Starting phenix.real_space_refine on Thu Feb 22 02:11:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufs_26479/02_2024/7ufs_26479.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufs_26479/02_2024/7ufs_26479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufs_26479/02_2024/7ufs_26479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufs_26479/02_2024/7ufs_26479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufs_26479/02_2024/7ufs_26479.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufs_26479/02_2024/7ufs_26479.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.889 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 140 5.16 5 C 20576 2.51 5 N 5776 2.21 5 O 6100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32596 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8148 Classifications: {'peptide': 1040} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 60, 'TRANS': 979} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8148 Classifications: {'peptide': 1040} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 60, 'TRANS': 979} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 8148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8148 Classifications: {'peptide': 1040} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 60, 'TRANS': 979} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 8148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8148 Classifications: {'peptide': 1040} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 60, 'TRANS': 979} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.90, per 1000 atoms: 0.55 Number of scatterers: 32596 At special positions: 0 Unit cell: (164.15, 142.71, 98.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 140 16.00 O 6100 8.00 N 5776 7.00 C 20576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.31 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 276 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 598 " pdb=" ZN B1101 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 598 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 276 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 598 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 276 " pdb=" ZN D1101 " pdb="ZN ZN D1101 " - pdb=" NE2 HIS D 598 " pdb="ZN ZN D1101 " - pdb=" NE2 HIS D 276 " 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7704 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 44 sheets defined 29.4% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 removed outlier: 3.680A pdb=" N GLU A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 198 through 218 removed outlier: 3.735A pdb=" N PHE A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.663A pdb=" N TRP A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.574A pdb=" N ALA A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 287 through 306 removed outlier: 4.120A pdb=" N GLU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 326 removed outlier: 3.705A pdb=" N TYR A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.906A pdb=" N GLU A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 376 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 451 through 461 removed outlier: 3.669A pdb=" N GLN A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 495 removed outlier: 3.549A pdb=" N THR A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.535A pdb=" N THR A 545 " --> pdb=" O GLY A 542 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 546 " --> pdb=" O THR A 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 542 through 546' Processing helix chain 'A' and resid 547 through 575 removed outlier: 3.878A pdb=" N LYS A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 575 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 589 Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 606 through 637 removed outlier: 3.673A pdb=" N HIS A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 614 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 637 " --> pdb=" O GLN A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.681A pdb=" N SER A 660 " --> pdb=" O PRO A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 844 removed outlier: 3.714A pdb=" N ALA A 844 " --> pdb=" O ARG A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 935 Processing helix chain 'B' and resid 4 through 19 removed outlier: 3.680A pdb=" N GLU B 10 " --> pdb=" O ASN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 44 through 55 Processing helix chain 'B' and resid 198 through 218 removed outlier: 3.735A pdb=" N PHE B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.663A pdb=" N TRP B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.574A pdb=" N ALA B 252 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'B' and resid 287 through 306 removed outlier: 4.120A pdb=" N GLU B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 326 removed outlier: 3.705A pdb=" N TYR B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.906A pdb=" N GLU B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 376 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 451 through 461 removed outlier: 3.669A pdb=" N GLN B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 495 removed outlier: 3.548A pdb=" N THR B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.534A pdb=" N THR B 545 " --> pdb=" O GLY B 542 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 546 " --> pdb=" O THR B 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 546' Processing helix chain 'B' and resid 547 through 575 removed outlier: 3.878A pdb=" N LYS B 551 " --> pdb=" O GLN B 547 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 589 Processing helix chain 'B' and resid 593 through 597 Processing helix chain 'B' and resid 606 through 638 removed outlier: 3.674A pdb=" N HIS B 610 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 614 " --> pdb=" O HIS B 610 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 637 " --> pdb=" O GLN B 633 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 638 " --> pdb=" O ALA B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 660 removed outlier: 3.681A pdb=" N SER B 660 " --> pdb=" O PRO B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 844 removed outlier: 3.714A pdb=" N ALA B 844 " --> pdb=" O ARG B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 935 Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.680A pdb=" N GLU C 10 " --> pdb=" O ASN C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 44 through 55 Processing helix chain 'C' and resid 198 through 218 removed outlier: 3.735A pdb=" N PHE C 202 " --> pdb=" O ASN C 198 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 237 removed outlier: 3.663A pdb=" N TRP C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.574A pdb=" N ALA C 252 " --> pdb=" O PRO C 248 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'C' and resid 287 through 306 removed outlier: 4.120A pdb=" N GLU C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 326 removed outlier: 3.705A pdb=" N TYR C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 340 removed outlier: 3.905A pdb=" N GLU C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 376 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 451 through 461 removed outlier: 3.669A pdb=" N GLN C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 495 removed outlier: 3.549A pdb=" N THR C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 493 " --> pdb=" O THR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.535A pdb=" N THR C 545 " --> pdb=" O GLY C 542 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 546 " --> pdb=" O THR C 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 542 through 546' Processing helix chain 'C' and resid 547 through 575 removed outlier: 3.878A pdb=" N LYS C 551 " --> pdb=" O GLN C 547 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN C 575 " --> pdb=" O ALA C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 589 Processing helix chain 'C' and resid 593 through 597 Processing helix chain 'C' and resid 606 through 638 removed outlier: 3.674A pdb=" N HIS C 610 " --> pdb=" O ILE C 606 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG C 614 " --> pdb=" O HIS C 610 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 637 " --> pdb=" O GLN C 633 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C 638 " --> pdb=" O ALA C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.680A pdb=" N SER C 660 " --> pdb=" O PRO C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 844 removed outlier: 3.716A pdb=" N ALA C 844 " --> pdb=" O ARG C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 935 Processing helix chain 'D' and resid 4 through 19 removed outlier: 3.680A pdb=" N GLU D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 44 through 55 Processing helix chain 'D' and resid 198 through 218 removed outlier: 3.735A pdb=" N PHE D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU D 217 " --> pdb=" O SER D 213 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 237 removed outlier: 3.664A pdb=" N TRP D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 246 through 255 removed outlier: 3.573A pdb=" N ALA D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 287 through 306 removed outlier: 4.121A pdb=" N GLU D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 326 removed outlier: 3.705A pdb=" N TYR D 319 " --> pdb=" O SER D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 340 removed outlier: 3.906A pdb=" N GLU D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY D 340 " --> pdb=" O ARG D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 376 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 451 through 461 removed outlier: 3.668A pdb=" N GLN D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 495 removed outlier: 3.549A pdb=" N THR D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 493 " --> pdb=" O THR D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 542 through 546 removed outlier: 3.535A pdb=" N THR D 545 " --> pdb=" O GLY D 542 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 546 " --> pdb=" O THR D 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 542 through 546' Processing helix chain 'D' and resid 547 through 575 removed outlier: 3.878A pdb=" N LYS D 551 " --> pdb=" O GLN D 547 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 589 Processing helix chain 'D' and resid 593 through 597 Processing helix chain 'D' and resid 606 through 638 removed outlier: 3.675A pdb=" N HIS D 610 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG D 614 " --> pdb=" O HIS D 610 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 637 " --> pdb=" O GLN D 633 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA D 638 " --> pdb=" O ALA D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.680A pdb=" N SER D 660 " --> pdb=" O PRO D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 844 removed outlier: 3.715A pdb=" N ALA D 844 " --> pdb=" O ARG D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 935 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 3.512A pdb=" N THR A 195 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 removed outlier: 4.645A pdb=" N LEU A 33 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 73 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 114 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS A 124 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 67 removed outlier: 4.461A pdb=" N GLY A 66 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 470 through 475 removed outlier: 3.699A pdb=" N ALA A 471 " --> pdb=" O ASN A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 384 through 385 removed outlier: 6.638A pdb=" N ILE A 384 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 679 through 682 removed outlier: 3.616A pdb=" N ILE A 688 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 696 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A 706 " --> pdb=" O ARG A 697 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 729 removed outlier: 6.838A pdb=" N LEU A 809 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY A 872 " --> pdb=" O SER A 895 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 873 " --> pdb=" O SER A 848 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 848 " --> pdb=" O SER A 873 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 762 removed outlier: 3.580A pdb=" N VAL A 773 " --> pdb=" O MET A 756 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N HIS A 771 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 760 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 769 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 768 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 821 through 826 removed outlier: 3.945A pdb=" N GLY A 829 " --> pdb=" O CYS A 826 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 950 through 951 removed outlier: 3.579A pdb=" N ALA A1030 " --> pdb=" O LEU A 989 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 958 through 965 removed outlier: 5.655A pdb=" N LEU A 960 " --> pdb=" O TYR A 978 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR A 978 " --> pdb=" O LEU A 960 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A1041 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.512A pdb=" N THR B 195 " --> pdb=" O GLU B 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 60 through 62 removed outlier: 4.645A pdb=" N LEU B 33 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 73 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 114 " --> pdb=" O GLU B 157 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B 124 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 66 through 67 removed outlier: 4.462A pdb=" N GLY B 66 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 470 through 475 removed outlier: 3.699A pdb=" N ALA B 471 " --> pdb=" O ASN B 268 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 384 through 385 removed outlier: 6.637A pdb=" N ILE B 384 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 679 through 682 removed outlier: 3.616A pdb=" N ILE B 688 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 696 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 706 " --> pdb=" O ARG B 697 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 726 through 729 removed outlier: 6.838A pdb=" N LEU B 809 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLY B 872 " --> pdb=" O SER B 895 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 873 " --> pdb=" O SER B 848 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 848 " --> pdb=" O SER B 873 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 755 through 762 removed outlier: 3.581A pdb=" N VAL B 773 " --> pdb=" O MET B 756 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N HIS B 771 " --> pdb=" O GLU B 758 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 760 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 769 " --> pdb=" O VAL B 760 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 768 " --> pdb=" O LEU B 787 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 821 through 826 removed outlier: 3.946A pdb=" N GLY B 829 " --> pdb=" O CYS B 826 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 950 through 951 removed outlier: 3.578A pdb=" N ALA B1030 " --> pdb=" O LEU B 989 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 958 through 965 removed outlier: 5.656A pdb=" N LEU B 960 " --> pdb=" O TYR B 978 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR B 978 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR B1041 " --> pdb=" O VAL B1003 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.513A pdb=" N THR C 195 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 60 through 62 removed outlier: 4.644A pdb=" N LEU C 33 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 73 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 114 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS C 124 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 66 through 67 removed outlier: 4.461A pdb=" N GLY C 66 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 470 through 475 removed outlier: 3.699A pdb=" N ALA C 471 " --> pdb=" O ASN C 268 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 384 through 385 removed outlier: 6.637A pdb=" N ILE C 384 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 679 through 682 removed outlier: 3.616A pdb=" N ILE C 688 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 696 " --> pdb=" O LEU C 689 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER C 706 " --> pdb=" O ARG C 697 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 726 through 729 removed outlier: 6.839A pdb=" N LEU C 809 " --> pdb=" O LEU C 896 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLY C 872 " --> pdb=" O SER C 895 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 873 " --> pdb=" O SER C 848 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 848 " --> pdb=" O SER C 873 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 755 through 762 removed outlier: 3.581A pdb=" N VAL C 773 " --> pdb=" O MET C 756 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N HIS C 771 " --> pdb=" O GLU C 758 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 760 " --> pdb=" O ALA C 769 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA C 769 " --> pdb=" O VAL C 760 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 768 " --> pdb=" O LEU C 787 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 821 through 826 removed outlier: 3.945A pdb=" N GLY C 829 " --> pdb=" O CYS C 826 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 950 through 951 removed outlier: 3.579A pdb=" N ALA C1030 " --> pdb=" O LEU C 989 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 958 through 965 removed outlier: 5.656A pdb=" N LEU C 960 " --> pdb=" O TYR C 978 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR C 978 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR C1041 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.512A pdb=" N THR D 195 " --> pdb=" O GLU D 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 60 through 62 removed outlier: 4.645A pdb=" N LEU D 33 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D 73 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 114 " --> pdb=" O GLU D 157 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS D 124 " --> pdb=" O VAL D 115 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 66 through 67 removed outlier: 4.462A pdb=" N GLY D 66 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 470 through 475 removed outlier: 3.699A pdb=" N ALA D 471 " --> pdb=" O ASN D 268 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 384 through 385 removed outlier: 6.638A pdb=" N ILE D 384 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 679 through 682 removed outlier: 3.616A pdb=" N ILE D 688 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 696 " --> pdb=" O LEU D 689 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER D 706 " --> pdb=" O ARG D 697 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 726 through 729 removed outlier: 6.838A pdb=" N LEU D 809 " --> pdb=" O LEU D 896 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY D 872 " --> pdb=" O SER D 895 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 873 " --> pdb=" O SER D 848 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER D 848 " --> pdb=" O SER D 873 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 755 through 762 removed outlier: 3.581A pdb=" N VAL D 773 " --> pdb=" O MET D 756 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N HIS D 771 " --> pdb=" O GLU D 758 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL D 760 " --> pdb=" O ALA D 769 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA D 769 " --> pdb=" O VAL D 760 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 768 " --> pdb=" O LEU D 787 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 821 through 826 removed outlier: 3.945A pdb=" N GLY D 829 " --> pdb=" O CYS D 826 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 950 through 951 removed outlier: 3.579A pdb=" N ALA D1030 " --> pdb=" O LEU D 989 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 958 through 965 removed outlier: 5.656A pdb=" N LEU D 960 " --> pdb=" O TYR D 978 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR D 978 " --> pdb=" O LEU D 960 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR D1041 " --> pdb=" O VAL D1003 " (cutoff:3.500A) 1256 hydrogen bonds defined for protein. 3540 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: 15.46 Time building geometry restraints manager: 13.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5627 1.32 - 1.44: 9030 1.44 - 1.57: 18507 1.57 - 1.69: 0 1.69 - 1.82: 244 Bond restraints: 33408 Sorted by residual: bond pdb=" C HIS D 276 " pdb=" O HIS D 276 " ideal model delta sigma weight residual 1.235 1.197 0.039 1.15e-02 7.56e+03 1.13e+01 bond pdb=" C HIS B 276 " pdb=" O HIS B 276 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" C HIS C 276 " pdb=" O HIS C 276 " ideal model delta sigma weight residual 1.235 1.198 0.037 1.15e-02 7.56e+03 1.04e+01 bond pdb=" CA ALA A 275 " pdb=" CB ALA A 275 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.46e-02 4.69e+03 8.39e+00 bond pdb=" N LEU A 282 " pdb=" CA LEU A 282 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.28e-02 6.10e+03 8.16e+00 ... (remaining 33403 not shown) Histogram of bond angle deviations from ideal: 98.92 - 106.00: 951 106.00 - 113.07: 17809 113.07 - 120.15: 11630 120.15 - 127.22: 14553 127.22 - 134.30: 521 Bond angle restraints: 45464 Sorted by residual: angle pdb=" CA TRP B 283 " pdb=" C TRP B 283 " pdb=" N PRO B 284 " ideal model delta sigma weight residual 118.33 124.48 -6.15 1.00e+00 1.00e+00 3.78e+01 angle pdb=" CA TRP C 283 " pdb=" C TRP C 283 " pdb=" N PRO C 284 " ideal model delta sigma weight residual 118.33 124.46 -6.13 1.00e+00 1.00e+00 3.75e+01 angle pdb=" CA TRP D 283 " pdb=" C TRP D 283 " pdb=" N PRO D 284 " ideal model delta sigma weight residual 118.33 124.44 -6.11 1.00e+00 1.00e+00 3.73e+01 angle pdb=" C ASP A 388 " pdb=" CA ASP A 388 " pdb=" CB ASP A 388 " ideal model delta sigma weight residual 111.43 104.73 6.70 1.24e+00 6.50e-01 2.92e+01 angle pdb=" C ASP C 388 " pdb=" CA ASP C 388 " pdb=" CB ASP C 388 " ideal model delta sigma weight residual 111.43 104.92 6.51 1.24e+00 6.50e-01 2.76e+01 ... (remaining 45459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.87: 17207 14.87 - 29.73: 1865 29.73 - 44.60: 710 44.60 - 59.47: 62 59.47 - 74.34: 28 Dihedral angle restraints: 19872 sinusoidal: 7904 harmonic: 11968 Sorted by residual: dihedral pdb=" CA TRP D 739 " pdb=" C TRP D 739 " pdb=" N ASP D 740 " pdb=" CA ASP D 740 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA TRP B 739 " pdb=" C TRP B 739 " pdb=" N ASP B 740 " pdb=" CA ASP B 740 " ideal model delta harmonic sigma weight residual -180.00 -160.68 -19.32 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA TRP C 739 " pdb=" C TRP C 739 " pdb=" N ASP C 740 " pdb=" CA ASP C 740 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 19869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3866 0.047 - 0.093: 786 0.093 - 0.140: 272 0.140 - 0.187: 10 0.187 - 0.233: 14 Chirality restraints: 4948 Sorted by residual: chirality pdb=" CA TRP C 281 " pdb=" N TRP C 281 " pdb=" C TRP C 281 " pdb=" CB TRP C 281 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TRP B 281 " pdb=" N TRP B 281 " pdb=" C TRP B 281 " pdb=" CB TRP B 281 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TRP D 281 " pdb=" N TRP D 281 " pdb=" C TRP D 281 " pdb=" CB TRP D 281 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 4945 not shown) Planarity restraints: 5996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 274 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C HIS A 274 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS A 274 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 275 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 476 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C GLY D 476 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY D 476 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE D 477 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 476 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C GLY C 476 " -0.046 2.00e-02 2.50e+03 pdb=" O GLY C 476 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE C 477 " 0.015 2.00e-02 2.50e+03 ... (remaining 5993 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 197 2.55 - 3.14: 24306 3.14 - 3.73: 49530 3.73 - 4.31: 65807 4.31 - 4.90: 114292 Nonbonded interactions: 254132 Sorted by model distance: nonbonded pdb=" OD2 ASP B 278 " pdb="ZN ZN B1101 " model vdw 1.969 2.230 nonbonded pdb=" OD2 ASP C 278 " pdb="ZN ZN C1101 " model vdw 1.990 2.230 nonbonded pdb=" OD2 ASP A 278 " pdb="ZN ZN A1101 " model vdw 2.090 2.230 nonbonded pdb=" OD2 ASP D 278 " pdb="ZN ZN D1101 " model vdw 2.105 2.230 nonbonded pdb=" OD2 ASP D 388 " pdb="ZN ZN D1101 " model vdw 2.128 2.230 ... (remaining 254127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 39.870 Check model and map are aligned: 0.530 Set scattering table: 0.300 Process input model: 95.140 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.200 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33408 Z= 0.189 Angle : 0.626 8.397 45464 Z= 0.351 Chirality : 0.044 0.233 4948 Planarity : 0.004 0.038 5996 Dihedral : 13.888 74.335 12168 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.12 % Allowed : 0.32 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4144 helix: 1.92 (0.16), residues: 1100 sheet: -0.13 (0.19), residues: 908 loop : -2.05 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 101 HIS 0.013 0.001 HIS D 598 PHE 0.010 0.001 PHE D 853 TYR 0.012 0.001 TYR C 204 ARG 0.008 0.000 ARG C 888 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 677 time to evaluate : 4.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7822 (ttt) cc_final: 0.7148 (ttm) REVERT: A 313 MET cc_start: 0.8703 (ttm) cc_final: 0.8340 (ttp) REVERT: A 411 GLN cc_start: 0.7345 (pp30) cc_final: 0.7090 (pp30) REVERT: A 1004 ASN cc_start: 0.8931 (p0) cc_final: 0.8723 (p0) REVERT: A 1046 ARG cc_start: 0.7201 (tmm160) cc_final: 0.6530 (ttt90) REVERT: B 192 MET cc_start: 0.7802 (ttt) cc_final: 0.7127 (ttm) REVERT: B 313 MET cc_start: 0.8699 (ttm) cc_final: 0.8344 (ttp) REVERT: B 411 GLN cc_start: 0.7325 (pp30) cc_final: 0.7082 (pp30) REVERT: B 1046 ARG cc_start: 0.7226 (tmm160) cc_final: 0.6542 (ttt90) REVERT: C 192 MET cc_start: 0.7811 (ttt) cc_final: 0.7138 (ttm) REVERT: C 313 MET cc_start: 0.8705 (ttm) cc_final: 0.8344 (ttp) REVERT: C 411 GLN cc_start: 0.7349 (pp30) cc_final: 0.7096 (pp30) REVERT: C 1046 ARG cc_start: 0.7217 (tmm160) cc_final: 0.6531 (ttt90) REVERT: D 192 MET cc_start: 0.7807 (ttt) cc_final: 0.7137 (ttm) REVERT: D 313 MET cc_start: 0.8683 (ttm) cc_final: 0.8334 (ttp) REVERT: D 411 GLN cc_start: 0.7324 (pp30) cc_final: 0.7069 (pp30) REVERT: D 657 PRO cc_start: 0.8805 (Cg_exo) cc_final: 0.8595 (Cg_endo) outliers start: 4 outliers final: 4 residues processed: 681 average time/residue: 0.4415 time to fit residues: 492.0358 Evaluate side-chains 531 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 527 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain D residue 599 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 6.9990 chunk 315 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 326 optimal weight: 0.1980 chunk 126 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 242 optimal weight: 0.0980 chunk 377 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 149 HIS A 274 HIS A 365 GLN A 424 HIS A 838 ASN B 130 ASN B 149 HIS B 274 HIS B 365 GLN B 424 HIS B 838 ASN C 130 ASN C 149 HIS C 274 HIS C 365 GLN C 424 HIS C 838 ASN D 130 ASN D 149 HIS D 274 HIS D 365 GLN D 424 HIS D 838 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33408 Z= 0.242 Angle : 0.568 7.595 45464 Z= 0.290 Chirality : 0.044 0.156 4948 Planarity : 0.004 0.043 5996 Dihedral : 4.446 48.004 4592 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.82 % Allowed : 10.93 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 4144 helix: 1.80 (0.16), residues: 1128 sheet: -0.53 (0.17), residues: 996 loop : -2.09 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 407 HIS 0.005 0.001 HIS D 598 PHE 0.012 0.001 PHE A 853 TYR 0.013 0.001 TYR B 225 ARG 0.006 0.000 ARG C 713 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 523 time to evaluate : 4.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 PRO cc_start: 0.8033 (Cg_exo) cc_final: 0.7707 (Cg_endo) REVERT: A 217 GLU cc_start: 0.7498 (pt0) cc_final: 0.6877 (pt0) REVERT: A 313 MET cc_start: 0.8814 (ttm) cc_final: 0.8611 (ttm) REVERT: A 411 GLN cc_start: 0.7359 (pp30) cc_final: 0.7030 (pp30) REVERT: A 456 MET cc_start: 0.7799 (mtp) cc_final: 0.7451 (mtp) REVERT: A 740 ASP cc_start: 0.6401 (t0) cc_final: 0.6087 (t0) REVERT: A 780 GLU cc_start: 0.8202 (pp20) cc_final: 0.7920 (pp20) REVERT: B 169 PRO cc_start: 0.8058 (Cg_exo) cc_final: 0.7736 (Cg_endo) REVERT: B 217 GLU cc_start: 0.7498 (pt0) cc_final: 0.6887 (pt0) REVERT: B 313 MET cc_start: 0.8824 (ttm) cc_final: 0.8618 (ttm) REVERT: B 411 GLN cc_start: 0.7360 (pp30) cc_final: 0.7032 (pp30) REVERT: B 456 MET cc_start: 0.7792 (mtp) cc_final: 0.7469 (mtp) REVERT: B 740 ASP cc_start: 0.6376 (t0) cc_final: 0.6048 (t0) REVERT: C 169 PRO cc_start: 0.8043 (Cg_exo) cc_final: 0.7722 (Cg_endo) REVERT: C 217 GLU cc_start: 0.7521 (pt0) cc_final: 0.6931 (pt0) REVERT: C 313 MET cc_start: 0.8817 (ttm) cc_final: 0.8607 (ttm) REVERT: C 411 GLN cc_start: 0.7360 (pp30) cc_final: 0.7032 (pp30) REVERT: C 456 MET cc_start: 0.7800 (mtp) cc_final: 0.7452 (mtp) REVERT: C 740 ASP cc_start: 0.6396 (t0) cc_final: 0.6071 (t0) REVERT: D 169 PRO cc_start: 0.8025 (Cg_exo) cc_final: 0.7708 (Cg_endo) REVERT: D 217 GLU cc_start: 0.7514 (pt0) cc_final: 0.6928 (pt0) REVERT: D 313 MET cc_start: 0.8808 (ttm) cc_final: 0.8600 (ttm) REVERT: D 411 GLN cc_start: 0.7350 (pp30) cc_final: 0.7004 (pp30) REVERT: D 456 MET cc_start: 0.7798 (mtp) cc_final: 0.7466 (mtp) REVERT: D 740 ASP cc_start: 0.6391 (t0) cc_final: 0.6052 (t0) outliers start: 62 outliers final: 51 residues processed: 557 average time/residue: 0.4389 time to fit residues: 408.0883 Evaluate side-chains 527 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 476 time to evaluate : 4.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 762 ASP Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 12 CYS Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 762 ASP Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 850 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain D residue 839 THR Chi-restraints excluded: chain D residue 850 THR Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 209 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 378 optimal weight: 5.9990 chunk 408 optimal weight: 7.9990 chunk 337 optimal weight: 2.9990 chunk 375 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 303 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 149 HIS A 735 HIS B 80 ASN B 149 HIS B 735 HIS C 80 ASN C 149 HIS C 735 HIS D 80 ASN D 149 HIS ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33408 Z= 0.233 Angle : 0.549 7.171 45464 Z= 0.281 Chirality : 0.044 0.187 4948 Planarity : 0.004 0.044 5996 Dihedral : 4.315 23.384 4584 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.75 % Allowed : 13.63 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.13), residues: 4144 helix: 1.79 (0.16), residues: 1128 sheet: -0.54 (0.17), residues: 992 loop : -2.07 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 407 HIS 0.006 0.001 HIS A 735 PHE 0.013 0.001 PHE A 853 TYR 0.014 0.001 TYR B 225 ARG 0.006 0.000 ARG C 713 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 509 time to evaluate : 3.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8278 (mpp) cc_final: 0.8039 (mpp) REVERT: A 169 PRO cc_start: 0.8148 (Cg_exo) cc_final: 0.7830 (Cg_endo) REVERT: A 217 GLU cc_start: 0.7536 (pt0) cc_final: 0.7142 (pt0) REVERT: A 411 GLN cc_start: 0.7344 (pp30) cc_final: 0.6974 (pp30) REVERT: A 456 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7502 (mtp) REVERT: A 740 ASP cc_start: 0.6515 (t0) cc_final: 0.6254 (t0) REVERT: A 742 GLN cc_start: 0.8252 (mp10) cc_final: 0.7838 (mp10) REVERT: B 16 MET cc_start: 0.8281 (mpp) cc_final: 0.8042 (mpp) REVERT: B 169 PRO cc_start: 0.8146 (Cg_exo) cc_final: 0.7831 (Cg_endo) REVERT: B 217 GLU cc_start: 0.7514 (pt0) cc_final: 0.7127 (pt0) REVERT: B 411 GLN cc_start: 0.7342 (pp30) cc_final: 0.6981 (pp30) REVERT: B 456 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7484 (mtp) REVERT: B 740 ASP cc_start: 0.6494 (t0) cc_final: 0.6214 (t0) REVERT: B 742 GLN cc_start: 0.8249 (mp10) cc_final: 0.7822 (mp10) REVERT: C 16 MET cc_start: 0.8276 (mpp) cc_final: 0.8038 (mpp) REVERT: C 169 PRO cc_start: 0.8138 (Cg_exo) cc_final: 0.7821 (Cg_endo) REVERT: C 217 GLU cc_start: 0.7519 (pt0) cc_final: 0.7118 (pt0) REVERT: C 411 GLN cc_start: 0.7342 (pp30) cc_final: 0.6978 (pp30) REVERT: C 456 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7478 (mtp) REVERT: C 740 ASP cc_start: 0.6514 (t0) cc_final: 0.6249 (t0) REVERT: C 742 GLN cc_start: 0.8252 (mp10) cc_final: 0.7832 (mp10) REVERT: D 16 MET cc_start: 0.8286 (mpp) cc_final: 0.8045 (mpp) REVERT: D 169 PRO cc_start: 0.8149 (Cg_exo) cc_final: 0.7838 (Cg_endo) REVERT: D 217 GLU cc_start: 0.7531 (pt0) cc_final: 0.7136 (pt0) REVERT: D 411 GLN cc_start: 0.7328 (pp30) cc_final: 0.6962 (pp30) REVERT: D 456 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7505 (mtp) REVERT: D 742 GLN cc_start: 0.8295 (mp10) cc_final: 0.7915 (mp10) outliers start: 94 outliers final: 71 residues processed: 554 average time/residue: 0.4110 time to fit residues: 374.1204 Evaluate side-chains 564 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 489 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 762 ASP Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 762 ASP Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 850 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 696 VAL Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 839 THR Chi-restraints excluded: chain D residue 848 SER Chi-restraints excluded: chain D residue 850 THR Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 373 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 254 optimal weight: 0.6980 chunk 379 optimal weight: 6.9990 chunk 402 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 359 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 838 ASN B 149 HIS B 838 ASN C 149 HIS C 838 ASN D 149 HIS ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 838 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33408 Z= 0.210 Angle : 0.538 6.649 45464 Z= 0.275 Chirality : 0.044 0.252 4948 Planarity : 0.003 0.044 5996 Dihedral : 4.283 23.135 4584 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.81 % Allowed : 16.00 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 4144 helix: 1.82 (0.16), residues: 1128 sheet: -0.27 (0.18), residues: 924 loop : -2.09 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 407 HIS 0.004 0.001 HIS D 598 PHE 0.013 0.001 PHE D 853 TYR 0.013 0.001 TYR D 225 ARG 0.007 0.000 ARG D 713 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 513 time to evaluate : 4.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8322 (mpp) cc_final: 0.8055 (mpp) REVERT: A 116 TYR cc_start: 0.9285 (m-80) cc_final: 0.8981 (m-80) REVERT: A 169 PRO cc_start: 0.8190 (Cg_exo) cc_final: 0.7884 (Cg_endo) REVERT: A 192 MET cc_start: 0.7343 (ttm) cc_final: 0.7131 (ttt) REVERT: A 217 GLU cc_start: 0.7472 (pt0) cc_final: 0.7055 (pt0) REVERT: A 411 GLN cc_start: 0.7249 (pp30) cc_final: 0.6766 (pp30) REVERT: A 456 MET cc_start: 0.7925 (mtp) cc_final: 0.7277 (mtp) REVERT: A 707 LEU cc_start: 0.9643 (tt) cc_final: 0.9300 (tt) REVERT: A 742 GLN cc_start: 0.8309 (mp10) cc_final: 0.7850 (mp10) REVERT: A 939 MET cc_start: 0.8812 (mmm) cc_final: 0.8522 (mmt) REVERT: B 16 MET cc_start: 0.8323 (mpp) cc_final: 0.8048 (mpp) REVERT: B 116 TYR cc_start: 0.9284 (m-80) cc_final: 0.9024 (m-80) REVERT: B 157 GLU cc_start: 0.8146 (tt0) cc_final: 0.7927 (tt0) REVERT: B 169 PRO cc_start: 0.8184 (Cg_exo) cc_final: 0.7879 (Cg_endo) REVERT: B 192 MET cc_start: 0.7338 (ttm) cc_final: 0.7120 (ttt) REVERT: B 217 GLU cc_start: 0.7453 (pt0) cc_final: 0.7041 (pt0) REVERT: B 360 GLU cc_start: 0.8172 (tp30) cc_final: 0.7521 (tp30) REVERT: B 411 GLN cc_start: 0.7249 (pp30) cc_final: 0.6769 (pp30) REVERT: B 456 MET cc_start: 0.7911 (mtp) cc_final: 0.7270 (mtp) REVERT: B 707 LEU cc_start: 0.9640 (tt) cc_final: 0.9308 (tt) REVERT: B 742 GLN cc_start: 0.8296 (mp10) cc_final: 0.7836 (mp10) REVERT: B 939 MET cc_start: 0.8811 (mmm) cc_final: 0.8534 (mmt) REVERT: C 16 MET cc_start: 0.8317 (mpp) cc_final: 0.8051 (mpp) REVERT: C 116 TYR cc_start: 0.9286 (m-80) cc_final: 0.9005 (m-80) REVERT: C 169 PRO cc_start: 0.8178 (Cg_exo) cc_final: 0.7867 (Cg_endo) REVERT: C 192 MET cc_start: 0.7331 (ttm) cc_final: 0.7116 (ttt) REVERT: C 217 GLU cc_start: 0.7475 (pt0) cc_final: 0.7076 (pt0) REVERT: C 360 GLU cc_start: 0.8185 (tp30) cc_final: 0.7537 (tp30) REVERT: C 411 GLN cc_start: 0.7248 (pp30) cc_final: 0.6765 (pp30) REVERT: C 456 MET cc_start: 0.7912 (mtp) cc_final: 0.7282 (mtp) REVERT: C 707 LEU cc_start: 0.9642 (tt) cc_final: 0.9304 (tt) REVERT: C 742 GLN cc_start: 0.8310 (mp10) cc_final: 0.7849 (mp10) REVERT: C 939 MET cc_start: 0.8809 (mmm) cc_final: 0.8531 (mmt) REVERT: D 16 MET cc_start: 0.8332 (mpp) cc_final: 0.8055 (mpp) REVERT: D 116 TYR cc_start: 0.9292 (m-80) cc_final: 0.9004 (m-80) REVERT: D 169 PRO cc_start: 0.8183 (Cg_exo) cc_final: 0.7884 (Cg_endo) REVERT: D 192 MET cc_start: 0.7333 (ttm) cc_final: 0.7107 (ttt) REVERT: D 217 GLU cc_start: 0.7453 (pt0) cc_final: 0.7063 (pt0) REVERT: D 360 GLU cc_start: 0.8181 (tp30) cc_final: 0.7483 (tp30) REVERT: D 411 GLN cc_start: 0.7237 (pp30) cc_final: 0.6753 (pp30) REVERT: D 456 MET cc_start: 0.7924 (mtp) cc_final: 0.7301 (mtp) REVERT: D 707 LEU cc_start: 0.9640 (tt) cc_final: 0.9306 (tt) REVERT: D 740 ASP cc_start: 0.6399 (t0) cc_final: 0.6158 (t0) REVERT: D 742 GLN cc_start: 0.8295 (mp10) cc_final: 0.8045 (mp10) outliers start: 96 outliers final: 83 residues processed: 572 average time/residue: 0.4228 time to fit residues: 396.3574 Evaluate side-chains 556 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 473 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 762 ASP Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 762 ASP Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 850 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 801 ASN Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 839 THR Chi-restraints excluded: chain D residue 848 SER Chi-restraints excluded: chain D residue 850 THR Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 334 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 299 optimal weight: 0.6980 chunk 165 optimal weight: 8.9990 chunk 343 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 205 optimal weight: 0.7980 chunk 360 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS B 149 HIS C 149 HIS D 149 HIS D 827 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33408 Z= 0.191 Angle : 0.532 6.917 45464 Z= 0.271 Chirality : 0.043 0.243 4948 Planarity : 0.003 0.044 5996 Dihedral : 4.254 23.461 4584 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.55 % Allowed : 17.03 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4144 helix: 1.88 (0.16), residues: 1128 sheet: -0.21 (0.18), residues: 924 loop : -2.08 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 283 HIS 0.004 0.001 HIS C 598 PHE 0.012 0.001 PHE A 853 TYR 0.013 0.001 TYR D 225 ARG 0.004 0.000 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 520 time to evaluate : 3.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9287 (m-80) cc_final: 0.9003 (m-80) REVERT: A 217 GLU cc_start: 0.7425 (pt0) cc_final: 0.7077 (pt0) REVERT: A 411 GLN cc_start: 0.7267 (pp30) cc_final: 0.6701 (pp30) REVERT: A 456 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7235 (mtp) REVERT: A 740 ASP cc_start: 0.6496 (t0) cc_final: 0.6186 (t0) REVERT: A 742 GLN cc_start: 0.8237 (mp10) cc_final: 0.7882 (mp10) REVERT: B 116 TYR cc_start: 0.9285 (m-80) cc_final: 0.9005 (m-80) REVERT: B 169 PRO cc_start: 0.8246 (Cg_exo) cc_final: 0.7958 (Cg_endo) REVERT: B 217 GLU cc_start: 0.7411 (pt0) cc_final: 0.7057 (pt0) REVERT: B 360 GLU cc_start: 0.8162 (tp30) cc_final: 0.7537 (tp30) REVERT: B 411 GLN cc_start: 0.7267 (pp30) cc_final: 0.6706 (pp30) REVERT: B 456 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7231 (mtp) REVERT: B 740 ASP cc_start: 0.6485 (t0) cc_final: 0.6176 (t0) REVERT: B 742 GLN cc_start: 0.8227 (mp10) cc_final: 0.7866 (mp10) REVERT: C 116 TYR cc_start: 0.9271 (m-80) cc_final: 0.8988 (m-80) REVERT: C 169 PRO cc_start: 0.8215 (Cg_exo) cc_final: 0.7925 (Cg_endo) REVERT: C 217 GLU cc_start: 0.7426 (pt0) cc_final: 0.7069 (pt0) REVERT: C 360 GLU cc_start: 0.8176 (tp30) cc_final: 0.7551 (tp30) REVERT: C 411 GLN cc_start: 0.7269 (pp30) cc_final: 0.6702 (pp30) REVERT: C 456 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7233 (mtp) REVERT: C 740 ASP cc_start: 0.6483 (t0) cc_final: 0.6179 (t0) REVERT: C 742 GLN cc_start: 0.8223 (mp10) cc_final: 0.7865 (mp10) REVERT: D 116 TYR cc_start: 0.9278 (m-80) cc_final: 0.8987 (m-80) REVERT: D 217 GLU cc_start: 0.7397 (pt0) cc_final: 0.7042 (pt0) REVERT: D 360 GLU cc_start: 0.8164 (tp30) cc_final: 0.7541 (tp30) REVERT: D 411 GLN cc_start: 0.7258 (pp30) cc_final: 0.6692 (pp30) REVERT: D 456 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7278 (mtp) REVERT: D 740 ASP cc_start: 0.6432 (t0) cc_final: 0.6211 (t0) REVERT: D 742 GLN cc_start: 0.8280 (mp10) cc_final: 0.7902 (mp10) outliers start: 121 outliers final: 93 residues processed: 589 average time/residue: 0.4421 time to fit residues: 427.2781 Evaluate side-chains 573 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 476 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 762 ASP Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 12 CYS Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 762 ASP Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 696 VAL Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 801 ASN Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 839 THR Chi-restraints excluded: chain D residue 848 SER Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 135 optimal weight: 6.9990 chunk 362 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 chunk 236 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 402 optimal weight: 10.0000 chunk 334 optimal weight: 0.1980 chunk 186 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 365 GLN A 838 ASN B 149 HIS B 838 ASN C 149 HIS C 838 ASN D 149 HIS D 838 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 33408 Z= 0.315 Angle : 0.597 8.459 45464 Z= 0.307 Chirality : 0.045 0.264 4948 Planarity : 0.004 0.046 5996 Dihedral : 4.503 22.933 4584 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.04 % Allowed : 17.67 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 4144 helix: 1.80 (0.16), residues: 1132 sheet: -0.53 (0.17), residues: 984 loop : -2.14 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 407 HIS 0.005 0.001 HIS B 598 PHE 0.016 0.001 PHE C 163 TYR 0.016 0.001 TYR B 225 ARG 0.007 0.000 ARG C 713 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 475 time to evaluate : 4.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8263 (mpp) cc_final: 0.7665 (mpp) REVERT: A 157 GLU cc_start: 0.8208 (tt0) cc_final: 0.7944 (tt0) REVERT: A 192 MET cc_start: 0.7509 (ttm) cc_final: 0.7247 (ttt) REVERT: A 217 GLU cc_start: 0.7442 (pt0) cc_final: 0.7084 (pt0) REVERT: A 243 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7228 (p0) REVERT: A 411 GLN cc_start: 0.7474 (pp30) cc_final: 0.6865 (pp30) REVERT: A 456 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7076 (mtp) REVERT: A 742 GLN cc_start: 0.8267 (mp10) cc_final: 0.8008 (mp10) REVERT: A 953 ASP cc_start: 0.8682 (m-30) cc_final: 0.8444 (m-30) REVERT: B 16 MET cc_start: 0.8242 (mpp) cc_final: 0.7687 (mpp) REVERT: B 157 GLU cc_start: 0.8193 (tt0) cc_final: 0.7971 (tt0) REVERT: B 169 PRO cc_start: 0.8447 (Cg_exo) cc_final: 0.8176 (Cg_endo) REVERT: B 192 MET cc_start: 0.7511 (ttm) cc_final: 0.7247 (ttt) REVERT: B 217 GLU cc_start: 0.7434 (pt0) cc_final: 0.7091 (pt0) REVERT: B 243 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7279 (p0) REVERT: B 360 GLU cc_start: 0.8364 (tp30) cc_final: 0.7710 (tp30) REVERT: B 411 GLN cc_start: 0.7484 (pp30) cc_final: 0.6879 (pp30) REVERT: B 456 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7078 (mtp) REVERT: B 742 GLN cc_start: 0.8259 (mp10) cc_final: 0.7995 (mp10) REVERT: B 953 ASP cc_start: 0.8687 (m-30) cc_final: 0.8447 (m-30) REVERT: C 16 MET cc_start: 0.8245 (mpp) cc_final: 0.7663 (mpp) REVERT: C 169 PRO cc_start: 0.8433 (Cg_exo) cc_final: 0.8166 (Cg_endo) REVERT: C 192 MET cc_start: 0.7503 (ttm) cc_final: 0.7242 (ttt) REVERT: C 217 GLU cc_start: 0.7435 (pt0) cc_final: 0.7079 (pt0) REVERT: C 243 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7259 (p0) REVERT: C 360 GLU cc_start: 0.8376 (tp30) cc_final: 0.7718 (tp30) REVERT: C 411 GLN cc_start: 0.7484 (pp30) cc_final: 0.6872 (pp30) REVERT: C 456 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7078 (mtp) REVERT: C 742 GLN cc_start: 0.8261 (mp10) cc_final: 0.7999 (mp10) REVERT: C 953 ASP cc_start: 0.8692 (m-30) cc_final: 0.8455 (m-30) REVERT: D 16 MET cc_start: 0.8263 (mpp) cc_final: 0.7661 (mpp) REVERT: D 192 MET cc_start: 0.7497 (ttm) cc_final: 0.7231 (ttt) REVERT: D 217 GLU cc_start: 0.7425 (pt0) cc_final: 0.7097 (pt0) REVERT: D 243 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7263 (p0) REVERT: D 360 GLU cc_start: 0.8361 (tp30) cc_final: 0.7709 (tp30) REVERT: D 411 GLN cc_start: 0.7469 (pp30) cc_final: 0.6860 (pp30) REVERT: D 456 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7120 (mtp) REVERT: D 742 GLN cc_start: 0.8283 (mp10) cc_final: 0.8008 (mp10) REVERT: D 953 ASP cc_start: 0.8679 (m-30) cc_final: 0.8437 (m-30) outliers start: 138 outliers final: 103 residues processed: 564 average time/residue: 0.4194 time to fit residues: 390.6575 Evaluate side-chains 562 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 451 time to evaluate : 3.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 762 ASP Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 12 CYS Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 762 ASP Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 838 ASN Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 696 VAL Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 801 ASN Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 839 THR Chi-restraints excluded: chain D residue 848 SER Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 388 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 293 optimal weight: 4.9990 chunk 227 optimal weight: 0.5980 chunk 338 optimal weight: 0.0980 chunk 224 optimal weight: 9.9990 chunk 400 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 185 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS B 149 HIS C 149 HIS D 149 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 33408 Z= 0.161 Angle : 0.557 9.443 45464 Z= 0.280 Chirality : 0.043 0.182 4948 Planarity : 0.003 0.044 5996 Dihedral : 4.318 23.655 4584 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.17 % Allowed : 19.81 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 4144 helix: 1.92 (0.16), residues: 1128 sheet: -0.17 (0.18), residues: 920 loop : -2.11 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 608 HIS 0.004 0.001 HIS C 598 PHE 0.012 0.001 PHE D 853 TYR 0.012 0.001 TYR D 225 ARG 0.005 0.000 ARG B 713 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 518 time to evaluate : 4.148 Fit side-chains REVERT: A 16 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7651 (mpp) REVERT: A 116 TYR cc_start: 0.9264 (m-80) cc_final: 0.9029 (m-80) REVERT: A 157 GLU cc_start: 0.8154 (tt0) cc_final: 0.7903 (tt0) REVERT: A 192 MET cc_start: 0.7377 (ttm) cc_final: 0.7160 (ttt) REVERT: A 217 GLU cc_start: 0.7371 (pt0) cc_final: 0.7067 (pt0) REVERT: A 305 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: A 411 GLN cc_start: 0.7264 (pp30) cc_final: 0.6681 (pp30) REVERT: A 453 ARG cc_start: 0.8438 (tmm-80) cc_final: 0.8095 (ttm170) REVERT: A 456 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7085 (mtp) REVERT: A 939 MET cc_start: 0.8611 (mmp) cc_final: 0.8345 (mmp) REVERT: A 1002 GLU cc_start: 0.7990 (pm20) cc_final: 0.7699 (pm20) REVERT: B 116 TYR cc_start: 0.9266 (m-80) cc_final: 0.9014 (m-80) REVERT: B 157 GLU cc_start: 0.8162 (tt0) cc_final: 0.7947 (tt0) REVERT: B 192 MET cc_start: 0.7376 (ttm) cc_final: 0.7159 (ttt) REVERT: B 217 GLU cc_start: 0.7341 (pt0) cc_final: 0.7005 (pt0) REVERT: B 360 GLU cc_start: 0.8131 (tp30) cc_final: 0.7500 (tp30) REVERT: B 411 GLN cc_start: 0.7272 (pp30) cc_final: 0.6696 (pp30) REVERT: B 456 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7064 (mtp) REVERT: B 939 MET cc_start: 0.8608 (mmp) cc_final: 0.8357 (mmp) REVERT: C 16 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7665 (mpp) REVERT: C 116 TYR cc_start: 0.9265 (m-80) cc_final: 0.9025 (m-80) REVERT: C 157 GLU cc_start: 0.8089 (tt0) cc_final: 0.7847 (tt0) REVERT: C 192 MET cc_start: 0.7379 (ttm) cc_final: 0.7160 (ttt) REVERT: C 217 GLU cc_start: 0.7373 (pt0) cc_final: 0.7080 (pt0) REVERT: C 360 GLU cc_start: 0.8144 (tp30) cc_final: 0.7511 (tp30) REVERT: C 411 GLN cc_start: 0.7278 (pp30) cc_final: 0.6700 (pp30) REVERT: C 456 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7073 (mtp) REVERT: C 939 MET cc_start: 0.8603 (mmp) cc_final: 0.8357 (mmp) REVERT: D 16 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7669 (mpp) REVERT: D 116 TYR cc_start: 0.9271 (m-80) cc_final: 0.9021 (m-80) REVERT: D 157 GLU cc_start: 0.8088 (tt0) cc_final: 0.7848 (tt0) REVERT: D 192 MET cc_start: 0.7377 (ttm) cc_final: 0.7159 (ttt) REVERT: D 217 GLU cc_start: 0.7349 (pt0) cc_final: 0.7046 (pt0) REVERT: D 360 GLU cc_start: 0.8127 (tp30) cc_final: 0.7520 (tp30) REVERT: D 411 GLN cc_start: 0.7262 (pp30) cc_final: 0.6682 (pp30) REVERT: D 456 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7087 (mtp) outliers start: 108 outliers final: 72 residues processed: 573 average time/residue: 0.4267 time to fit residues: 403.7197 Evaluate side-chains 572 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 492 time to evaluate : 3.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 762 ASP Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 762 ASP Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 696 VAL Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 801 ASN Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 839 THR Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 248 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 239 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 chunk 254 optimal weight: 0.0770 chunk 273 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 315 optimal weight: 6.9990 overall best weight: 2.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 838 ASN B 149 HIS B 838 ASN C 149 HIS C 838 ASN D 149 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33408 Z= 0.245 Angle : 0.578 8.139 45464 Z= 0.292 Chirality : 0.044 0.256 4948 Planarity : 0.004 0.045 5996 Dihedral : 4.373 23.827 4584 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.25 % Allowed : 20.19 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.13), residues: 4144 helix: 1.91 (0.16), residues: 1128 sheet: -0.46 (0.17), residues: 984 loop : -2.14 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 407 HIS 0.005 0.001 HIS C 598 PHE 0.014 0.001 PHE A 853 TYR 0.014 0.001 TYR D 225 ARG 0.008 0.000 ARG C 713 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 471 time to evaluate : 4.216 Fit side-chains REVERT: A 7 GLN cc_start: 0.7875 (tt0) cc_final: 0.7486 (mm110) REVERT: A 16 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7667 (mpp) REVERT: A 116 TYR cc_start: 0.9279 (m-80) cc_final: 0.9067 (m-80) REVERT: A 157 GLU cc_start: 0.8179 (tt0) cc_final: 0.7943 (tt0) REVERT: A 217 GLU cc_start: 0.7360 (pt0) cc_final: 0.7067 (pt0) REVERT: A 243 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.6985 (p0) REVERT: A 411 GLN cc_start: 0.7449 (pp30) cc_final: 0.6860 (pp30) REVERT: A 453 ARG cc_start: 0.8477 (tmm-80) cc_final: 0.8130 (ttm170) REVERT: A 456 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7080 (mtp) REVERT: A 584 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: A 953 ASP cc_start: 0.8659 (m-30) cc_final: 0.8437 (m-30) REVERT: A 1002 GLU cc_start: 0.8117 (pm20) cc_final: 0.7865 (pm20) REVERT: B 16 MET cc_start: 0.8192 (mpp) cc_final: 0.7719 (mpp) REVERT: B 157 GLU cc_start: 0.8190 (tt0) cc_final: 0.7978 (tt0) REVERT: B 217 GLU cc_start: 0.7345 (pt0) cc_final: 0.7053 (pt0) REVERT: B 360 GLU cc_start: 0.8293 (tp30) cc_final: 0.7680 (tp30) REVERT: B 411 GLN cc_start: 0.7456 (pp30) cc_final: 0.6868 (pp30) REVERT: B 456 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7069 (mtp) REVERT: B 953 ASP cc_start: 0.8667 (m-30) cc_final: 0.8442 (m-30) REVERT: C 16 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7687 (mpp) REVERT: C 116 TYR cc_start: 0.9273 (m-80) cc_final: 0.9066 (m-80) REVERT: C 217 GLU cc_start: 0.7368 (pt0) cc_final: 0.7066 (pt0) REVERT: C 360 GLU cc_start: 0.8304 (tp30) cc_final: 0.7691 (tp30) REVERT: C 411 GLN cc_start: 0.7457 (pp30) cc_final: 0.6863 (pp30) REVERT: C 456 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7074 (mtp) REVERT: C 953 ASP cc_start: 0.8673 (m-30) cc_final: 0.8449 (m-30) REVERT: D 16 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7656 (mpp) REVERT: D 116 TYR cc_start: 0.9279 (m-80) cc_final: 0.9056 (m-80) REVERT: D 157 GLU cc_start: 0.8164 (tt0) cc_final: 0.7940 (tt0) REVERT: D 192 MET cc_start: 0.7441 (ttm) cc_final: 0.7229 (ttt) REVERT: D 217 GLU cc_start: 0.7325 (pt0) cc_final: 0.7010 (pt0) REVERT: D 243 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7226 (p0) REVERT: D 360 GLU cc_start: 0.8294 (tp30) cc_final: 0.7683 (tp30) REVERT: D 411 GLN cc_start: 0.7444 (pp30) cc_final: 0.6853 (pp30) REVERT: D 456 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7058 (mtp) REVERT: D 488 MET cc_start: 0.9119 (ptp) cc_final: 0.8910 (mtm) REVERT: D 742 GLN cc_start: 0.7915 (mp10) cc_final: 0.7324 (mp10) REVERT: D 953 ASP cc_start: 0.8661 (m-30) cc_final: 0.8433 (m-30) outliers start: 111 outliers final: 81 residues processed: 536 average time/residue: 0.4128 time to fit residues: 367.2595 Evaluate side-chains 557 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 466 time to evaluate : 4.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 762 ASP Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 762 ASP Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 801 ASN Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 839 THR Chi-restraints excluded: chain D residue 848 SER Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 364 optimal weight: 0.3980 chunk 384 optimal weight: 7.9990 chunk 350 optimal weight: 3.9990 chunk 373 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 293 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 337 optimal weight: 1.9990 chunk 353 optimal weight: 0.9990 chunk 372 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS B 149 HIS C 149 HIS D 149 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33408 Z= 0.184 Angle : 0.562 7.863 45464 Z= 0.283 Chirality : 0.043 0.247 4948 Planarity : 0.003 0.044 5996 Dihedral : 4.300 24.038 4584 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.34 % Allowed : 20.40 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4144 helix: 1.92 (0.16), residues: 1128 sheet: -0.15 (0.18), residues: 920 loop : -2.16 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 407 HIS 0.004 0.001 HIS A 598 PHE 0.013 0.001 PHE A 853 TYR 0.012 0.001 TYR D 225 ARG 0.007 0.000 ARG B 713 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 496 time to evaluate : 4.151 Fit side-chains REVERT: A 7 GLN cc_start: 0.7838 (tt0) cc_final: 0.7369 (mm-40) REVERT: A 16 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7671 (mpp) REVERT: A 116 TYR cc_start: 0.9262 (m-80) cc_final: 0.9049 (m-80) REVERT: A 157 GLU cc_start: 0.8129 (tt0) cc_final: 0.7873 (tt0) REVERT: A 217 GLU cc_start: 0.7311 (pt0) cc_final: 0.7019 (pt0) REVERT: A 411 GLN cc_start: 0.7376 (pp30) cc_final: 0.6778 (pp30) REVERT: A 453 ARG cc_start: 0.8437 (tmm-80) cc_final: 0.8097 (ttm170) REVERT: A 456 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7059 (mtp) REVERT: A 584 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: A 939 MET cc_start: 0.8637 (mmp) cc_final: 0.8384 (mmp) REVERT: A 953 ASP cc_start: 0.8650 (m-30) cc_final: 0.8430 (m-30) REVERT: A 1002 GLU cc_start: 0.8097 (pm20) cc_final: 0.7894 (pm20) REVERT: B 16 MET cc_start: 0.8197 (mpp) cc_final: 0.7799 (mpp) REVERT: B 157 GLU cc_start: 0.8147 (tt0) cc_final: 0.7916 (tt0) REVERT: B 217 GLU cc_start: 0.7293 (pt0) cc_final: 0.7007 (pt0) REVERT: B 243 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6953 (p0) REVERT: B 360 GLU cc_start: 0.8199 (tp30) cc_final: 0.7567 (tp30) REVERT: B 411 GLN cc_start: 0.7377 (pp30) cc_final: 0.6772 (pp30) REVERT: B 456 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7051 (mtp) REVERT: B 584 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: B 939 MET cc_start: 0.8630 (mmp) cc_final: 0.8383 (mmp) REVERT: B 953 ASP cc_start: 0.8655 (m-30) cc_final: 0.8433 (m-30) REVERT: C 16 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7664 (mpp) REVERT: C 116 TYR cc_start: 0.9254 (m-80) cc_final: 0.9047 (m-80) REVERT: C 217 GLU cc_start: 0.7305 (pt0) cc_final: 0.7009 (pt0) REVERT: C 243 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.6956 (p0) REVERT: C 360 GLU cc_start: 0.8211 (tp30) cc_final: 0.7581 (tp30) REVERT: C 411 GLN cc_start: 0.7378 (pp30) cc_final: 0.6769 (pp30) REVERT: C 456 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7053 (mtp) REVERT: C 584 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: C 939 MET cc_start: 0.8628 (mmp) cc_final: 0.8386 (mmp) REVERT: C 953 ASP cc_start: 0.8658 (m-30) cc_final: 0.8436 (m-30) REVERT: D 16 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7672 (mpp) REVERT: D 116 TYR cc_start: 0.9264 (m-80) cc_final: 0.9043 (m-80) REVERT: D 157 GLU cc_start: 0.8145 (tt0) cc_final: 0.7914 (tt0) REVERT: D 217 GLU cc_start: 0.7291 (pt0) cc_final: 0.6996 (pt0) REVERT: D 360 GLU cc_start: 0.8203 (tp30) cc_final: 0.7599 (tp30) REVERT: D 411 GLN cc_start: 0.7365 (pp30) cc_final: 0.6760 (pp30) REVERT: D 456 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7058 (mtp) REVERT: D 584 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: D 742 GLN cc_start: 0.7885 (mp10) cc_final: 0.7327 (mp10) REVERT: D 953 ASP cc_start: 0.8653 (m-30) cc_final: 0.8430 (m-30) outliers start: 114 outliers final: 80 residues processed: 562 average time/residue: 0.4162 time to fit residues: 385.5484 Evaluate side-chains 578 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 485 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 762 ASP Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 762 ASP Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 801 ASN Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 839 THR Chi-restraints excluded: chain D residue 848 SER Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 245 optimal weight: 0.9990 chunk 395 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 274 optimal weight: 0.7980 chunk 414 optimal weight: 0.0970 chunk 381 optimal weight: 7.9990 chunk 330 optimal weight: 0.0980 chunk 34 optimal weight: 0.0020 chunk 254 optimal weight: 0.7980 chunk 202 optimal weight: 8.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 365 GLN B 149 HIS C 149 HIS D 149 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33408 Z= 0.152 Angle : 0.572 9.542 45464 Z= 0.282 Chirality : 0.043 0.239 4948 Planarity : 0.003 0.043 5996 Dihedral : 4.158 22.918 4584 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.17 % Allowed : 21.89 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4144 helix: 1.87 (0.16), residues: 1144 sheet: 0.08 (0.19), residues: 884 loop : -2.19 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 283 HIS 0.004 0.001 HIS A 598 PHE 0.013 0.001 PHE D 853 TYR 0.010 0.001 TYR A 225 ARG 0.008 0.000 ARG A 888 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 554 time to evaluate : 4.019 Fit side-chains REVERT: A 16 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7711 (mpp) REVERT: A 157 GLU cc_start: 0.8055 (tt0) cc_final: 0.7467 (tm-30) REVERT: A 192 MET cc_start: 0.7219 (ttm) cc_final: 0.6964 (ttt) REVERT: A 217 GLU cc_start: 0.7259 (pt0) cc_final: 0.6998 (pt0) REVERT: A 411 GLN cc_start: 0.7236 (pp30) cc_final: 0.6686 (pp30) REVERT: A 456 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7015 (mtp) REVERT: A 939 MET cc_start: 0.8572 (mmp) cc_final: 0.8327 (mmp) REVERT: A 1002 GLU cc_start: 0.7994 (pm20) cc_final: 0.7726 (pm20) REVERT: B 16 MET cc_start: 0.8158 (mpp) cc_final: 0.7784 (mpp) REVERT: B 157 GLU cc_start: 0.8153 (tt0) cc_final: 0.7911 (tt0) REVERT: B 192 MET cc_start: 0.7223 (ttm) cc_final: 0.6973 (ttt) REVERT: B 217 GLU cc_start: 0.7236 (pt0) cc_final: 0.6984 (pt0) REVERT: B 243 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6956 (p0) REVERT: B 360 GLU cc_start: 0.8019 (tp30) cc_final: 0.7431 (tp30) REVERT: B 411 GLN cc_start: 0.7242 (pp30) cc_final: 0.6683 (pp30) REVERT: B 456 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7017 (mtp) REVERT: B 584 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: B 801 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8349 (m110) REVERT: B 832 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7789 (mm-30) REVERT: B 939 MET cc_start: 0.8564 (mmp) cc_final: 0.8324 (mmp) REVERT: C 16 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7681 (mpp) REVERT: C 116 TYR cc_start: 0.9220 (m-80) cc_final: 0.8966 (m-80) REVERT: C 157 GLU cc_start: 0.8038 (tt0) cc_final: 0.7428 (tm-30) REVERT: C 192 MET cc_start: 0.7224 (ttm) cc_final: 0.6976 (ttt) REVERT: C 217 GLU cc_start: 0.7258 (pt0) cc_final: 0.6904 (pt0) REVERT: C 243 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6952 (p0) REVERT: C 360 GLU cc_start: 0.8032 (tp30) cc_final: 0.7446 (tp30) REVERT: C 411 GLN cc_start: 0.7242 (pp30) cc_final: 0.6671 (pp30) REVERT: C 456 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7000 (mtp) REVERT: C 584 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: C 801 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8364 (m110) REVERT: C 832 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7775 (mm-30) REVERT: C 939 MET cc_start: 0.8564 (mmp) cc_final: 0.8331 (mmp) REVERT: D 16 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7708 (mpp) REVERT: D 116 TYR cc_start: 0.9218 (m-80) cc_final: 0.8959 (m-80) REVERT: D 157 GLU cc_start: 0.8106 (tt0) cc_final: 0.7398 (tm-30) REVERT: D 217 GLU cc_start: 0.7198 (pt0) cc_final: 0.6947 (pt0) REVERT: D 360 GLU cc_start: 0.8021 (tp30) cc_final: 0.7435 (tp30) REVERT: D 411 GLN cc_start: 0.7227 (pp30) cc_final: 0.6672 (pp30) REVERT: D 456 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7039 (mtp) REVERT: D 584 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8171 (mp0) outliers start: 74 outliers final: 53 residues processed: 594 average time/residue: 0.4130 time to fit residues: 406.4081 Evaluate side-chains 576 residues out of total 3416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 509 time to evaluate : 4.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 850 THR Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 262 optimal weight: 7.9990 chunk 351 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 330 optimal weight: 7.9990 chunk 138 optimal weight: 0.6980 chunk 339 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS B 149 HIS C 149 HIS D 149 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.110712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.092704 restraints weight = 58801.351| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.17 r_work: 0.2893 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33408 Z= 0.266 Angle : 0.605 8.258 45464 Z= 0.303 Chirality : 0.044 0.280 4948 Planarity : 0.004 0.045 5996 Dihedral : 4.310 24.190 4584 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.52 % Allowed : 21.86 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4144 helix: 1.97 (0.16), residues: 1136 sheet: -0.25 (0.18), residues: 960 loop : -2.17 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 407 HIS 0.005 0.001 HIS C 598 PHE 0.014 0.001 PHE D 163 TYR 0.014 0.001 TYR D 225 ARG 0.008 0.000 ARG D 888 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8104.16 seconds wall clock time: 149 minutes 7.63 seconds (8947.63 seconds total)