Starting phenix.real_space_refine on Thu Oct 10 05:54:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh1_43231/10_2024/8vh1_43231_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh1_43231/10_2024/8vh1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh1_43231/10_2024/8vh1_43231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh1_43231/10_2024/8vh1_43231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh1_43231/10_2024/8vh1_43231_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh1_43231/10_2024/8vh1_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-5477/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: 16.86, per 1000 atoms: 0.37 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: 9.06 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: 3.61 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: 15.35 Time building geometry restraints manager: 11.01 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: 0.00 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.610 Extract box with map and model: 1.390 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 73.740 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.160 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:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.250 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 2.906 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: 0.6720 time to fit residues: 124.1366 Evaluate side-chains 97 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 2.895 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 2.883 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: 0.6468 time to fit residues: 117.9656 Evaluate side-chains 100 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 270 optimal weight: 20.0000 chunk 291 optimal weight: 20.0000 chunk 240 optimal weight: 3.9990 chunk 267 optimal weight: 0.2980 chunk 92 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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** F 611 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23705 Z= 0.319 Angle : 0.649 6.558 32190 Z= 0.357 Chirality : 0.046 0.180 3648 Planarity : 0.004 0.056 4103 Dihedral : 6.652 26.858 3194 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.50 % Favored : 89.26 % Rotamer: Outliers : 0.04 % Allowed : 1.99 % Favored : 97.97 % 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: -2.18 (0.15), residues: 2932 helix: -1.06 (0.26), residues: 366 sheet: -0.68 (0.18), residues: 869 loop : -2.02 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 50 HIS 0.007 0.001 HIS K 35 PHE 0.016 0.002 PHE L 118 TYR 0.018 0.002 TYR K 59 ARG 0.004 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 123 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 2.865 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: K 87 THR cc_start: 0.9038 (m) cc_final: 0.8831 (t) outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.6396 time to fit residues: 124.9138 Evaluate side-chains 103 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 271 optimal weight: 10.0000 chunk 287 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 GLN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 23705 Z= 0.366 Angle : 0.660 6.562 32190 Z= 0.363 Chirality : 0.046 0.162 3648 Planarity : 0.005 0.053 4103 Dihedral : 6.656 29.065 3194 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.11 % Favored : 87.72 % Rotamer: Outliers : 0.04 % Allowed : 2.52 % Favored : 97.44 % 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: -2.31 (0.15), residues: 2932 helix: -1.02 (0.26), residues: 369 sheet: -0.75 (0.18), residues: 863 loop : -2.14 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 50 HIS 0.011 0.002 HIS C 35 PHE 0.017 0.002 PHE L 118 TYR 0.015 0.002 TYR C 59 ARG 0.002 0.000 ARG I 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 114 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 2.893 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: K 48 MET cc_start: 0.8580 (mmm) cc_final: 0.8288 (mmm) REVERT: K 87 THR cc_start: 0.9039 (m) cc_final: 0.8814 (t) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.6159 time to fit residues: 113.2310 Evaluate side-chains 98 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 32 ASN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23705 Z= 0.218 Angle : 0.597 6.241 32190 Z= 0.324 Chirality : 0.044 0.159 3648 Planarity : 0.004 0.051 4103 Dihedral : 6.321 25.795 3194 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.72 % Favored : 90.11 % Rotamer: Outliers : 0.04 % Allowed : 1.30 % Favored : 98.66 % 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: -2.09 (0.15), residues: 2932 helix: -0.74 (0.27), residues: 351 sheet: -0.74 (0.18), residues: 863 loop : -1.93 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP G 50 HIS 0.004 0.001 HIS A 72 PHE 0.017 0.002 PHE L 118 TYR 0.012 0.001 TYR J 586 ARG 0.002 0.000 ARG B 617 *********************** 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 131 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 2.858 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: G 87 THR cc_start: 0.9134 (m) cc_final: 0.8871 (t) REVERT: I 396 MET cc_start: 0.6669 (pmm) cc_final: 0.5546 (mtp) REVERT: K 87 THR cc_start: 0.9014 (m) cc_final: 0.8788 (t) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.6258 time to fit residues: 130.7053 Evaluate side-chains 105 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 8.9990 chunk 258 optimal weight: 0.0470 chunk 56 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 287 optimal weight: 1.9990 chunk 238 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- 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 ** D 32 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23705 Z= 0.306 Angle : 0.621 6.457 32190 Z= 0.338 Chirality : 0.045 0.157 3648 Planarity : 0.004 0.048 4103 Dihedral : 6.313 27.509 3194 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.02 % Favored : 88.85 % Rotamer: Outliers : 0.04 % Allowed : 1.49 % Favored : 98.47 % 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: -0.70 (0.27), residues: 369 sheet: -0.76 (0.18), residues: 863 loop : -2.05 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 50 HIS 0.005 0.001 HIS C 35 PHE 0.016 0.002 PHE L 118 TYR 0.030 0.002 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 fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 3.442 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: E 473 MET cc_start: 0.7831 (pmm) cc_final: 0.7607 (pmm) REVERT: G 87 THR cc_start: 0.9186 (m) cc_final: 0.8912 (t) REVERT: I 396 MET cc_start: 0.6723 (pmm) cc_final: 0.5556 (mtp) REVERT: I 473 MET cc_start: 0.7942 (pmm) cc_final: 0.7728 (pmm) REVERT: K 87 THR cc_start: 0.9026 (m) cc_final: 0.8824 (t) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.6289 time to fit residues: 120.8769 Evaluate side-chains 99 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 209 optimal weight: 0.4980 chunk 162 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 160 optimal weight: 0.0870 chunk 286 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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 D 166 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23705 Z= 0.161 Angle : 0.562 6.487 32190 Z= 0.302 Chirality : 0.044 0.162 3648 Planarity : 0.004 0.045 4103 Dihedral : 5.952 24.683 3194 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.22 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -1.84 (0.15), residues: 2932 helix: -0.29 (0.28), residues: 345 sheet: -0.67 (0.18), residues: 869 loop : -1.76 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 50 HIS 0.003 0.001 HIS I 374 PHE 0.017 0.001 PHE L 118 TYR 0.021 0.001 TYR C 33 ARG 0.020 0.000 ARG E 478 *********************** 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 122 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.897 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: D 185 ASP cc_start: 0.6103 (m-30) cc_final: 0.5360 (t0) REVERT: G 87 THR cc_start: 0.9153 (m) cc_final: 0.8860 (t) REVERT: I 396 MET cc_start: 0.6661 (pmm) cc_final: 0.5518 (mtp) REVERT: I 434 MET cc_start: 0.7728 (ttm) cc_final: 0.7473 (mtp) REVERT: K 87 THR cc_start: 0.9010 (m) cc_final: 0.8798 (t) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.6234 time to fit residues: 122.6228 Evaluate side-chains 103 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 23705 Z= 0.387 Angle : 0.647 6.595 32190 Z= 0.353 Chirality : 0.045 0.167 3648 Planarity : 0.005 0.044 4103 Dihedral : 6.243 26.974 3194 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.43 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: -2.15 (0.15), residues: 2932 helix: -0.58 (0.27), residues: 372 sheet: -0.77 (0.18), residues: 854 loop : -2.04 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 50 HIS 0.006 0.001 HIS I 287 PHE 0.016 0.002 PHE L 118 TYR 0.039 0.002 TYR K 33 ARG 0.008 0.000 ARG E 478 *********************** 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 111 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 3.845 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: G 87 THR cc_start: 0.9161 (m) cc_final: 0.8898 (t) REVERT: I 95 MET cc_start: 0.7792 (ptm) cc_final: 0.7519 (ptm) REVERT: J 535 MET cc_start: 0.3584 (tpt) cc_final: 0.3071 (tpt) REVERT: K 87 THR cc_start: 0.9036 (m) cc_final: 0.8829 (t) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.6827 time to fit residues: 122.6695 Evaluate side-chains 95 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 252 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23705 Z= 0.304 Angle : 0.614 6.708 32190 Z= 0.333 Chirality : 0.045 0.161 3648 Planarity : 0.004 0.045 4103 Dihedral : 6.206 27.106 3194 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.40 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -2.13 (0.15), residues: 2932 helix: -0.51 (0.27), residues: 372 sheet: -0.78 (0.18), residues: 857 loop : -2.03 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 50 HIS 0.005 0.001 HIS I 287 PHE 0.017 0.002 PHE L 118 TYR 0.032 0.002 TYR C 33 ARG 0.009 0.000 ARG E 478 *********************** 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 110 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.931 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: 0.7208 (pmm) cc_final: 0.5288 (mtt) REVERT: F 530 MET cc_start: 0.6836 (mmp) cc_final: 0.6617 (mmp) REVERT: G 87 THR cc_start: 0.9166 (m) cc_final: 0.8894 (t) REVERT: I 95 MET cc_start: 0.7835 (ptm) cc_final: 0.7499 (ptm) REVERT: I 473 MET cc_start: 0.7871 (pmm) cc_final: 0.7645 (pmm) REVERT: J 535 MET cc_start: 0.3460 (tpt) cc_final: 0.2974 (tpt) REVERT: K 87 THR cc_start: 0.9018 (m) cc_final: 0.8804 (t) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.6390 time to fit residues: 111.8087 Evaluate side-chains 97 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 7.9990 chunk 282 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 196 optimal weight: 20.0000 chunk 295 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 144 optimal weight: 30.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 276 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23705 Z= 0.340 Angle : 0.634 8.802 32190 Z= 0.345 Chirality : 0.045 0.157 3648 Planarity : 0.005 0.193 4103 Dihedral : 6.263 29.137 3194 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.94 % Favored : 87.86 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -0.46 (0.27), residues: 366 sheet: -0.86 (0.18), residues: 860 loop : -2.05 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 50 HIS 0.005 0.001 HIS I 287 PHE 0.017 0.002 PHE L 118 TYR 0.032 0.002 TYR C 33 ARG 0.030 0.001 ARG K 210 ********************** 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 109 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.888 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 396 MET cc_start: 0.7204 (pmm) cc_final: 0.5335 (mtt) REVERT: G 87 THR cc_start: 0.9153 (m) cc_final: 0.8892 (t) REVERT: I 95 MET cc_start: 0.7857 (ptm) cc_final: 0.7499 (ptm) REVERT: I 100 MET cc_start: 0.8002 (ptp) cc_final: 0.7727 (ptp) REVERT: J 535 MET cc_start: 0.3494 (tpt) cc_final: 0.3018 (tpt) REVERT: K 87 THR cc_start: 0.9026 (m) cc_final: 0.8815 (t) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.6849 time to fit residues: 119.2819 Evaluate side-chains 92 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 217 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 235 optimal weight: 0.2980 chunk 98 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- 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** F 658 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 = 0.3682 r_free = 0.3682 target = 0.078370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.062860 restraints weight = 265346.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.064742 restraints weight = 127427.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.065876 restraints weight = 77588.964| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23705 Z= 0.221 Angle : 0.577 6.091 32190 Z= 0.312 Chirality : 0.044 0.167 3648 Planarity : 0.004 0.045 4103 Dihedral : 6.015 25.991 3194 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.75 % Favored : 90.04 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % 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: -1.97 (0.15), residues: 2932 helix: -0.17 (0.28), residues: 363 sheet: -0.79 (0.18), residues: 860 loop : -1.90 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 50 HIS 0.004 0.001 HIS K 35 PHE 0.017 0.002 PHE L 118 TYR 0.025 0.001 TYR C 33 ARG 0.007 0.000 ARG E 478 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4937.26 seconds wall clock time: 92 minutes 2.95 seconds (5522.95 seconds total)