Starting phenix.real_space_refine on Sun Feb 18 23:42:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8q_12089/02_2024/7b8q_12089.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8q_12089/02_2024/7b8q_12089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8q_12089/02_2024/7b8q_12089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8q_12089/02_2024/7b8q_12089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8q_12089/02_2024/7b8q_12089.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8q_12089/02_2024/7b8q_12089.pdb" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 14987 2.51 5 N 3770 2.21 5 O 4286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "A PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ASP 739": "OD1" <-> "OD2" Residue "A ARG 771": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 825": "OD1" <-> "OD2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A GLU 861": "OE1" <-> "OE2" Residue "A PHE 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ASP 189": "OD1" <-> "OD2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B ASP 597": "OD1" <-> "OD2" Residue "B ASP 600": "OD1" <-> "OD2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 678": "OD1" <-> "OD2" Residue "B TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 723": "OD1" <-> "OD2" Residue "B PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "B TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 836": "OE1" <-> "OE2" Residue "B TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 857": "OE1" <-> "OE2" Residue "B PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 945": "OE1" <-> "OE2" Residue "B GLU 952": "OE1" <-> "OE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 407": "OD1" <-> "OD2" Residue "C ASP 429": "OD1" <-> "OD2" Residue "C PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 518": "OD1" <-> "OD2" Residue "C PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 582": "OE1" <-> "OE2" Residue "C ASP 597": "OD1" <-> "OD2" Residue "C ASP 600": "OD1" <-> "OD2" Residue "C PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 678": "OD1" <-> "OD2" Residue "C TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 723": "OD1" <-> "OD2" Residue "C PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "C GLU 767": "OE1" <-> "OE2" Residue "C TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 836": "OE1" <-> "OE2" Residue "C TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 857": "OE1" <-> "OE2" Residue "C PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 945": "OE1" <-> "OE2" Residue "C GLU 952": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23178 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7710 Classifications: {'peptide': 1011} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 964} Chain breaks: 2 Chain: "B" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7734 Classifications: {'peptide': 1015} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 968} Chain breaks: 1 Chain: "C" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7734 Classifications: {'peptide': 1015} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 968} Chain breaks: 1 Time building chain proxies: 11.83, per 1000 atoms: 0.51 Number of scatterers: 23178 At special positions: 0 Unit cell: (118.65, 113.4, 139.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 4286 8.00 N 3770 7.00 C 14987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.30 Conformation dependent library (CDL) restraints added in 4.4 seconds 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5670 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 23 sheets defined 59.7% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.513A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.701A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.572A pdb=" N ALA A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.691A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.817A pdb=" N VAL A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 265' Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 329 through 360 Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.716A pdb=" N THR A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 386 Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 423 removed outlier: 4.510A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 5.483A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 460 through 496 removed outlier: 3.523A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 512 through 533 removed outlier: 3.973A pdb=" N SER A 516 " --> pdb=" O TRP A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 555 Processing helix chain 'A' and resid 580 through 597 removed outlier: 4.460A pdb=" N ASP A 597 " --> pdb=" O ASN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 removed outlier: 3.763A pdb=" N ARG A 632 " --> pdb=" O PHE A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 648 Processing helix chain 'A' and resid 683 through 700 Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 771 Processing helix chain 'A' and resid 774 through 780 Processing helix chain 'A' and resid 791 through 794 Processing helix chain 'A' and resid 827 through 840 removed outlier: 3.617A pdb=" N ALA A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 860 removed outlier: 3.631A pdb=" N LYS A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 removed outlier: 4.363A pdb=" N PHE A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 894 removed outlier: 4.139A pdb=" N SER A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 892 " --> pdb=" O ILE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 911 removed outlier: 3.666A pdb=" N GLY A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 946 removed outlier: 3.642A pdb=" N GLU A 946 " --> pdb=" O MET A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 982 removed outlier: 4.230A pdb=" N VAL A 955 " --> pdb=" O ILE A 951 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 986 through 1022 removed outlier: 3.660A pdb=" N GLN A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.951A pdb=" N ARG B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 27 removed outlier: 3.613A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.855A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.515A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 150 through 162 removed outlier: 3.568A pdb=" N VAL B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 314 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 329 through 360 Processing helix chain 'B' and resid 361 through 370 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 423 removed outlier: 4.329A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 453 removed outlier: 6.281A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 3.775A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 461 through 496 removed outlier: 4.090A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 512 through 534 removed outlier: 3.768A pdb=" N HIS B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 580 through 595 Processing helix chain 'B' and resid 635 through 646 removed outlier: 3.651A pdb=" N ASP B 642 " --> pdb=" O LYS B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 698 Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 747 removed outlier: 3.634A pdb=" N VAL B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER B 747 " --> pdb=" O THR B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 removed outlier: 4.416A pdb=" N ARG B 771 " --> pdb=" O ALA B 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 768 through 771' Processing helix chain 'B' and resid 773 through 778 removed outlier: 3.971A pdb=" N ILE B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 795 No H-bonds generated for 'chain 'B' and resid 793 through 795' Processing helix chain 'B' and resid 827 through 841 Processing helix chain 'B' and resid 852 through 862 Processing helix chain 'B' and resid 863 through 884 removed outlier: 3.574A pdb=" N LEU B 867 " --> pdb=" O GLN B 863 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 868 " --> pdb=" O MET B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 894 Processing helix chain 'B' and resid 895 through 911 Processing helix chain 'B' and resid 915 through 946 removed outlier: 3.784A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 982 removed outlier: 4.611A pdb=" N ARG B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Proline residue: B 964 - end of helix Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 986 through 1007 removed outlier: 4.168A pdb=" N GLN B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1022 removed outlier: 4.121A pdb=" N VAL B1014 " --> pdb=" O PHE B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.951A pdb=" N ARG C 7 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 27 removed outlier: 3.677A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.854A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.792A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 360 Processing helix chain 'C' and resid 361 through 370 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 423 removed outlier: 4.328A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA C 409 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 453 removed outlier: 6.280A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 3.777A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 461 through 488 removed outlier: 4.090A pdb=" N GLN C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 Processing helix chain 'C' and resid 512 through 534 removed outlier: 3.768A pdb=" N HIS C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 556 Processing helix chain 'C' and resid 580 through 595 Processing helix chain 'C' and resid 635 through 646 removed outlier: 3.651A pdb=" N ASP C 642 " --> pdb=" O LYS C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 698 removed outlier: 4.020A pdb=" N ALA C 686 " --> pdb=" O LEU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 747 removed outlier: 3.597A pdb=" N VAL C 737 " --> pdb=" O LYS C 733 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER C 747 " --> pdb=" O THR C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 771 Processing helix chain 'C' and resid 773 through 778 removed outlier: 3.954A pdb=" N ILE C 777 " --> pdb=" O GLN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 841 Processing helix chain 'C' and resid 852 through 862 Processing helix chain 'C' and resid 863 through 884 removed outlier: 3.575A pdb=" N LEU C 867 " --> pdb=" O GLN C 863 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 868 " --> pdb=" O MET C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 894 Processing helix chain 'C' and resid 895 through 911 Processing helix chain 'C' and resid 915 through 946 removed outlier: 3.784A pdb=" N ILE C 936 " --> pdb=" O ASN C 932 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 982 removed outlier: 4.610A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 986 through 1007 removed outlier: 4.168A pdb=" N GLN C 990 " --> pdb=" O SER C 986 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1022 removed outlier: 4.121A pdb=" N VAL C1014 " --> pdb=" O PHE C1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.496A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.496A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.682A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU A 293 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE A 136 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N LEU A 137 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASP A 328 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.769A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 603 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 605 " --> pdb=" O PHE A 623 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.540A pdb=" N LYS A 182 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLN A 761 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 796 through 804 removed outlier: 8.334A pdb=" N SER B 235 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE A 718 " --> pdb=" O SER B 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 782 through 783 Processing sheet with id=AA8, first strand: chain 'B' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 821 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.623A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.831A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 605 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 572 " --> pdb=" O MET B 656 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.776A pdb=" N LYS B 182 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE B 763 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET B 184 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN B 765 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE B 186 " --> pdb=" O GLN B 765 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AB5, first strand: chain 'B' and resid 715 through 719 Processing sheet with id=AB6, first strand: chain 'B' and resid 781 through 783 Processing sheet with id=AB7, first strand: chain 'C' and resid 127 through 132 removed outlier: 4.678A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 821 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET C 706 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 127 through 132 removed outlier: 4.678A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.622A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.832A pdb=" N ILE C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR C 605 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER C 572 " --> pdb=" O MET C 656 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.777A pdb=" N LYS C 182 " --> pdb=" O GLN C 761 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE C 763 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N MET C 184 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLN C 765 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE C 186 " --> pdb=" O GLN C 765 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 250 through 252 Processing sheet with id=AC4, first strand: chain 'C' and resid 715 through 722 Processing sheet with id=AC5, first strand: chain 'C' and resid 781 through 783 1575 hydrogen bonds defined for protein. 4566 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: 9.72 Time building geometry restraints manager: 11.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3817 1.31 - 1.44: 5659 1.44 - 1.56: 13851 1.56 - 1.69: 4 1.69 - 1.81: 264 Bond restraints: 23595 Sorted by residual: bond pdb=" C GLU A 423 " pdb=" N GLY A 424 " ideal model delta sigma weight residual 1.329 1.404 -0.075 1.09e-02 8.42e+03 4.76e+01 bond pdb=" CA LEU B 198 " pdb=" C LEU B 198 " ideal model delta sigma weight residual 1.526 1.593 -0.068 1.36e-02 5.41e+03 2.50e+01 bond pdb=" N LEU B 720 " pdb=" CA LEU B 720 " ideal model delta sigma weight residual 1.454 1.398 0.056 1.15e-02 7.56e+03 2.40e+01 bond pdb=" CA LEU C 198 " pdb=" C LEU C 198 " ideal model delta sigma weight residual 1.526 1.591 -0.066 1.36e-02 5.41e+03 2.35e+01 bond pdb=" CA VAL B 259 " pdb=" CB VAL B 259 " ideal model delta sigma weight residual 1.533 1.481 0.052 1.13e-02 7.83e+03 2.15e+01 ... (remaining 23590 not shown) Histogram of bond angle deviations from ideal: 96.81 - 104.53: 519 104.53 - 112.25: 12156 112.25 - 119.96: 8616 119.96 - 127.68: 10543 127.68 - 135.40: 170 Bond angle restraints: 32004 Sorted by residual: angle pdb=" N ILE C 750 " pdb=" CA ILE C 750 " pdb=" C ILE C 750 " ideal model delta sigma weight residual 111.67 125.08 -13.41 9.50e-01 1.11e+00 1.99e+02 angle pdb=" N ILE B 750 " pdb=" CA ILE B 750 " pdb=" C ILE B 750 " ideal model delta sigma weight residual 111.67 124.70 -13.03 9.50e-01 1.11e+00 1.88e+02 angle pdb=" N SER A 132 " pdb=" CA SER A 132 " pdb=" C SER A 132 " ideal model delta sigma weight residual 111.52 126.06 -14.54 1.40e+00 5.10e-01 1.08e+02 angle pdb=" N LYS B 226 " pdb=" CA LYS B 226 " pdb=" C LYS B 226 " ideal model delta sigma weight residual 110.24 96.81 13.43 1.47e+00 4.63e-01 8.35e+01 angle pdb=" C GLY A 238 " pdb=" N GLN A 239 " pdb=" CA GLN A 239 " ideal model delta sigma weight residual 123.00 135.40 -12.40 1.38e+00 5.25e-01 8.08e+01 ... (remaining 31999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 12663 17.69 - 35.38: 1281 35.38 - 53.07: 283 53.07 - 70.76: 61 70.76 - 88.45: 20 Dihedral angle restraints: 14308 sinusoidal: 5547 harmonic: 8761 Sorted by residual: dihedral pdb=" CA TYR C 49 " pdb=" C TYR C 49 " pdb=" N PRO C 50 " pdb=" CA PRO C 50 " ideal model delta harmonic sigma weight residual -180.00 -159.24 -20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR B 49 " pdb=" C TYR B 49 " pdb=" N PRO B 50 " pdb=" CA PRO B 50 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C ASN A 248 " pdb=" N ASN A 248 " pdb=" CA ASN A 248 " pdb=" CB ASN A 248 " ideal model delta harmonic sigma weight residual -122.60 -132.82 10.22 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 14305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3470 0.092 - 0.183: 341 0.183 - 0.275: 29 0.275 - 0.367: 4 0.367 - 0.458: 4 Chirality restraints: 3848 Sorted by residual: chirality pdb=" CA SER A 132 " pdb=" N SER A 132 " pdb=" C SER A 132 " pdb=" CB SER A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA ASN A 248 " pdb=" N ASN A 248 " pdb=" C ASN A 248 " pdb=" CB ASN A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CA LYS C 254 " pdb=" N LYS C 254 " pdb=" C LYS C 254 " pdb=" CB LYS C 254 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 3845 not shown) Planarity restraints: 4027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 666 " 0.020 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C LEU A 666 " -0.068 2.00e-02 2.50e+03 pdb=" O LEU A 666 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY A 667 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 561 " 0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO A 562 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 562 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 562 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 35 " -0.061 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO B 36 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " -0.049 5.00e-02 4.00e+02 ... (remaining 4024 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 695 2.70 - 3.25: 24659 3.25 - 3.80: 37121 3.80 - 4.35: 47745 4.35 - 4.90: 80392 Nonbonded interactions: 190612 Sorted by model distance: nonbonded pdb=" O GLU A 654 " pdb=" OE1 GLU A 654 " model vdw 2.150 3.040 nonbonded pdb=" N ASP B 723 " pdb=" O VAL B 795 " model vdw 2.197 2.520 nonbonded pdb=" O PRO C 216 " pdb=" O LEU C 234 " model vdw 2.229 3.040 nonbonded pdb=" O SER A 747 " pdb=" OG SER A 747 " model vdw 2.238 2.440 nonbonded pdb=" O VAL B 212 " pdb=" O GLY B 238 " model vdw 2.324 3.040 ... (remaining 190607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 502 or resid 511 through 1023)) selection = (chain 'B' and (resid 1 through 253 or resid 259 through 1023)) selection = (chain 'C' and (resid 1 through 253 or resid 259 through 1023)) } 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.780 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 63.610 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.167 23595 Z= 0.346 Angle : 1.008 18.491 32004 Z= 0.688 Chirality : 0.057 0.458 3848 Planarity : 0.006 0.097 4027 Dihedral : 15.131 88.451 8638 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.79 % Allowed : 13.39 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.93 (0.14), residues: 3027 helix: -1.04 (0.12), residues: 1660 sheet: -2.72 (0.21), residues: 464 loop : -2.92 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 886 HIS 0.002 0.001 HIS B 360 PHE 0.015 0.001 PHE B 917 TYR 0.016 0.001 TYR B 49 ARG 0.005 0.000 ARG C 724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 923 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 VAL cc_start: 0.8476 (t) cc_final: 0.8254 (p) REVERT: A 477 SER cc_start: 0.8947 (t) cc_final: 0.8638 (m) REVERT: A 563 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7152 (mt-10) REVERT: A 647 MET cc_start: 0.8439 (mmp) cc_final: 0.7818 (mmm) REVERT: A 701 ASN cc_start: 0.7099 (t0) cc_final: 0.5972 (t0) REVERT: A 759 MET cc_start: 0.8389 (mmm) cc_final: 0.7574 (mmt) REVERT: A 848 TYR cc_start: 0.8485 (p90) cc_final: 0.8220 (p90) REVERT: A 926 ILE cc_start: 0.9577 (mm) cc_final: 0.9209 (mm) REVERT: A 943 LEU cc_start: 0.8598 (mt) cc_final: 0.8348 (tp) REVERT: A 987 SER cc_start: 0.8951 (p) cc_final: 0.8723 (m) REVERT: B 44 ASN cc_start: 0.8222 (m-40) cc_final: 0.7894 (m-40) REVERT: B 49 TYR cc_start: 0.8754 (t80) cc_final: 0.8517 (t80) REVERT: B 102 MET cc_start: 0.8321 (mmm) cc_final: 0.8059 (mmm) REVERT: B 106 ASP cc_start: 0.7627 (m-30) cc_final: 0.7352 (m-30) REVERT: B 240 LEU cc_start: 0.8388 (mt) cc_final: 0.8129 (mt) REVERT: B 272 SER cc_start: 0.9298 (p) cc_final: 0.8987 (m) REVERT: B 404 ILE cc_start: 0.7800 (mt) cc_final: 0.7351 (mt) REVERT: B 460 SER cc_start: 0.8620 (m) cc_final: 0.8382 (p) REVERT: B 570 MET cc_start: 0.8313 (mtm) cc_final: 0.8064 (mtm) REVERT: B 574 GLN cc_start: 0.8474 (tp40) cc_final: 0.7821 (tm-30) REVERT: B 604 ASN cc_start: 0.9016 (t0) cc_final: 0.8681 (t0) REVERT: B 727 LEU cc_start: 0.7779 (mt) cc_final: 0.7272 (mt) REVERT: B 848 TYR cc_start: 0.8084 (p90) cc_final: 0.7786 (p90) REVERT: B 919 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7936 (mttp) REVERT: B 922 LEU cc_start: 0.9264 (tp) cc_final: 0.8912 (tt) REVERT: B 962 LEU cc_start: 0.9017 (tp) cc_final: 0.8778 (tp) REVERT: C 44 ASN cc_start: 0.8028 (m-40) cc_final: 0.7726 (m-40) REVERT: C 102 MET cc_start: 0.8355 (mmm) cc_final: 0.7461 (tpp) REVERT: C 185 ARG cc_start: 0.8960 (mmm-85) cc_final: 0.8597 (mmt180) REVERT: C 196 TYR cc_start: 0.7960 (m-80) cc_final: 0.7440 (m-80) REVERT: C 398 MET cc_start: 0.8643 (mtt) cc_final: 0.8431 (mtt) REVERT: C 404 ILE cc_start: 0.9086 (mt) cc_final: 0.8806 (mt) REVERT: C 474 MET cc_start: 0.7875 (mtm) cc_final: 0.7649 (mtm) REVERT: C 524 TYR cc_start: 0.8677 (t80) cc_final: 0.8394 (t80) REVERT: C 545 ILE cc_start: 0.8616 (mt) cc_final: 0.8369 (mt) REVERT: C 604 ASN cc_start: 0.8487 (t0) cc_final: 0.7876 (t0) REVERT: C 697 MET cc_start: 0.7747 (mtp) cc_final: 0.7546 (mtm) REVERT: C 864 MET cc_start: 0.7767 (ptm) cc_final: 0.7541 (tpp) REVERT: C 904 ILE cc_start: 0.8900 (mm) cc_final: 0.8206 (mm) outliers start: 20 outliers final: 1 residues processed: 931 average time/residue: 0.3398 time to fit residues: 489.7846 Evaluate side-chains 534 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 532 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 919 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 6.9990 chunk 229 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 237 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 144 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN A 276 ASN A 604 ASN A 677 GLN A 691 GLN A 709 ASN A 779 ASN B 128 GLN B 228 GLN B 239 GLN B 415 ASN B 574 GLN B 617 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 ASN B 805 GLN B 823 ASN B 863 GLN C 128 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 191 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN C 415 ASN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23595 Z= 0.246 Angle : 0.649 10.329 32004 Z= 0.329 Chirality : 0.042 0.194 3848 Planarity : 0.005 0.058 4027 Dihedral : 4.001 27.002 3183 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.52 % Allowed : 18.53 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.06 (0.15), residues: 3027 helix: 0.50 (0.13), residues: 1685 sheet: -2.30 (0.21), residues: 487 loop : -1.97 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 568 HIS 0.004 0.001 HIS C 342 PHE 0.023 0.002 PHE B 470 TYR 0.019 0.002 TYR C 77 ARG 0.006 0.001 ARG B 758 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 573 time to evaluate : 2.779 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 61 VAL cc_start: 0.8678 (t) cc_final: 0.8333 (p) REVERT: A 112 LYS cc_start: 0.8074 (tptt) cc_final: 0.7782 (tptp) REVERT: A 352 PHE cc_start: 0.8290 (t80) cc_final: 0.7955 (t80) REVERT: A 435 MET cc_start: 0.9429 (mmm) cc_final: 0.9216 (mmt) REVERT: A 477 SER cc_start: 0.8941 (t) cc_final: 0.8603 (m) REVERT: A 549 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8105 (p) REVERT: A 639 MET cc_start: 0.8228 (tpp) cc_final: 0.7832 (mmt) REVERT: A 647 MET cc_start: 0.8302 (mmp) cc_final: 0.7746 (mmm) REVERT: A 695 MET cc_start: 0.8174 (tpp) cc_final: 0.7694 (mmm) REVERT: A 848 TYR cc_start: 0.8550 (p90) cc_final: 0.8252 (p90) REVERT: A 987 SER cc_start: 0.8952 (p) cc_final: 0.8709 (m) REVERT: B 49 TYR cc_start: 0.8819 (t80) cc_final: 0.8583 (t80) REVERT: B 404 ILE cc_start: 0.8313 (mt) cc_final: 0.7868 (mt) REVERT: B 435 MET cc_start: 0.6765 (mmm) cc_final: 0.6535 (mmm) REVERT: B 534 HIS cc_start: 0.6488 (OUTLIER) cc_final: 0.6264 (m170) REVERT: B 656 MET cc_start: 0.8765 (mtp) cc_final: 0.7306 (mtp) REVERT: B 701 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7766 (m-40) REVERT: B 759 MET cc_start: 0.8049 (mmm) cc_final: 0.7779 (mmp) REVERT: B 832 MET cc_start: 0.8690 (mtp) cc_final: 0.8207 (mtp) REVERT: B 962 LEU cc_start: 0.9085 (tp) cc_final: 0.8867 (tp) REVERT: C 102 MET cc_start: 0.8443 (mmm) cc_final: 0.7577 (mpp) REVERT: C 398 MET cc_start: 0.8638 (mtt) cc_final: 0.8422 (mtt) REVERT: C 439 THR cc_start: 0.8167 (t) cc_final: 0.7916 (m) REVERT: C 515 ARG cc_start: 0.8043 (mtt90) cc_final: 0.7816 (ttp80) REVERT: C 524 TYR cc_start: 0.8650 (t80) cc_final: 0.8365 (t80) REVERT: C 545 ILE cc_start: 0.8589 (mt) cc_final: 0.8322 (mt) REVERT: C 595 LEU cc_start: 0.8738 (pp) cc_final: 0.8461 (pp) REVERT: C 604 ASN cc_start: 0.8308 (t0) cc_final: 0.7983 (t0) REVERT: C 694 LEU cc_start: 0.9154 (tt) cc_final: 0.8743 (tp) REVERT: C 706 MET cc_start: 0.6379 (ttt) cc_final: 0.5552 (ttp) REVERT: C 770 SER cc_start: 0.8743 (m) cc_final: 0.8422 (t) outliers start: 115 outliers final: 60 residues processed: 647 average time/residue: 0.3146 time to fit residues: 333.3785 Evaluate side-chains 521 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 458 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 436 LYS Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 512 TRP Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 275 optimal weight: 0.0060 chunk 297 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 221 optimal weight: 4.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS A 618 ASN ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN C 176 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 GLN ** C 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23595 Z= 0.266 Angle : 0.622 9.404 32004 Z= 0.315 Chirality : 0.042 0.220 3848 Planarity : 0.005 0.057 4027 Dihedral : 3.940 17.328 3178 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.91 % Allowed : 20.34 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 3027 helix: 1.00 (0.13), residues: 1688 sheet: -2.03 (0.22), residues: 485 loop : -1.53 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 800 HIS 0.006 0.001 HIS C 342 PHE 0.026 0.002 PHE B 629 TYR 0.021 0.002 TYR C 883 ARG 0.004 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 505 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 VAL cc_start: 0.8784 (t) cc_final: 0.8416 (p) REVERT: A 112 LYS cc_start: 0.8078 (tptt) cc_final: 0.7817 (tptp) REVERT: A 202 ASP cc_start: 0.8014 (t0) cc_final: 0.7569 (t0) REVERT: A 477 SER cc_start: 0.8954 (t) cc_final: 0.8664 (m) REVERT: A 549 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.8040 (p) REVERT: A 575 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8224 (mt) REVERT: A 639 MET cc_start: 0.8243 (tpp) cc_final: 0.7881 (mmt) REVERT: A 647 MET cc_start: 0.8374 (mmp) cc_final: 0.7009 (mmm) REVERT: A 695 MET cc_start: 0.8199 (tpp) cc_final: 0.7825 (mmm) REVERT: A 848 TYR cc_start: 0.8633 (p90) cc_final: 0.8236 (p90) REVERT: A 987 SER cc_start: 0.8856 (p) cc_final: 0.8607 (m) REVERT: B 232 ILE cc_start: 0.9191 (mt) cc_final: 0.8964 (mt) REVERT: B 404 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8029 (mt) REVERT: B 435 MET cc_start: 0.7197 (mmm) cc_final: 0.6737 (mmm) REVERT: B 438 ILE cc_start: 0.8675 (pp) cc_final: 0.8398 (pp) REVERT: B 638 LYS cc_start: 0.9049 (tmtt) cc_final: 0.8419 (tmtt) REVERT: B 656 MET cc_start: 0.8689 (mtp) cc_final: 0.7691 (mtp) REVERT: B 745 MET cc_start: 0.6095 (mmm) cc_final: 0.5749 (mmm) REVERT: B 832 MET cc_start: 0.8680 (mtp) cc_final: 0.8142 (mtp) REVERT: B 864 MET cc_start: 0.8533 (tpp) cc_final: 0.8330 (tpp) REVERT: C 130 GLU cc_start: 0.8079 (pp20) cc_final: 0.7715 (pp20) REVERT: C 398 MET cc_start: 0.8707 (mtt) cc_final: 0.8495 (mtt) REVERT: C 439 THR cc_start: 0.8396 (t) cc_final: 0.8116 (m) REVERT: C 474 MET cc_start: 0.8102 (mtm) cc_final: 0.7727 (mtm) REVERT: C 524 TYR cc_start: 0.8634 (t80) cc_final: 0.8370 (t80) REVERT: C 595 LEU cc_start: 0.8772 (pp) cc_final: 0.8517 (pp) REVERT: C 604 ASN cc_start: 0.8398 (t0) cc_final: 0.7516 (t0) REVERT: C 697 MET cc_start: 0.7960 (ttp) cc_final: 0.7736 (ttp) REVERT: C 1011 PHE cc_start: 0.8934 (m-80) cc_final: 0.8676 (m-80) outliers start: 125 outliers final: 85 residues processed: 589 average time/residue: 0.3196 time to fit residues: 309.2172 Evaluate side-chains 534 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 446 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 436 LYS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 143 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 262 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 805 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23595 Z= 0.190 Angle : 0.581 8.521 32004 Z= 0.293 Chirality : 0.041 0.168 3848 Planarity : 0.004 0.055 4027 Dihedral : 3.856 16.168 3178 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.71 % Allowed : 21.63 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 3027 helix: 1.22 (0.13), residues: 1690 sheet: -1.70 (0.22), residues: 496 loop : -1.07 (0.23), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 556 HIS 0.007 0.001 HIS C 342 PHE 0.020 0.002 PHE B 629 TYR 0.029 0.001 TYR C 883 ARG 0.005 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 512 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8103 (tptt) cc_final: 0.7735 (tptp) REVERT: A 202 ASP cc_start: 0.8028 (t0) cc_final: 0.7823 (t70) REVERT: A 383 MET cc_start: 0.8561 (ttm) cc_final: 0.8259 (mtt) REVERT: A 477 SER cc_start: 0.8864 (t) cc_final: 0.8632 (m) REVERT: A 575 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8221 (mt) REVERT: A 639 MET cc_start: 0.8188 (tpp) cc_final: 0.7866 (mmt) REVERT: A 647 MET cc_start: 0.8360 (mmp) cc_final: 0.6925 (mmm) REVERT: A 695 MET cc_start: 0.8148 (tpp) cc_final: 0.7823 (mmm) REVERT: A 848 TYR cc_start: 0.8601 (p90) cc_final: 0.8198 (p90) REVERT: A 967 MET cc_start: 0.7966 (ttt) cc_final: 0.7410 (ttt) REVERT: A 987 SER cc_start: 0.8791 (p) cc_final: 0.8570 (m) REVERT: B 404 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.7873 (mt) REVERT: B 435 MET cc_start: 0.7459 (mmm) cc_final: 0.7116 (mmm) REVERT: B 438 ILE cc_start: 0.8535 (pp) cc_final: 0.8322 (pp) REVERT: B 638 LYS cc_start: 0.9040 (tmtt) cc_final: 0.8578 (tmtt) REVERT: B 645 SER cc_start: 0.8788 (p) cc_final: 0.8562 (m) REVERT: B 832 MET cc_start: 0.8602 (mtp) cc_final: 0.8302 (mtp) REVERT: B 834 GLU cc_start: 0.8301 (tp30) cc_final: 0.8059 (tm-30) REVERT: B 857 GLU cc_start: 0.8724 (tt0) cc_final: 0.8209 (tt0) REVERT: B 864 MET cc_start: 0.8574 (tpp) cc_final: 0.8361 (tpp) REVERT: B 962 LEU cc_start: 0.9149 (tp) cc_final: 0.8907 (tt) REVERT: C 68 GLU cc_start: 0.8139 (mp0) cc_final: 0.7920 (mp0) REVERT: C 130 GLU cc_start: 0.8168 (pp20) cc_final: 0.7778 (pp20) REVERT: C 346 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: C 439 THR cc_start: 0.8366 (t) cc_final: 0.8153 (m) REVERT: C 474 MET cc_start: 0.7999 (mtm) cc_final: 0.7656 (mtm) REVERT: C 524 TYR cc_start: 0.8618 (t80) cc_final: 0.8332 (t80) REVERT: C 592 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6827 (mm-30) REVERT: C 604 ASN cc_start: 0.8482 (t0) cc_final: 0.7944 (t0) outliers start: 120 outliers final: 80 residues processed: 599 average time/residue: 0.3003 time to fit residues: 295.1708 Evaluate side-chains 534 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 451 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 243 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 249 optimal weight: 0.8980 chunk 202 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS A 598 ASN B 109 ASN B 691 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23595 Z= 0.201 Angle : 0.592 11.165 32004 Z= 0.294 Chirality : 0.041 0.176 3848 Planarity : 0.004 0.053 4027 Dihedral : 3.832 18.477 3178 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.75 % Allowed : 22.77 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 3027 helix: 1.33 (0.13), residues: 1686 sheet: -1.50 (0.23), residues: 494 loop : -0.88 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 556 HIS 0.009 0.001 HIS C 342 PHE 0.028 0.001 PHE B 629 TYR 0.014 0.001 TYR B 49 ARG 0.006 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 477 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8046 (tptt) cc_final: 0.7735 (tptp) REVERT: A 383 MET cc_start: 0.8582 (ttm) cc_final: 0.8301 (mtt) REVERT: A 477 SER cc_start: 0.8862 (t) cc_final: 0.8608 (m) REVERT: A 534 HIS cc_start: 0.6510 (OUTLIER) cc_final: 0.6189 (m90) REVERT: A 575 LEU cc_start: 0.8650 (mm) cc_final: 0.8367 (mp) REVERT: A 647 MET cc_start: 0.8368 (mmp) cc_final: 0.7083 (mmm) REVERT: A 987 SER cc_start: 0.8777 (p) cc_final: 0.8563 (m) REVERT: B 20 ILE cc_start: 0.9238 (mm) cc_final: 0.8949 (mt) REVERT: B 48 THR cc_start: 0.9101 (m) cc_final: 0.8695 (p) REVERT: B 193 LEU cc_start: 0.8251 (mt) cc_final: 0.7967 (mm) REVERT: B 404 ILE cc_start: 0.8449 (mt) cc_final: 0.7919 (mt) REVERT: B 449 LEU cc_start: 0.8927 (mm) cc_final: 0.8650 (mm) REVERT: B 638 LYS cc_start: 0.9096 (tmtt) cc_final: 0.8615 (tmtt) REVERT: B 679 ARG cc_start: 0.7933 (mtt-85) cc_final: 0.7393 (mtt-85) REVERT: B 832 MET cc_start: 0.8707 (mtp) cc_final: 0.8290 (mtp) REVERT: B 857 GLU cc_start: 0.8689 (tt0) cc_final: 0.8390 (tp30) REVERT: C 102 MET cc_start: 0.8473 (mmm) cc_final: 0.7748 (mpp) REVERT: C 346 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: C 439 THR cc_start: 0.8415 (t) cc_final: 0.8180 (m) REVERT: C 474 MET cc_start: 0.7987 (mtm) cc_final: 0.7629 (mtm) REVERT: C 524 TYR cc_start: 0.8593 (t80) cc_final: 0.8330 (t80) REVERT: C 592 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6920 (mm-30) REVERT: C 604 ASN cc_start: 0.8401 (t0) cc_final: 0.7928 (t0) REVERT: C 857 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7655 (tm-30) outliers start: 121 outliers final: 93 residues processed: 568 average time/residue: 0.2985 time to fit residues: 279.7645 Evaluate side-chains 542 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 447 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 0.8980 chunk 263 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 293 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 153 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS B 109 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23595 Z= 0.187 Angle : 0.598 13.113 32004 Z= 0.295 Chirality : 0.041 0.234 3848 Planarity : 0.004 0.051 4027 Dihedral : 3.840 19.359 3178 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.03 % Allowed : 23.52 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 3027 helix: 1.39 (0.13), residues: 1673 sheet: -1.35 (0.23), residues: 496 loop : -0.77 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 556 HIS 0.029 0.002 HIS A 534 PHE 0.027 0.001 PHE C 669 TYR 0.012 0.001 TYR A 524 ARG 0.007 0.000 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 487 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7989 (tptt) cc_final: 0.7665 (tptp) REVERT: A 193 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 383 MET cc_start: 0.8581 (ttm) cc_final: 0.8300 (mtt) REVERT: A 477 SER cc_start: 0.8844 (t) cc_final: 0.8636 (m) REVERT: A 534 HIS cc_start: 0.6616 (m90) cc_final: 0.6399 (m170) REVERT: A 575 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8366 (mp) REVERT: A 647 MET cc_start: 0.8361 (mmp) cc_final: 0.7168 (mmm) REVERT: B 20 ILE cc_start: 0.9256 (mm) cc_final: 0.8964 (mt) REVERT: B 48 THR cc_start: 0.8995 (m) cc_final: 0.8571 (p) REVERT: B 68 GLU cc_start: 0.7617 (mp0) cc_final: 0.7304 (mp0) REVERT: B 114 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8543 (m) REVERT: B 193 LEU cc_start: 0.8270 (mt) cc_final: 0.8059 (mt) REVERT: B 279 ILE cc_start: 0.9334 (mm) cc_final: 0.9124 (mm) REVERT: B 449 LEU cc_start: 0.8958 (mm) cc_final: 0.8750 (mm) REVERT: B 483 LEU cc_start: 0.9050 (tt) cc_final: 0.8753 (tp) REVERT: B 638 LYS cc_start: 0.9110 (tmtt) cc_final: 0.8643 (tmtt) REVERT: B 745 MET cc_start: 0.6271 (mmm) cc_final: 0.6028 (mmm) REVERT: B 832 MET cc_start: 0.8704 (mtp) cc_final: 0.8371 (mtp) REVERT: B 842 LEU cc_start: 0.8933 (mt) cc_final: 0.8709 (mm) REVERT: B 857 GLU cc_start: 0.8646 (tt0) cc_final: 0.8254 (tt0) REVERT: C 102 MET cc_start: 0.8520 (mmm) cc_final: 0.7797 (mpp) REVERT: C 130 GLU cc_start: 0.8357 (pp20) cc_final: 0.7812 (pp20) REVERT: C 346 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: C 433 LYS cc_start: 0.8570 (tttt) cc_final: 0.8229 (tppt) REVERT: C 439 THR cc_start: 0.8278 (t) cc_final: 0.8030 (m) REVERT: C 474 MET cc_start: 0.7968 (mtm) cc_final: 0.7645 (mtm) REVERT: C 524 TYR cc_start: 0.8608 (t80) cc_final: 0.8342 (t80) REVERT: C 592 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6958 (tp30) REVERT: C 857 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7561 (tm-30) outliers start: 128 outliers final: 93 residues processed: 578 average time/residue: 0.2945 time to fit residues: 280.8647 Evaluate side-chains 541 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 444 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 512 TRP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 167 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 246 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 292 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 chunk 178 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 292 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23595 Z= 0.188 Angle : 0.604 9.577 32004 Z= 0.298 Chirality : 0.041 0.263 3848 Planarity : 0.004 0.048 4027 Dihedral : 3.838 19.629 3178 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.26 % Allowed : 24.42 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 3027 helix: 1.39 (0.13), residues: 1685 sheet: -1.25 (0.24), residues: 488 loop : -0.70 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 556 HIS 0.008 0.001 HIS C 342 PHE 0.027 0.001 PHE C 669 TYR 0.012 0.001 TYR A 524 ARG 0.007 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 473 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7971 (tptt) cc_final: 0.7611 (tptp) REVERT: A 193 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7997 (mp) REVERT: A 383 MET cc_start: 0.8530 (ttm) cc_final: 0.8292 (mtt) REVERT: A 477 SER cc_start: 0.8827 (t) cc_final: 0.8502 (m) REVERT: A 534 HIS cc_start: 0.6570 (m90) cc_final: 0.6351 (m170) REVERT: A 575 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 647 MET cc_start: 0.8358 (mmp) cc_final: 0.7245 (mmm) REVERT: A 948 MET cc_start: 0.7827 (tmm) cc_final: 0.7351 (ttt) REVERT: B 20 ILE cc_start: 0.9277 (mm) cc_final: 0.8975 (mt) REVERT: B 68 GLU cc_start: 0.7576 (mp0) cc_final: 0.7166 (mp0) REVERT: B 114 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8562 (m) REVERT: B 193 LEU cc_start: 0.8142 (mt) cc_final: 0.7828 (mm) REVERT: B 279 ILE cc_start: 0.9372 (mm) cc_final: 0.9158 (mm) REVERT: B 483 LEU cc_start: 0.9031 (tt) cc_final: 0.8747 (tp) REVERT: B 638 LYS cc_start: 0.9100 (tmtt) cc_final: 0.8638 (tmtt) REVERT: B 695 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8858 (mmm) REVERT: B 832 MET cc_start: 0.8683 (mtp) cc_final: 0.8322 (mtp) REVERT: B 857 GLU cc_start: 0.8580 (tt0) cc_final: 0.8221 (tt0) REVERT: B 942 MET cc_start: 0.8077 (mtt) cc_final: 0.7702 (mtt) REVERT: B 998 PHE cc_start: 0.8811 (t80) cc_final: 0.8591 (t80) REVERT: C 102 MET cc_start: 0.8496 (mmm) cc_final: 0.7699 (mpp) REVERT: C 130 GLU cc_start: 0.8343 (pp20) cc_final: 0.7801 (pp20) REVERT: C 346 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: C 405 ILE cc_start: 0.8986 (mp) cc_final: 0.8754 (mp) REVERT: C 433 LYS cc_start: 0.8557 (tttt) cc_final: 0.8236 (tppt) REVERT: C 439 THR cc_start: 0.8306 (t) cc_final: 0.8040 (m) REVERT: C 474 MET cc_start: 0.8014 (mtm) cc_final: 0.7639 (mtm) REVERT: C 524 TYR cc_start: 0.8605 (t80) cc_final: 0.8325 (t80) REVERT: C 857 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7429 (tm-30) REVERT: C 952 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6914 (tm-30) REVERT: C 1018 PHE cc_start: 0.8453 (t80) cc_final: 0.8228 (t80) outliers start: 134 outliers final: 97 residues processed: 564 average time/residue: 0.3024 time to fit residues: 282.0256 Evaluate side-chains 544 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 442 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 749 TYR Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 512 TRP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 180 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 229 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23595 Z= 0.186 Angle : 0.612 11.445 32004 Z= 0.299 Chirality : 0.041 0.200 3848 Planarity : 0.004 0.046 4027 Dihedral : 3.834 20.149 3178 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.40 % Allowed : 25.17 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 3027 helix: 1.43 (0.13), residues: 1687 sheet: -1.09 (0.24), residues: 476 loop : -0.64 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 556 HIS 0.008 0.001 HIS C 342 PHE 0.028 0.001 PHE C 669 TYR 0.011 0.001 TYR A 524 ARG 0.004 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 479 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7828 (tm-30) REVERT: A 112 LYS cc_start: 0.7841 (tptt) cc_final: 0.7619 (tptp) REVERT: A 193 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7960 (mp) REVERT: A 355 MET cc_start: 0.8098 (tpp) cc_final: 0.7796 (tpp) REVERT: A 383 MET cc_start: 0.8501 (ttm) cc_final: 0.8253 (mtt) REVERT: A 477 SER cc_start: 0.8761 (t) cc_final: 0.8480 (m) REVERT: A 639 MET cc_start: 0.8340 (tpp) cc_final: 0.8002 (mmt) REVERT: A 647 MET cc_start: 0.8371 (mmp) cc_final: 0.7288 (mmm) REVERT: A 848 TYR cc_start: 0.8406 (p90) cc_final: 0.8168 (p90) REVERT: A 948 MET cc_start: 0.7707 (tmm) cc_final: 0.7386 (ttt) REVERT: B 20 ILE cc_start: 0.9306 (mm) cc_final: 0.8999 (mt) REVERT: B 68 GLU cc_start: 0.7546 (mp0) cc_final: 0.7211 (mp0) REVERT: B 91 THR cc_start: 0.9077 (m) cc_final: 0.8663 (p) REVERT: B 114 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8506 (m) REVERT: B 193 LEU cc_start: 0.8151 (mt) cc_final: 0.7773 (mm) REVERT: B 279 ILE cc_start: 0.9372 (mm) cc_final: 0.9160 (mm) REVERT: B 449 LEU cc_start: 0.8948 (mm) cc_final: 0.8650 (mm) REVERT: B 483 LEU cc_start: 0.9020 (tt) cc_final: 0.8728 (tp) REVERT: B 638 LYS cc_start: 0.9086 (tmtt) cc_final: 0.8614 (tmtt) REVERT: B 695 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8904 (mmm) REVERT: B 832 MET cc_start: 0.8606 (mtp) cc_final: 0.8266 (mtp) REVERT: B 857 GLU cc_start: 0.8525 (tt0) cc_final: 0.8206 (tt0) REVERT: C 102 MET cc_start: 0.8415 (mmm) cc_final: 0.7732 (mpp) REVERT: C 130 GLU cc_start: 0.8382 (pp20) cc_final: 0.7822 (pp20) REVERT: C 346 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: C 433 LYS cc_start: 0.8577 (tttt) cc_final: 0.8225 (tppt) REVERT: C 439 THR cc_start: 0.8297 (t) cc_final: 0.8024 (m) REVERT: C 474 MET cc_start: 0.7985 (mtm) cc_final: 0.7593 (mtm) REVERT: C 656 MET cc_start: 0.8341 (mmm) cc_final: 0.8054 (mmm) REVERT: C 1018 PHE cc_start: 0.8469 (t80) cc_final: 0.8202 (t80) outliers start: 112 outliers final: 92 residues processed: 556 average time/residue: 0.3030 time to fit residues: 277.6871 Evaluate side-chains 539 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 443 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 749 TYR Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 512 TRP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 272 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 213 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 271 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN A 534 HIS ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 292 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 23595 Z= 0.239 Angle : 0.640 10.709 32004 Z= 0.316 Chirality : 0.042 0.342 3848 Planarity : 0.004 0.045 4027 Dihedral : 3.951 22.990 3178 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.71 % Allowed : 25.48 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 3027 helix: 1.43 (0.13), residues: 1685 sheet: -1.02 (0.24), residues: 460 loop : -0.69 (0.23), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 556 HIS 0.012 0.002 HIS B 342 PHE 0.028 0.002 PHE C 669 TYR 0.016 0.001 TYR A 356 ARG 0.004 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 456 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7898 (mp) REVERT: A 355 MET cc_start: 0.8155 (tpp) cc_final: 0.7854 (tpp) REVERT: A 383 MET cc_start: 0.8565 (ttm) cc_final: 0.8283 (mtt) REVERT: A 400 LEU cc_start: 0.9030 (mt) cc_final: 0.8817 (mt) REVERT: A 477 SER cc_start: 0.8764 (t) cc_final: 0.8451 (m) REVERT: A 574 GLN cc_start: 0.8254 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 647 MET cc_start: 0.8388 (mmp) cc_final: 0.7100 (mmm) REVERT: A 783 MET cc_start: 0.7619 (tpt) cc_final: 0.7120 (tpt) REVERT: A 848 TYR cc_start: 0.8524 (p90) cc_final: 0.8280 (p90) REVERT: A 948 MET cc_start: 0.7679 (tmm) cc_final: 0.7371 (ttt) REVERT: B 20 ILE cc_start: 0.9413 (mm) cc_final: 0.9137 (mt) REVERT: B 474 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6841 (mtt) REVERT: B 483 LEU cc_start: 0.9031 (tt) cc_final: 0.8724 (tp) REVERT: B 638 LYS cc_start: 0.9109 (tmtt) cc_final: 0.8634 (tmtt) REVERT: B 832 MET cc_start: 0.8718 (mtp) cc_final: 0.8342 (mtp) REVERT: B 857 GLU cc_start: 0.8589 (tt0) cc_final: 0.8260 (tt0) REVERT: B 938 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7274 (tm-30) REVERT: C 102 MET cc_start: 0.8522 (mmm) cc_final: 0.7776 (mpp) REVERT: C 130 GLU cc_start: 0.8462 (pp20) cc_final: 0.7835 (pp20) REVERT: C 433 LYS cc_start: 0.8615 (tttt) cc_final: 0.8286 (tppt) REVERT: C 439 THR cc_start: 0.8496 (t) cc_final: 0.8226 (m) REVERT: C 472 LEU cc_start: 0.8920 (tt) cc_final: 0.8520 (tp) REVERT: C 474 MET cc_start: 0.8044 (mtm) cc_final: 0.7642 (mtm) REVERT: C 853 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7996 (mp) REVERT: C 857 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7522 (tm-30) REVERT: C 913 MET cc_start: 0.7806 (mmm) cc_final: 0.7299 (mmm) REVERT: C 1018 PHE cc_start: 0.8422 (t80) cc_final: 0.8215 (t80) outliers start: 120 outliers final: 93 residues processed: 542 average time/residue: 0.3223 time to fit residues: 288.4409 Evaluate side-chains 532 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 436 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 749 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 512 TRP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 178 optimal weight: 6.9990 chunk 287 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 301 optimal weight: 0.7980 chunk 277 optimal weight: 0.8980 chunk 240 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23595 Z= 0.206 Angle : 0.647 12.527 32004 Z= 0.316 Chirality : 0.042 0.287 3848 Planarity : 0.004 0.045 4027 Dihedral : 3.944 24.460 3178 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.04 % Allowed : 26.50 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.16), residues: 3027 helix: 1.46 (0.13), residues: 1683 sheet: -0.94 (0.24), residues: 460 loop : -0.61 (0.23), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 512 HIS 0.013 0.001 HIS B 342 PHE 0.031 0.001 PHE B 352 TYR 0.013 0.001 TYR A 356 ARG 0.006 0.000 ARG C 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 459 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7656 (tm-30) REVERT: A 193 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7886 (mp) REVERT: A 355 MET cc_start: 0.8156 (tpp) cc_final: 0.7943 (tpp) REVERT: A 400 LEU cc_start: 0.9001 (mt) cc_final: 0.8785 (mt) REVERT: A 477 SER cc_start: 0.8687 (t) cc_final: 0.8363 (m) REVERT: A 647 MET cc_start: 0.8377 (mmp) cc_final: 0.7148 (mmm) REVERT: A 783 MET cc_start: 0.7605 (tpt) cc_final: 0.7103 (tpt) REVERT: A 948 MET cc_start: 0.7664 (tmm) cc_final: 0.7363 (ttt) REVERT: B 20 ILE cc_start: 0.9415 (mm) cc_final: 0.9128 (mt) REVERT: B 68 GLU cc_start: 0.7491 (mp0) cc_final: 0.7245 (mp0) REVERT: B 449 LEU cc_start: 0.8959 (mm) cc_final: 0.8642 (mm) REVERT: B 483 LEU cc_start: 0.9021 (tt) cc_final: 0.8695 (tp) REVERT: B 638 LYS cc_start: 0.9101 (tmtt) cc_final: 0.8644 (tmtt) REVERT: B 832 MET cc_start: 0.8708 (mtp) cc_final: 0.8328 (mtp) REVERT: B 857 GLU cc_start: 0.8562 (tt0) cc_final: 0.8249 (tt0) REVERT: C 102 MET cc_start: 0.8481 (mmm) cc_final: 0.7704 (mpp) REVERT: C 130 GLU cc_start: 0.8453 (pp20) cc_final: 0.7821 (pp20) REVERT: C 327 TYR cc_start: 0.9030 (t80) cc_final: 0.8787 (t80) REVERT: C 433 LYS cc_start: 0.8615 (tttt) cc_final: 0.8289 (tppt) REVERT: C 439 THR cc_start: 0.8453 (t) cc_final: 0.8204 (m) REVERT: C 472 LEU cc_start: 0.8840 (tt) cc_final: 0.8449 (tp) REVERT: C 474 MET cc_start: 0.7984 (mtm) cc_final: 0.7599 (mtm) REVERT: C 848 TYR cc_start: 0.8375 (p90) cc_final: 0.8013 (p90) REVERT: C 853 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7960 (mp) REVERT: C 857 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7441 (tm-30) REVERT: C 913 MET cc_start: 0.7807 (mmm) cc_final: 0.7272 (mmm) outliers start: 103 outliers final: 95 residues processed: 530 average time/residue: 0.3001 time to fit residues: 263.2072 Evaluate side-chains 539 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 442 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 749 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 512 TRP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 0.9990 chunk 256 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 247 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** 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 = 0.3309 r_free = 0.3309 target = 0.113540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.097803 restraints weight = 41235.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.100480 restraints weight = 21756.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102288 restraints weight = 13818.684| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23595 Z= 0.218 Angle : 0.659 13.760 32004 Z= 0.323 Chirality : 0.042 0.288 3848 Planarity : 0.004 0.057 4027 Dihedral : 3.948 23.969 3178 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.28 % Allowed : 26.46 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 3027 helix: 1.46 (0.13), residues: 1686 sheet: -0.90 (0.24), residues: 460 loop : -0.59 (0.23), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 512 HIS 0.013 0.001 HIS B 342 PHE 0.026 0.001 PHE C 669 TYR 0.013 0.001 TYR A 356 ARG 0.008 0.000 ARG B 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5604.38 seconds wall clock time: 102 minutes 19.89 seconds (6139.89 seconds total)