cc_start: 0.6126 (ttp) cc_final: 0.5337 (tpp) REVERT: D 641 ILE cc_start: 0.9462 (tt) cc_final: 0.9192 (tp) REVERT: D 732 ASP cc_start: 0.7431 (t0) cc_final: 0.7175 (t0) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.2902 time to fit residues: 166.0803 Evaluate side-chains 270 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 0.0060 chunk 120 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 237 optimal weight: 8.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS B 703 HIS D 782 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24144 Z= 0.234 Angle : 0.585 9.972 32912 Z= 0.309 Chirality : 0.044 0.365 3858 Planarity : 0.005 0.146 4182 Dihedral : 5.370 46.122 3374 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.82 % Favored : 91.14 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.95 (0.15), residues: 3128 helix: -0.12 (0.15), residues: 1206 sheet: -2.34 (0.24), residues: 442 loop : -1.93 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 632 HIS 0.004 0.001 HIS B 840 PHE 0.031 0.002 PHE C 137 TYR 0.009 0.001 TYR D 282 ARG 0.004 0.000 ARG A 776 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7771 (tpp) cc_final: 0.7369 (mmt) REVERT: A 235 LEU cc_start: 0.8658 (mp) cc_final: 0.8334 (mp) REVERT: A 292 LEU cc_start: 0.6371 (tp) cc_final: 0.5115 (pt) REVERT: A 491 MET cc_start: 0.5934 (mtt) cc_final: 0.5714 (mtt) REVERT: A 530 GLN cc_start: 0.8315 (tp-100) cc_final: 0.8001 (tp-100) REVERT: A 628 MET cc_start: 0.8483 (mmm) cc_final: 0.8203 (mmm) REVERT: A 662 MET cc_start: 0.9326 (tmm) cc_final: 0.8857 (tmm) REVERT: A 834 MET cc_start: 0.9191 (mtp) cc_final: 0.8882 (mtp) REVERT: B 73 MET cc_start: 0.7506 (ttm) cc_final: 0.7281 (ttm) REVERT: B 201 GLU cc_start: 0.8068 (mp0) cc_final: 0.7853 (mp0) REVERT: B 641 ILE cc_start: 0.9454 (tt) cc_final: 0.9173 (tp) REVERT: B 681 PHE cc_start: 0.6659 (m-10) cc_final: 0.6422 (m-80) REVERT: B 732 ASP cc_start: 0.7477 (t0) cc_final: 0.7269 (t0) REVERT: B 777 ASP cc_start: 0.8388 (m-30) cc_final: 0.8122 (m-30) REVERT: B 824 MET cc_start: 0.5777 (mmt) cc_final: 0.5536 (mmt) REVERT: C 74 MET cc_start: 0.7846 (tpp) cc_final: 0.7292 (mmt) REVERT: C 163 ILE cc_start: 0.9080 (pt) cc_final: 0.8867 (pt) REVERT: C 235 LEU cc_start: 0.8616 (mp) cc_final: 0.8215 (mp) REVERT: C 628 MET cc_start: 0.8452 (mmm) cc_final: 0.8150 (mmm) REVERT: C 662 MET cc_start: 0.9335 (tmm) cc_final: 0.8863 (tmm) REVERT: C 716 ARG cc_start: 0.7973 (ptm160) cc_final: 0.7625 (ttt-90) REVERT: C 723 MET cc_start: 0.8987 (mtp) cc_final: 0.8364 (mtm) REVERT: C 834 MET cc_start: 0.9189 (mtp) cc_final: 0.8919 (mtp) REVERT: D 73 MET cc_start: 0.7585 (ttm) cc_final: 0.7279 (ttm) REVERT: D 307 MET cc_start: 0.6332 (ttp) cc_final: 0.5494 (tpp) REVERT: D 641 ILE cc_start: 0.9468 (tt) cc_final: 0.9195 (tp) REVERT: D 677 PHE cc_start: 0.8129 (t80) cc_final: 0.7687 (t80) REVERT: D 732 ASP cc_start: 0.7473 (t0) cc_final: 0.7223 (t0) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.3033 time to fit residues: 165.4226 Evaluate side-chains 274 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 264 optimal weight: 30.0000 chunk 282 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 221 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 266 optimal weight: 0.6980 chunk 281 optimal weight: 2.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN D 782 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24144 Z= 0.189 Angle : 0.558 11.326 32912 Z= 0.294 Chirality : 0.044 0.461 3858 Planarity : 0.004 0.143 4182 Dihedral : 5.170 45.837 3374 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.15), residues: 3128 helix: 0.03 (0.16), residues: 1202 sheet: -2.22 (0.24), residues: 452 loop : -1.83 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 607 HIS 0.004 0.001 HIS B 840 PHE 0.020 0.001 PHE C 774 TYR 0.010 0.001 TYR D 282 ARG 0.003 0.000 ARG A 776 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8609 (mp) cc_final: 0.8263 (mp) REVERT: A 530 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7951 (tp-100) REVERT: A 585 LEU cc_start: 0.8698 (mm) cc_final: 0.8491 (mm) REVERT: A 628 MET cc_start: 0.8477 (mmm) cc_final: 0.8172 (mmm) REVERT: A 662 MET cc_start: 0.9369 (tmm) cc_final: 0.8965 (tmm) REVERT: A 723 MET cc_start: 0.8947 (mtp) cc_final: 0.8219 (mtm) REVERT: A 834 MET cc_start: 0.9213 (mtp) cc_final: 0.8958 (mtp) REVERT: B 73 MET cc_start: 0.7650 (ttm) cc_final: 0.7396 (ttm) REVERT: B 201 GLU cc_start: 0.8071 (mp0) cc_final: 0.7852 (mp0) REVERT: B 307 MET cc_start: 0.6125 (ttp) cc_final: 0.5397 (tpp) REVERT: B 641 ILE cc_start: 0.9431 (tt) cc_final: 0.9154 (tp) REVERT: B 677 PHE cc_start: 0.8149 (t80) cc_final: 0.7898 (t80) REVERT: B 681 PHE cc_start: 0.6724 (m-10) cc_final: 0.6457 (m-80) REVERT: B 732 ASP cc_start: 0.7430 (t0) cc_final: 0.7179 (t0) REVERT: B 777 ASP cc_start: 0.8440 (m-30) cc_final: 0.8133 (m-30) REVERT: B 786 ASP cc_start: 0.8218 (m-30) cc_final: 0.7763 (m-30) REVERT: B 824 MET cc_start: 0.5743 (mmt) cc_final: 0.5463 (mmp) REVERT: C 74 MET cc_start: 0.7846 (tpp) cc_final: 0.7295 (mmt) REVERT: C 235 LEU cc_start: 0.8557 (mp) cc_final: 0.8150 (mp) REVERT: C 585 LEU cc_start: 0.8736 (mm) cc_final: 0.8505 (mm) REVERT: C 628 MET cc_start: 0.8471 (mmm) cc_final: 0.8180 (mmm) REVERT: C 662 MET cc_start: 0.9375 (tmm) cc_final: 0.8954 (tmm) REVERT: C 716 ARG cc_start: 0.7933 (ptm160) cc_final: 0.7620 (ttt180) REVERT: C 723 MET cc_start: 0.8990 (mtp) cc_final: 0.8355 (mtm) REVERT: C 834 MET cc_start: 0.9227 (mtp) cc_final: 0.8953 (mtp) REVERT: D 73 MET cc_start: 0.7615 (ttm) cc_final: 0.7295 (ttm) REVERT: D 132 MET cc_start: 0.7404 (mmp) cc_final: 0.7176 (mmm) REVERT: D 307 MET cc_start: 0.6239 (ttp) cc_final: 0.5470 (tpp) REVERT: D 544 THR cc_start: 0.8129 (t) cc_final: 0.7916 (t) REVERT: D 641 ILE cc_start: 0.9425 (tt) cc_final: 0.9145 (tp) REVERT: D 732 ASP cc_start: 0.7426 (t0) cc_final: 0.7194 (t0) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.3072 time to fit residues: 177.8095 Evaluate side-chains 282 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 chunk 182 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 312 optimal weight: 0.7980 chunk 287 optimal weight: 0.2980 chunk 249 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 192 optimal weight: 0.0470 chunk 152 optimal weight: 5.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 24144 Z= 0.159 Angle : 0.539 9.249 32912 Z= 0.283 Chirality : 0.043 0.335 3858 Planarity : 0.005 0.143 4182 Dihedral : 4.992 46.285 3374 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.58 (0.15), residues: 3128 helix: 0.13 (0.16), residues: 1212 sheet: -1.87 (0.26), residues: 420 loop : -1.78 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 607 HIS 0.004 0.001 HIS A 162 PHE 0.018 0.001 PHE C 774 TYR 0.010 0.001 TYR D 282 ARG 0.003 0.000 ARG A 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7690 (tpp) cc_final: 0.7201 (mmt) REVERT: A 163 ILE cc_start: 0.8825 (pt) cc_final: 0.8547 (pt) REVERT: A 235 LEU cc_start: 0.8591 (mp) cc_final: 0.8238 (mp) REVERT: A 523 MET cc_start: 0.8507 (mmm) cc_final: 0.8178 (mtp) REVERT: A 585 LEU cc_start: 0.8678 (mm) cc_final: 0.8422 (mm) REVERT: A 662 MET cc_start: 0.9400 (tmm) cc_final: 0.9018 (tmm) REVERT: A 716 ARG cc_start: 0.8328 (ptm160) cc_final: 0.7938 (ttt180) REVERT: A 723 MET cc_start: 0.8867 (mtp) cc_final: 0.8076 (mtm) REVERT: B 73 MET cc_start: 0.7687 (ttm) cc_final: 0.7438 (ttm) REVERT: B 307 MET cc_start: 0.6033 (ttp) cc_final: 0.5362 (tpp) REVERT: B 641 ILE cc_start: 0.9425 (tt) cc_final: 0.9151 (tp) REVERT: B 732 ASP cc_start: 0.7401 (t0) cc_final: 0.7158 (t0) REVERT: B 777 ASP cc_start: 0.8467 (m-30) cc_final: 0.8214 (m-30) REVERT: B 786 ASP cc_start: 0.7978 (m-30) cc_final: 0.7620 (m-30) REVERT: B 824 MET cc_start: 0.5715 (mmt) cc_final: 0.5426 (mmp) REVERT: C 74 MET cc_start: 0.7835 (tpp) cc_final: 0.7299 (mmt) REVERT: C 130 ASP cc_start: 0.7944 (m-30) cc_final: 0.7700 (m-30) REVERT: C 155 MET cc_start: 0.7971 (mtt) cc_final: 0.7620 (mmm) REVERT: C 235 LEU cc_start: 0.8515 (mp) cc_final: 0.8128 (mp) REVERT: C 336 TRP cc_start: 0.5672 (t60) cc_final: 0.5425 (t60) REVERT: C 491 MET cc_start: 0.7004 (mmm) cc_final: 0.6628 (mtt) REVERT: C 585 LEU cc_start: 0.8723 (mm) cc_final: 0.8430 (mm) REVERT: C 662 MET cc_start: 0.9402 (tmm) cc_final: 0.8971 (tmm) REVERT: C 716 ARG cc_start: 0.7974 (ptm160) cc_final: 0.7725 (ttt180) REVERT: C 723 MET cc_start: 0.8896 (mtp) cc_final: 0.8248 (mtm) REVERT: D 73 MET cc_start: 0.7087 (ttm) cc_final: 0.6757 (ttm) REVERT: D 132 MET cc_start: 0.7496 (mmp) cc_final: 0.7227 (mmm) REVERT: D 307 MET cc_start: 0.5927 (ttp) cc_final: 0.5334 (tpp) REVERT: D 544 THR cc_start: 0.8104 (t) cc_final: 0.7868 (t) REVERT: D 641 ILE cc_start: 0.9413 (tt) cc_final: 0.9131 (tp) REVERT: D 732 ASP cc_start: 0.7340 (t0) cc_final: 0.7107 (t0) REVERT: D 786 ASP cc_start: 0.8273 (m-30) cc_final: 0.7891 (m-30) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2979 time to fit residues: 175.6516 Evaluate side-chains 278 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 3.9990 chunk 265 optimal weight: 0.0370 chunk 76 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 chunk 104 optimal weight: 0.0470 chunk 256 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.117648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.098233 restraints weight = 57122.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099966 restraints weight = 41102.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101134 restraints weight = 32664.251| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 24144 Z= 0.142 Angle : 0.519 8.388 32912 Z= 0.272 Chirality : 0.042 0.339 3858 Planarity : 0.005 0.112 4182 Dihedral : 4.652 45.377 3374 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.36 (0.15), residues: 3128 helix: 0.36 (0.16), residues: 1188 sheet: -1.69 (0.24), residues: 472 loop : -1.67 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 844 HIS 0.004 0.001 HIS C 592 PHE 0.017 0.001 PHE C 774 TYR 0.010 0.001 TYR D 282 ARG 0.002 0.000 ARG D 682 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4260.77 seconds wall clock time: 78 minutes 0.93 seconds (4680.93 seconds total)