Starting phenix.real_space_refine on Tue Jan 14 23:37:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vh1_43231/01_2025/8vh1_43231_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vh1_43231/01_2025/8vh1_43231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vh1_43231/01_2025/8vh1_43231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vh1_43231/01_2025/8vh1_43231.map" model { file = "/net/cci-nas-00/data/ceres_data/8vh1_43231/01_2025/8vh1_43231_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vh1_43231/01_2025/8vh1_43231_neut.cif" } resolution = 4.08 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= 0.006 sd= 0.171 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4992 atoms to isotropic. 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 S 144 5.16 5 C 14589 2.51 5 N 4002 2.21 5 O 4485 1.98 5 H 22827 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 46047 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6945 Classifications: {'peptide': 443} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 421} Chain breaks: 3 Chain: "B" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3287 Classifications: {'peptide': 220} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Chain breaks: 1 Chain: "D" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3197 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 200} Chain: "E" Number of atoms: 6945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6945 Classifications: {'peptide': 443} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 421} Chain breaks: 3 Chain: "F" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3287 Classifications: {'peptide': 220} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Chain breaks: 1 Chain: "H" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3197 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 200} Chain: "I" Number of atoms: 6945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6945 Classifications: {'peptide': 443} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 421} Chain breaks: 4 Chain: "J" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "K" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3287 Classifications: {'peptide': 220} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Chain breaks: 1 Chain: "L" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3197 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 200} Time building chain proxies: 16.02, per 1000 atoms: 0.35 Number of scatterers: 46047 At special positions: 0 Unit cell: (182.52, 172.8, 123.12, 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) S 144 16.00 O 4485 8.00 N 4002 7.00 C 14589 6.00 H 22827 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 499 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 499 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.81 Conformation dependent library (CDL) restraints added in 2.7 seconds 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5574 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 61 sheets defined 15.3% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.523A pdb=" N TRP A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 removed outlier: 3.582A pdb=" N THR A 198 " --> pdb=" O ASN A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 198' Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.707A pdb=" N LYS A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.865A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 4.390A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 573 through 597 removed outlier: 3.839A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 628 through 636 removed outlier: 3.684A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.649A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.570A pdb=" N ASN C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 121 through 128 removed outlier: 3.771A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.871A pdb=" N TRP E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 350 removed outlier: 3.725A pdb=" N LYS E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 473 through 479 removed outlier: 3.865A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 4.319A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 573 through 596 removed outlier: 3.749A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.914A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.640A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN F 652 " --> pdb=" O GLU F 648 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU F 654 " --> pdb=" O GLN F 650 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS F 655 " --> pdb=" O ASN F 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.739A pdb=" N ASN G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 121 through 126 removed outlier: 3.549A pdb=" N LEU H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 Processing helix chain 'I' and resid 99 through 117 removed outlier: 3.890A pdb=" N TRP I 112 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 350 removed outlier: 3.711A pdb=" N LYS I 350 " --> pdb=" O SER I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 473 through 479 removed outlier: 3.901A pdb=" N TRP I 477 " --> pdb=" O MET I 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 543 removed outlier: 3.756A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 596 removed outlier: 3.868A pdb=" N LEU J 592 " --> pdb=" O ARG J 588 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY J 594 " --> pdb=" O GLN J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.938A pdb=" N TRP J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 662 removed outlier: 3.577A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN J 653 " --> pdb=" O SER J 649 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU J 654 " --> pdb=" O GLN J 650 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS J 655 " --> pdb=" O ASN J 651 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU J 660 " --> pdb=" O ASN J 656 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.598A pdb=" N ASN K 31 " --> pdb=" O THR K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 182 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 493 through 497 removed outlier: 3.622A pdb=" N VAL A 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.679A pdb=" N MET A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.725A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.842A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.663A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LYS A 293 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASN A 334 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.130A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.663A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.789A pdb=" N SER C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.775A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR C 33 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.775A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR C 33 " --> pdb=" O ASP C 95 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.812A pdb=" N PHE C 122 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU C 141 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.812A pdb=" N PHE C 122 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU C 141 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 175 " --> pdb=" O GLN C 171 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AB7, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.500A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.691A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.622A pdb=" N SER D 114 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC3, first strand: chain 'E' and resid 493 through 497 removed outlier: 3.603A pdb=" N VAL E 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS F 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AC7, first strand: chain 'E' and resid 158 through 162 Processing sheet with id=AC8, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.789A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.868A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.682A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LYS E 293 " --> pdb=" O ASN E 334 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN E 334 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU E 295 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.079A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.682A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 304 through 309 removed outlier: 4.129A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.934A pdb=" N SER G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.012A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR G 33 " --> pdb=" O ASP G 95 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.012A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR G 33 " --> pdb=" O ASP G 95 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.821A pdb=" N PHE G 122 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU G 141 " --> pdb=" O PHE G 122 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.821A pdb=" N PHE G 122 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU G 141 " --> pdb=" O PHE G 122 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU G 175 " --> pdb=" O GLN G 171 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 151 through 154 Processing sheet with id=AD9, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.527A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.494A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.572A pdb=" N SER H 114 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.572A pdb=" N SER H 114 " --> pdb=" O ASN H 137 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN H 137 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU H 175 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 153 through 154 Processing sheet with id=AE5, first strand: chain 'I' and resid 493 through 497 removed outlier: 3.643A pdb=" N VAL I 38 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS J 604 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.679A pdb=" N MET I 84 " --> pdb=" O THR I 244 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AE8, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AE9, first strand: chain 'I' and resid 158 through 162 Processing sheet with id=AF1, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.757A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 260 through 261 removed outlier: 6.868A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.696A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.248A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS I 293 " --> pdb=" O ASN I 334 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN I 334 " --> pdb=" O LYS I 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 271 through 274 removed outlier: 7.087A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 10.248A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.696A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 304 through 308 Processing sheet with id=AF5, first strand: chain 'K' and resid 6 through 7 removed outlier: 3.823A pdb=" N SER K 7 " --> pdb=" O SER K 21 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER K 21 " --> pdb=" O SER K 7 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.815A pdb=" N TYR K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 11 through 12 removed outlier: 4.210A pdb=" N TYR K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 120 through 122 removed outlier: 3.821A pdb=" N PHE K 122 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU K 141 " --> pdb=" O PHE K 122 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR K 176 " --> pdb=" O ASP K 144 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 120 through 122 removed outlier: 3.821A pdb=" N PHE K 122 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU K 141 " --> pdb=" O PHE K 122 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR K 176 " --> pdb=" O ASP K 144 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU K 175 " --> pdb=" O GLN K 171 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 151 through 154 Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.500A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.754A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.595A pdb=" N SER L 114 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.595A pdb=" N SER L 114 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 153 through 154 869 hydrogen bonds defined for protein. 2247 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: 15.32 Time building geometry restraints manager: 10.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.26: 26637 1.26 - 1.70: 19698 1.70 - 2.13: 195 2.13 - 2.56: 0 2.56 - 2.99: 2 Bond restraints: 46532 Sorted by residual: bond pdb=" C ILE E 309 " pdb=" N GLY E 312 " ideal model delta sigma weight residual 1.330 2.994 -1.664 1.49e-02 4.50e+03 1.25e+04 bond pdb=" C ILE A 309 " pdb=" N GLY A 312 " ideal model delta sigma weight residual 1.330 2.977 -1.647 1.49e-02 4.50e+03 1.22e+04 bond pdb=" CB TRP L 96 " pdb=" CG TRP L 96 " ideal model delta sigma weight residual 1.498 1.431 0.067 3.10e-02 1.04e+03 4.63e+00 bond pdb=" N GLU A 32 " pdb=" CA GLU A 32 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" CB PHE L 118 " pdb=" CG PHE L 118 " ideal model delta sigma weight residual 1.502 1.461 0.041 2.30e-02 1.89e+03 3.10e+00 ... (remaining 46527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.01: 83903 15.01 - 30.02: 1 30.02 - 45.03: 1 45.03 - 60.04: 0 60.04 - 75.05: 4 Bond angle restraints: 83909 Sorted by residual: angle pdb=" O ILE A 309 " pdb=" C ILE A 309 " pdb=" N GLY A 312 " ideal model delta sigma weight residual 122.57 47.52 75.05 1.25e+00 6.40e-01 3.61e+03 angle pdb=" O ILE E 309 " pdb=" C ILE E 309 " pdb=" N GLY E 312 " ideal model delta sigma weight residual 122.57 56.58 65.99 1.25e+00 6.40e-01 2.79e+03 angle pdb=" CA ILE A 309 " pdb=" C ILE A 309 " pdb=" N GLY A 312 " ideal model delta sigma weight residual 116.60 149.03 -32.43 1.45e+00 4.76e-01 5.00e+02 angle pdb=" C ILE A 309 " pdb=" N GLY A 312 " pdb=" H GLY A 312 " ideal model delta sigma weight residual 124.21 58.49 65.72 3.00e+00 1.11e-01 4.80e+02 angle pdb=" C ILE E 309 " pdb=" N GLY E 312 " pdb=" H GLY E 312 " ideal model delta sigma weight residual 124.21 58.93 65.28 3.00e+00 1.11e-01 4.74e+02 ... (remaining 83904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 20013 17.97 - 35.94: 1571 35.94 - 53.92: 410 53.92 - 71.89: 130 71.89 - 89.86: 60 Dihedral angle restraints: 22184 sinusoidal: 12093 harmonic: 10091 Sorted by residual: dihedral pdb=" CA ILE A 309 " pdb=" C ILE A 309 " pdb=" N GLY A 312 " pdb=" CA GLY A 312 " ideal model delta harmonic sigma weight residual 180.00 -131.96 -48.04 0 5.00e+00 4.00e-02 9.23e+01 dihedral pdb=" CA ILE E 309 " pdb=" C ILE E 309 " pdb=" N GLY E 312 " pdb=" CA GLY E 312 " ideal model delta harmonic sigma weight residual 180.00 -144.48 -35.52 0 5.00e+00 4.00e-02 5.05e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 39.27 53.73 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 22181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2169 0.034 - 0.067: 995 0.067 - 0.101: 289 0.101 - 0.135: 176 0.135 - 0.168: 19 Chirality restraints: 3648 Sorted by residual: chirality pdb=" CA VAL D 132 " pdb=" N VAL D 132 " pdb=" C VAL D 132 " pdb=" CB VAL D 132 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA VAL J 518 " pdb=" N VAL J 518 " pdb=" C VAL J 518 " pdb=" CB VAL J 518 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA VAL F 518 " pdb=" N VAL F 518 " pdb=" C VAL F 518 " pdb=" CB VAL F 518 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 3645 not shown) Planarity restraints: 6931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 309 " 0.012 2.00e-02 2.50e+03 2.30e-01 5.28e+02 pdb=" N GLY A 312 " 0.358 2.00e-02 2.50e+03 pdb=" CA GLY A 312 " -0.100 2.00e-02 2.50e+03 pdb=" H GLY A 312 " -0.270 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 309 " 0.017 2.00e-02 2.50e+03 2.27e-01 5.16e+02 pdb=" N GLY E 312 " 0.351 2.00e-02 2.50e+03 pdb=" CA GLY E 312 " -0.098 2.00e-02 2.50e+03 pdb=" H GLY E 312 " -0.271 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 309 " 0.209 2.00e-02 2.50e+03 2.20e-01 4.85e+02 pdb=" C ILE E 309 " -0.371 2.00e-02 2.50e+03 pdb=" O ILE E 309 " 0.084 2.00e-02 2.50e+03 pdb=" N GLY E 312 " 0.077 2.00e-02 2.50e+03 ... (remaining 6928 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 692 2.04 - 2.68: 70294 2.68 - 3.32: 127765 3.32 - 3.96: 162572 3.96 - 4.60: 255458 Nonbonded interactions: 616781 Sorted by model distance: nonbonded pdb=" OE1 GLU I 47 " pdb=" H GLU I 47 " model vdw 1.400 2.450 nonbonded pdb=" H ARG G 3 " pdb=" OG SER G 25 " model vdw 1.480 2.450 nonbonded pdb=" H ARG C 3 " pdb=" OG SER C 25 " model vdw 1.508 2.450 nonbonded pdb=" H ARG K 3 " pdb=" OG SER K 25 " model vdw 1.535 2.450 nonbonded pdb=" OE1 GLU F 648 " pdb="HD21 ASN F 651 " model vdw 1.542 2.450 ... (remaining 616776 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.590 Extract box with map and model: 1.250 Check model and map are aligned: 0.260 Set scattering table: 0.310 Process input model: 72.890 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.016 1.664 23705 Z= 1.196 Angle : 0.956 75.053 32190 Z= 0.642 Chirality : 0.046 0.168 3648 Planarity : 0.007 0.220 4103 Dihedral : 13.536 89.859 8603 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.59 % Favored : 89.14 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -2.16 (0.15), residues: 2928 helix: -1.74 (0.27), residues: 348 sheet: -0.74 (0.17), residues: 888 loop : -1.79 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 148 HIS 0.005 0.001 HIS E 72 PHE 0.023 0.003 PHE L 118 TYR 0.034 0.002 TYR G 176 ARG 0.003 0.001 ARG E 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.6687 time to fit residues: 124.1268 Evaluate side-chains 97 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 10.0000 chunk 225 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 232 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 269 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN B 658 GLN E 334 ASN J 540 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.077085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.061501 restraints weight = 267970.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.063324 restraints weight = 129836.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.064439 restraints weight = 80051.922| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 23705 Z= 0.405 Angle : 0.706 6.856 32190 Z= 0.390 Chirality : 0.047 0.247 3648 Planarity : 0.005 0.060 4103 Dihedral : 6.881 29.340 3194 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.05 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -2.17 (0.15), residues: 2932 helix: -1.16 (0.27), residues: 348 sheet: -0.69 (0.18), residues: 860 loop : -1.96 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 50 HIS 0.006 0.002 HIS H 198 PHE 0.020 0.002 PHE L 118 TYR 0.018 0.002 TYR F 586 ARG 0.004 0.000 ARG I 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.6493 time to fit residues: 118.9141 Evaluate side-chains 100 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 124 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 210 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 611 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.080280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.064685 restraints weight = 264931.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.066549 restraints weight = 127273.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.067663 restraints weight = 78465.682| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23705 Z= 0.163 Angle : 0.588 6.393 32190 Z= 0.318 Chirality : 0.045 0.163 3648 Planarity : 0.004 0.053 4103 Dihedral : 6.206 24.774 3194 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.37 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.15), residues: 2932 helix: -0.76 (0.27), residues: 339 sheet: -0.54 (0.18), residues: 875 loop : -1.66 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP G 50 HIS 0.007 0.001 HIS K 35 PHE 0.016 0.001 PHE L 118 TYR 0.019 0.001 TYR K 59 ARG 0.003 0.000 ARG E 344 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 MET cc_start: 0.7322 (pmm) cc_final: 0.5194 (mtt) REVERT: F 530 MET cc_start: 0.6561 (mmp) cc_final: 0.6307 (mmp) REVERT: H 4 MET cc_start: 0.5877 (ttp) cc_final: 0.5621 (ttp) REVERT: I 396 MET cc_start: 0.7046 (pmm) cc_final: 0.5523 (mtp) REVERT: K 100 LEU cc_start: 0.8865 (mt) cc_final: 0.8657 (pp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.6608 time to fit residues: 141.7523 Evaluate side-chains 100 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 7 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 171 optimal weight: 0.0470 chunk 101 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 GLN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.078056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.062529 restraints weight = 265074.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.064372 restraints weight = 126850.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.065503 restraints weight = 77538.196| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 23705 Z= 0.331 Angle : 0.626 6.546 32190 Z= 0.343 Chirality : 0.045 0.157 3648 Planarity : 0.004 0.051 4103 Dihedral : 6.334 27.489 3194 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.71 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -2.00 (0.15), residues: 2932 helix: -0.75 (0.26), residues: 366 sheet: -0.60 (0.18), residues: 830 loop : -1.89 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 50 HIS 0.010 0.001 HIS C 35 PHE 0.017 0.002 PHE L 118 TYR 0.015 0.002 TYR K 59 ARG 0.003 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.7976 (ttm) cc_final: 0.7680 (mtp) REVERT: A 473 MET cc_start: 0.7332 (pmm) cc_final: 0.7074 (pmm) REVERT: E 473 MET cc_start: 0.7687 (pmm) cc_final: 0.7447 (pmm) REVERT: K 48 MET cc_start: 0.8138 (mmm) cc_final: 0.7810 (mmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.6188 time to fit residues: 118.8280 Evaluate side-chains 97 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 80 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 ASN L 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.078172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.062617 restraints weight = 264833.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.064474 restraints weight = 126616.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.065607 restraints weight = 77260.410| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23705 Z= 0.276 Angle : 0.602 6.263 32190 Z= 0.328 Chirality : 0.045 0.161 3648 Planarity : 0.004 0.049 4103 Dihedral : 6.215 25.937 3194 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.99 % Favored : 89.84 % Rotamer: Outliers : 0.08 % Allowed : 1.80 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -2.00 (0.15), residues: 2932 helix: -0.68 (0.27), residues: 369 sheet: -0.68 (0.18), residues: 854 loop : -1.87 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 50 HIS 0.005 0.001 HIS A 72 PHE 0.016 0.002 PHE L 118 TYR 0.013 0.001 TYR J 586 ARG 0.005 0.000 ARG I 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.7787 (ttm) cc_final: 0.7525 (mtp) REVERT: A 473 MET cc_start: 0.7324 (pmm) cc_final: 0.7119 (pmm) REVERT: D 185 ASP cc_start: 0.6481 (m-30) cc_final: 0.5540 (t0) REVERT: I 396 MET cc_start: 0.7041 (pmm) cc_final: 0.5435 (mtp) REVERT: I 473 MET cc_start: 0.7731 (pmm) cc_final: 0.7520 (pmm) REVERT: J 535 MET cc_start: 0.3877 (tpt) cc_final: 0.3146 (tpt) REVERT: K 48 MET cc_start: 0.8030 (mmm) cc_final: 0.7738 (mmm) outliers start: 2 outliers final: 1 residues processed: 121 average time/residue: 0.6293 time to fit residues: 125.1211 Evaluate side-chains 103 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 94 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.078592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.063030 restraints weight = 264444.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.064907 restraints weight = 126240.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.066046 restraints weight = 76660.058| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23705 Z= 0.234 Angle : 0.584 6.157 32190 Z= 0.317 Chirality : 0.044 0.158 3648 Planarity : 0.004 0.046 4103 Dihedral : 6.056 25.007 3194 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.06 % Favored : 89.80 % Rotamer: Outliers : 0.04 % Allowed : 0.99 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.15), residues: 2932 helix: -0.52 (0.27), residues: 369 sheet: -0.66 (0.18), residues: 860 loop : -1.83 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 50 HIS 0.005 0.001 HIS C 35 PHE 0.016 0.002 PHE L 118 TYR 0.042 0.001 TYR C 33 ARG 0.002 0.000 ARG I 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 185 ASP cc_start: 0.6497 (m-30) cc_final: 0.5543 (t0) REVERT: I 396 MET cc_start: 0.7031 (pmm) cc_final: 0.5420 (mtp) REVERT: I 434 MET cc_start: 0.7841 (ttm) cc_final: 0.7381 (mtp) REVERT: I 473 MET cc_start: 0.7642 (pmm) cc_final: 0.7441 (pmm) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.6060 time to fit residues: 120.0266 Evaluate side-chains 101 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 12 optimal weight: 4.9990 chunk 266 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 ASN L 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.077734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.062221 restraints weight = 267824.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.064071 restraints weight = 128032.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.065195 restraints weight = 78344.913| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23705 Z= 0.320 Angle : 0.614 8.541 32190 Z= 0.334 Chirality : 0.045 0.161 3648 Planarity : 0.004 0.045 4103 Dihedral : 6.154 26.156 3194 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.32 % Favored : 88.51 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -2.03 (0.15), residues: 2932 helix: -0.56 (0.27), residues: 372 sheet: -0.71 (0.18), residues: 860 loop : -1.93 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 50 HIS 0.005 0.001 HIS A 72 PHE 0.016 0.002 PHE L 118 TYR 0.026 0.002 TYR C 33 ARG 0.002 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 473 MET cc_start: 0.7668 (pmm) cc_final: 0.7457 (pmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.6413 time to fit residues: 117.3636 Evaluate side-chains 97 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 82 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 275 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 231 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 284 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.079416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.063959 restraints weight = 262701.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.065885 restraints weight = 124342.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.067022 restraints weight = 75135.630| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23705 Z= 0.155 Angle : 0.555 6.068 32190 Z= 0.298 Chirality : 0.044 0.157 3648 Planarity : 0.004 0.043 4103 Dihedral : 5.815 23.338 3194 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.59 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.15), residues: 2932 helix: -0.23 (0.28), residues: 351 sheet: -0.62 (0.18), residues: 860 loop : -1.69 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 50 HIS 0.003 0.001 HIS K 100D PHE 0.017 0.001 PHE L 118 TYR 0.040 0.001 TYR K 33 ARG 0.002 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 MET cc_start: 0.7433 (pmm) cc_final: 0.5025 (mtt) REVERT: A 473 MET cc_start: 0.7263 (pmm) cc_final: 0.7034 (pmm) REVERT: D 185 ASP cc_start: 0.6437 (m-30) cc_final: 0.5410 (t0) REVERT: K 48 MET cc_start: 0.7866 (mmm) cc_final: 0.7586 (mmm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.6455 time to fit residues: 129.7564 Evaluate side-chains 104 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 76 optimal weight: 6.9990 chunk 247 optimal weight: 0.8980 chunk 222 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.079008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.063522 restraints weight = 263360.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.065424 restraints weight = 125661.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.066573 restraints weight = 76054.273| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23705 Z= 0.209 Angle : 0.558 6.234 32190 Z= 0.301 Chirality : 0.043 0.155 3648 Planarity : 0.004 0.044 4103 Dihedral : 5.741 23.528 3194 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.79 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.15), residues: 2932 helix: -0.07 (0.28), residues: 366 sheet: -0.62 (0.18), residues: 860 loop : -1.68 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 50 HIS 0.006 0.001 HIS K 35 PHE 0.018 0.002 PHE L 118 TYR 0.028 0.001 TYR K 33 ARG 0.002 0.000 ARG E 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 MET cc_start: 0.7475 (pmm) cc_final: 0.5170 (mtt) REVERT: I 95 MET cc_start: 0.7907 (ptm) cc_final: 0.7661 (ptm) REVERT: I 473 MET cc_start: 0.7538 (pmm) cc_final: 0.7335 (pmm) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.6083 time to fit residues: 114.2842 Evaluate side-chains 98 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 191 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.078395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.062855 restraints weight = 265287.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.064733 restraints weight = 125850.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.065907 restraints weight = 76285.826| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23705 Z= 0.270 Angle : 0.586 6.087 32190 Z= 0.317 Chirality : 0.044 0.157 3648 Planarity : 0.004 0.041 4103 Dihedral : 5.839 24.004 3194 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.37 % Favored : 89.46 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.15), residues: 2932 helix: -0.14 (0.27), residues: 372 sheet: -0.65 (0.18), residues: 860 loop : -1.78 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 50 HIS 0.005 0.001 HIS C 35 PHE 0.024 0.002 PHE F 522 TYR 0.032 0.001 TYR K 33 ARG 0.002 0.000 ARG E 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5864 Ramachandran restraints generated. 2932 Oldfield, 0 Emsley, 2932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 MET cc_start: 0.7440 (pmm) cc_final: 0.5182 (mtt) REVERT: A 473 MET cc_start: 0.7348 (pmm) cc_final: 0.7140 (pmm) REVERT: F 530 MET cc_start: 0.7085 (mmp) cc_final: 0.6795 (mmp) REVERT: I 95 MET cc_start: 0.8003 (ptm) cc_final: 0.7563 (ptm) REVERT: I 473 MET cc_start: 0.7589 (pmm) cc_final: 0.7386 (pmm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.6355 time to fit residues: 110.3972 Evaluate side-chains 92 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 653 GLN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.077748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.062209 restraints weight = 266673.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.064080 restraints weight = 128504.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.065211 restraints weight = 78283.789| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 23705 Z= 0.332 Angle : 0.615 6.533 32190 Z= 0.334 Chirality : 0.045 0.159 3648 Planarity : 0.004 0.042 4103 Dihedral : 6.007 24.821 3194 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.63 % Favored : 88.20 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 2932 helix: -0.23 (0.27), residues: 372 sheet: -0.74 (0.18), residues: 860 loop : -1.90 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 50 HIS 0.006 0.001 HIS I 287 PHE 0.018 0.002 PHE F 522 TYR 0.029 0.002 TYR K 33 ARG 0.004 0.000 ARG C 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7846.35 seconds wall clock time: 136 minutes 44.29 seconds (8204.29 seconds total)