Starting phenix.real_space_refine on Mon Feb 19 06:33:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjk_40092/02_2024/8gjk_40092_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjk_40092/02_2024/8gjk_40092.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjk_40092/02_2024/8gjk_40092_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjk_40092/02_2024/8gjk_40092_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjk_40092/02_2024/8gjk_40092_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjk_40092/02_2024/8gjk_40092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjk_40092/02_2024/8gjk_40092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjk_40092/02_2024/8gjk_40092_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjk_40092/02_2024/8gjk_40092_trim_updated.pdb" } resolution = 3.16 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= 0.001 sd= 0.034 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 85 5.16 5 C 15505 2.51 5 N 3850 2.21 5 O 4461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 8": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 701": "NH1" <-> "NH2" Residue "B ARG 703": "NH1" <-> "NH2" Residue "B GLU 839": "OE1" <-> "OE2" Residue "B GLU 848": "OE1" <-> "OE2" Residue "B GLU 860": "OE1" <-> "OE2" Residue "B GLU 887": "OE1" <-> "OE2" Residue "B GLU 946": "OE1" <-> "OE2" Residue "B GLU 1028": "OE1" <-> "OE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A GLU 887": "OE1" <-> "OE2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A GLU 1024": "OE1" <-> "OE2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 587": "OE1" <-> "OE2" Residue "C PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 635": "OE1" <-> "OE2" Residue "C GLU 698": "OE1" <-> "OE2" Residue "C GLU 839": "OE1" <-> "OE2" Residue "C GLU 941": "OE1" <-> "OE2" Residue "C GLU 945": "OE1" <-> "OE2" Residue "C PHE 1014": "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: 23901 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 7954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7954 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 7952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7952 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 7995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7995 Unusual residues: {'ZZ7': 1} Classifications: {'peptide': 1032, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990, None: 1} Not linked: pdbres="LYS C1032 " pdbres="ZZ7 C1101 " Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 11.81, per 1000 atoms: 0.49 Number of scatterers: 23901 At special positions: 0 Unit cell: (119.84, 124.12, 146.59, 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 85 16.00 O 4461 8.00 N 3850 7.00 C 15505 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: 10.53 Conformation dependent library (CDL) restraints added in 4.6 seconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 25 sheets defined 54.3% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.59 Creating SS restraints... Processing helix chain 'B' and resid 2 through 8 removed outlier: 3.923A pdb=" N PHE B 6 " --> pdb=" O PHE B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 30 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 100 through 117 removed outlier: 3.730A pdb=" N ALA B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 201 through 211 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 263 through 266 No H-bonds generated for 'chain 'B' and resid 263 through 266' Processing helix chain 'B' and resid 300 through 317 removed outlier: 3.547A pdb=" N LYS B 316 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 359 removed outlier: 3.738A pdb=" N LEU B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 387 Proline residue: B 369 - end of helix Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 393 through 423 removed outlier: 4.816A pdb=" N GLY B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 458 removed outlier: 3.515A pdb=" N MET B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N SER B 442 " --> pdb=" O ASN B 438 " (cutoff:3.500A) Proline residue: B 443 - end of helix Proline residue: B 457 - end of helix Processing helix chain 'B' and resid 464 through 488 removed outlier: 3.758A pdb=" N PHE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'B' and resid 509 through 533 Processing helix chain 'B' and resid 535 through 554 removed outlier: 3.534A pdb=" N GLY B 547 " --> pdb=" O CYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 597 Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'B' and resid 686 through 700 Processing helix chain 'B' and resid 726 through 731 Processing helix chain 'B' and resid 736 through 746 Processing helix chain 'B' and resid 770 through 773 Processing helix chain 'B' and resid 776 through 781 removed outlier: 4.024A pdb=" N LEU B 779 " --> pdb=" O GLN B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 797 No H-bonds generated for 'chain 'B' and resid 794 through 797' Processing helix chain 'B' and resid 830 through 843 removed outlier: 3.519A pdb=" N ILE B 834 " --> pdb=" O SER B 830 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 835 " --> pdb=" O GLY B 831 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 836 " --> pdb=" O GLN B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 863 Processing helix chain 'B' and resid 869 through 886 Processing helix chain 'B' and resid 891 through 913 removed outlier: 3.636A pdb=" N THR B 897 " --> pdb=" O ALA B 894 " (cutoff:3.500A) Proline residue: B 900 - end of helix removed outlier: 3.544A pdb=" N VAL B 910 " --> pdb=" O ILE B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 950 removed outlier: 3.780A pdb=" N ALA B 936 " --> pdb=" O SER B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 980 removed outlier: 4.218A pdb=" N ARG B 967 " --> pdb=" O LYS B 963 " (cutoff:3.500A) Proline residue: B 968 - end of helix Processing helix chain 'B' and resid 982 through 984 No H-bonds generated for 'chain 'B' and resid 982 through 984' Processing helix chain 'B' and resid 991 through 1031 removed outlier: 3.935A pdb=" N GLY B1000 " --> pdb=" O SER B 996 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B1001 " --> pdb=" O LEU B 997 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B1012 " --> pdb=" O ALA B1008 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE B1013 " --> pdb=" O SER B1009 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B1014 " --> pdb=" O THR B1010 " (cutoff:3.500A) Proline residue: B1017 - end of helix Processing helix chain 'A' and resid 2 through 8 removed outlier: 4.070A pdb=" N PHE A 6 " --> pdb=" O PHE A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 30 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 63 through 70 Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.570A pdb=" N LEU A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 191 through 197 Processing helix chain 'A' and resid 201 through 211 Processing helix chain 'A' and resid 244 through 247 No H-bonds generated for 'chain 'A' and resid 244 through 247' Processing helix chain 'A' and resid 263 through 266 No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 300 through 317 removed outlier: 4.027A pdb=" N ASN A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 359 removed outlier: 3.713A pdb=" N LEU A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 387 removed outlier: 3.704A pdb=" N ILE A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.618A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Proline residue: A 374 - end of helix removed outlier: 3.554A pdb=" N ALA A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 removed outlier: 4.631A pdb=" N GLY A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASP A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 460 removed outlier: 4.680A pdb=" N SER A 442 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix removed outlier: 3.505A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Proline residue: A 457 - end of helix removed outlier: 3.619A pdb=" N PHE A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 488 removed outlier: 4.303A pdb=" N GLN A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 475 " --> pdb=" O GLN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'A' and resid 508 through 533 removed outlier: 3.563A pdb=" N PHE A 513 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 554 removed outlier: 3.589A pdb=" N VAL A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 597 removed outlier: 3.672A pdb=" N LYS A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 648 Processing helix chain 'A' and resid 686 through 702 removed outlier: 3.513A pdb=" N GLN A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'A' and resid 736 through 746 Processing helix chain 'A' and resid 777 through 781 Processing helix chain 'A' and resid 830 through 845 Processing helix chain 'A' and resid 855 through 863 Processing helix chain 'A' and resid 866 through 886 Processing helix chain 'A' and resid 890 through 912 removed outlier: 4.031A pdb=" N ALA A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Proline residue: A 900 - end of helix Processing helix chain 'A' and resid 919 through 948 removed outlier: 3.697A pdb=" N GLY A 930 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 939 " --> pdb=" O ASN A 935 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 984 removed outlier: 4.929A pdb=" N ARG A 967 " --> pdb=" O LYS A 963 " (cutoff:3.500A) Proline residue: A 968 - end of helix Proline residue: A 982 - end of helix Processing helix chain 'A' and resid 991 through 1031 removed outlier: 3.600A pdb=" N GLY A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE A1013 " --> pdb=" O SER A1009 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) Proline residue: A1017 - end of helix Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 10 through 30 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 63 through 70 Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.545A pdb=" N ALA C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 162 through 168 removed outlier: 3.510A pdb=" N LEU C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 201 through 211 Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 263 through 266 No H-bonds generated for 'chain 'C' and resid 263 through 266' Processing helix chain 'C' and resid 300 through 316 Processing helix chain 'C' and resid 330 through 360 Processing helix chain 'C' and resid 366 through 386 Proline residue: C 374 - end of helix removed outlier: 3.888A pdb=" N THR C 380 " --> pdb=" O SER C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 423 removed outlier: 3.915A pdb=" N GLY C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 460 removed outlier: 4.695A pdb=" N SER C 442 " --> pdb=" O ASN C 438 " (cutoff:3.500A) Proline residue: C 443 - end of helix Proline residue: C 457 - end of helix Processing helix chain 'C' and resid 464 through 488 removed outlier: 3.599A pdb=" N PHE C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 475 " --> pdb=" O GLN C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 498 Processing helix chain 'C' and resid 508 through 533 Processing helix chain 'C' and resid 535 through 555 Processing helix chain 'C' and resid 581 through 597 removed outlier: 3.538A pdb=" N ASN C 594 " --> pdb=" O THR C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 648 Processing helix chain 'C' and resid 686 through 702 Processing helix chain 'C' and resid 726 through 731 Processing helix chain 'C' and resid 736 through 746 Processing helix chain 'C' and resid 770 through 773 No H-bonds generated for 'chain 'C' and resid 770 through 773' Processing helix chain 'C' and resid 776 through 781 removed outlier: 3.876A pdb=" N LEU C 779 " --> pdb=" O GLN C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 797 No H-bonds generated for 'chain 'C' and resid 794 through 797' Processing helix chain 'C' and resid 830 through 844 Processing helix chain 'C' and resid 856 through 861 Processing helix chain 'C' and resid 866 through 886 Processing helix chain 'C' and resid 891 through 913 Proline residue: C 900 - end of helix removed outlier: 3.608A pdb=" N VAL C 903 " --> pdb=" O PRO C 900 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 906 " --> pdb=" O VAL C 903 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 909 " --> pdb=" O SER C 906 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C 910 " --> pdb=" O ILE C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 948 Processing helix chain 'C' and resid 954 through 964 removed outlier: 3.758A pdb=" N ALA C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 984 Proline residue: C 982 - end of helix Processing helix chain 'C' and resid 991 through 1010 removed outlier: 3.680A pdb=" N GLY C1000 " --> pdb=" O SER C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1031 Proline residue: C1017 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 127 through 130 removed outlier: 3.507A pdb=" N TYR B 78 " --> pdb=" O TYR B 93 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 322 through 324 removed outlier: 6.694A pdb=" N ILE B 292 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL B 139 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE B 290 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER B 141 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 288 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 174 " --> pdb=" O ASN B 293 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 267 through 273 Processing sheet with id= D, first strand: chain 'B' and resid 279 through 282 removed outlier: 6.773A pdb=" N ILE B 627 " --> pdb=" O SER B 602 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER B 604 " --> pdb=" O PHE B 625 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE B 625 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER B 606 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 623 " --> pdb=" O SER B 606 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE B 608 " --> pdb=" O ALA B 621 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA B 621 " --> pdb=" O ILE B 608 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 626 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET B 570 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 850 through 854 removed outlier: 4.372A pdb=" N GLU B 675 " --> pdb=" O SER B 854 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 676 " --> pdb=" O ILE B 820 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 818 " --> pdb=" O ALA B 678 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN B 708 " --> pdb=" O ASP B 823 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 717 through 724 Processing sheet with id= G, first strand: chain 'B' and resid 754 through 757 Processing sheet with id= H, first strand: chain 'B' and resid 783 through 785 Processing sheet with id= I, first strand: chain 'B' and resid 251 through 254 removed outlier: 6.774A pdb=" N LEU B 261 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.116A pdb=" N THR A 43 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS A 810 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 322 through 325 removed outlier: 6.999A pdb=" N ILE A 292 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 139 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE A 290 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER A 141 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 288 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 174 " --> pdb=" O ASN A 293 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 267 through 273 removed outlier: 8.202A pdb=" N ASN A 761 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N MET A 185 " --> pdb=" O ASN A 761 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN A 763 " --> pdb=" O MET A 185 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE A 187 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN A 765 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU A 189 " --> pdb=" O ASN A 765 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG A 767 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 753 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE A 766 " --> pdb=" O TYR A 751 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR A 751 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 279 through 282 removed outlier: 6.877A pdb=" N ILE A 627 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER A 604 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 625 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER A 606 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 623 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE A 608 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA A 621 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 718 through 724 Processing sheet with id= O, first strand: chain 'A' and resid 783 through 785 Processing sheet with id= P, first strand: chain 'A' and resid 251 through 254 removed outlier: 6.724A pdb=" N LEU A 261 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 127 through 131 Processing sheet with id= R, first strand: chain 'C' and resid 322 through 325 removed outlier: 6.983A pdb=" N ILE C 292 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL C 139 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE C 290 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER C 141 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL C 288 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 267 through 273 removed outlier: 7.898A pdb=" N TYR C 183 " --> pdb=" O ASN C 761 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN C 763 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN C 753 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE C 766 " --> pdb=" O TYR C 751 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TYR C 751 " --> pdb=" O ILE C 766 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 215 through 220 Processing sheet with id= U, first strand: chain 'C' and resid 280 through 282 removed outlier: 3.553A pdb=" N SER C 603 " --> pdb=" O ILE C 627 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 819 through 821 removed outlier: 4.394A pdb=" N GLU C 675 " --> pdb=" O SER C 854 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 718 through 724 Processing sheet with id= X, first strand: chain 'C' and resid 783 through 785 Processing sheet with id= Y, first strand: chain 'C' and resid 251 through 254 removed outlier: 6.679A pdb=" N LEU C 261 " --> pdb=" O LEU C 252 " (cutoff:3.500A) 1351 hydrogen bonds defined for protein. 3903 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: 9.66 Time building geometry restraints manager: 11.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5143 1.32 - 1.45: 5125 1.45 - 1.57: 13931 1.57 - 1.69: 0 1.69 - 1.81: 164 Bond restraints: 24363 Sorted by residual: bond pdb=" C12 ZZ7 C1101 " pdb=" N3 ZZ7 C1101 " ideal model delta sigma weight residual 1.814 1.441 0.373 2.00e-02 2.50e+03 3.48e+02 bond pdb=" C6 ZZ7 C1101 " pdb=" S1 ZZ7 C1101 " ideal model delta sigma weight residual 1.518 1.768 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C12 ZZ7 C1101 " pdb=" C2 ZZ7 C1101 " ideal model delta sigma weight residual 1.262 1.498 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C3 ZZ7 C1101 " pdb=" N1 ZZ7 C1101 " ideal model delta sigma weight residual 1.456 1.329 0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C THR A 40 " pdb=" N PRO A 41 " ideal model delta sigma weight residual 1.329 1.376 -0.047 1.18e-02 7.18e+03 1.59e+01 ... (remaining 24358 not shown) Histogram of bond angle deviations from ideal: 95.43 - 103.61: 366 103.61 - 111.79: 11250 111.79 - 119.97: 10917 119.97 - 128.15: 10450 128.15 - 136.33: 125 Bond angle restraints: 33108 Sorted by residual: angle pdb=" N ASP B 257 " pdb=" CA ASP B 257 " pdb=" C ASP B 257 " ideal model delta sigma weight residual 112.88 97.69 15.19 1.29e+00 6.01e-01 1.39e+02 angle pdb=" N ASP C 257 " pdb=" CA ASP C 257 " pdb=" C ASP C 257 " ideal model delta sigma weight residual 112.57 100.54 12.03 1.13e+00 7.83e-01 1.13e+02 angle pdb=" N ASP A 777 " pdb=" CA ASP A 777 " pdb=" C ASP A 777 " ideal model delta sigma weight residual 111.36 101.05 10.31 1.09e+00 8.42e-01 8.95e+01 angle pdb=" N ILE C 427 " pdb=" CA ILE C 427 " pdb=" C ILE C 427 " ideal model delta sigma weight residual 109.30 121.22 -11.92 1.31e+00 5.83e-01 8.28e+01 angle pdb=" C THR A 61 " pdb=" N VAL A 62 " pdb=" CA VAL A 62 " ideal model delta sigma weight residual 123.08 114.15 8.93 1.01e+00 9.80e-01 7.81e+01 ... (remaining 33103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 13556 17.82 - 35.64: 883 35.64 - 53.46: 163 53.46 - 71.28: 25 71.28 - 89.10: 3 Dihedral angle restraints: 14630 sinusoidal: 5591 harmonic: 9039 Sorted by residual: dihedral pdb=" C VAL A1016 " pdb=" N VAL A1016 " pdb=" CA VAL A1016 " pdb=" CB VAL A1016 " ideal model delta harmonic sigma weight residual -122.00 -135.02 13.02 0 2.50e+00 1.60e-01 2.71e+01 dihedral pdb=" C ILE C 427 " pdb=" N ILE C 427 " pdb=" CA ILE C 427 " pdb=" CB ILE C 427 " ideal model delta harmonic sigma weight residual -122.00 -133.57 11.57 0 2.50e+00 1.60e-01 2.14e+01 dihedral pdb=" N VAL A1016 " pdb=" C VAL A1016 " pdb=" CA VAL A1016 " pdb=" CB VAL A1016 " ideal model delta harmonic sigma weight residual 123.40 134.78 -11.38 0 2.50e+00 1.60e-01 2.07e+01 ... (remaining 14627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2835 0.089 - 0.178: 846 0.178 - 0.267: 212 0.267 - 0.356: 35 0.356 - 0.445: 18 Chirality restraints: 3946 Sorted by residual: chirality pdb=" CA PHE A 538 " pdb=" N PHE A 538 " pdb=" C PHE A 538 " pdb=" CB PHE A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA MET C 891 " pdb=" N MET C 891 " pdb=" C MET C 891 " pdb=" CB MET C 891 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA LEU A 890 " pdb=" N LEU A 890 " pdb=" C LEU A 890 " pdb=" CB LEU A 890 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 3943 not shown) Planarity restraints: 4196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 899 " -0.059 5.00e-02 4.00e+02 9.04e-02 1.31e+01 pdb=" N PRO C 900 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO C 900 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 900 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 368 " -0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO A 369 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 369 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 369 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B1016 " -0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO B1017 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B1017 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B1017 " -0.047 5.00e-02 4.00e+02 ... (remaining 4193 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7372 2.82 - 3.34: 24159 3.34 - 3.86: 41399 3.86 - 4.38: 50572 4.38 - 4.90: 82563 Nonbonded interactions: 206065 Sorted by model distance: nonbonded pdb=" N ASP B 257 " pdb=" N LYS B 258 " model vdw 2.295 2.560 nonbonded pdb=" N ASP C 257 " pdb=" N LYS C 258 " model vdw 2.437 2.560 nonbonded pdb=" N ASP A 257 " pdb=" N LYS A 258 " model vdw 2.485 2.560 nonbonded pdb=" N GLN A 245 " pdb=" N GLU A 246 " model vdw 2.493 2.560 nonbonded pdb=" N SER C 787 " pdb=" N ASP C 788 " model vdw 2.494 2.560 ... (remaining 206060 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 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 360 or (resid 361 and (name N or \ name CA or name C or name O or name CB )) or resid 362 through 536 or (resid 53 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 538 through \ 944 or (resid 945 and (name N or name CA or name C or name O or name CB )) or re \ sid 946 through 955 or (resid 956 through 958 and (name N or name CA or name C o \ r name O or name CB )) or resid 959 through 964 or (resid 965 and (name N or nam \ e CA or name C or name O or name CB )) or resid 966 through 1032)) selection = (chain 'B' and (resid 1 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 502 or (resid 503 and (name N or \ name CA or name C or name O or name CB )) or resid 504 through 652 or (resid 65 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 654 through \ 771 or (resid 772 through 773 and (name N or name CA or name C or name O or name \ CB )) or resid 774 through 775 or (resid 776 and (name N or name CA or name C o \ r name O or name CB )) or resid 777 through 1032)) selection = (chain 'C' and (resid 1 through 360 or (resid 361 and (name N or name CA or name \ C or name O or name CB )) or resid 362 through 536 or (resid 537 and (name N or \ name CA or name C or name O or name CB )) or resid 538 through 652 or (resid 65 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 654 through \ 771 or (resid 772 through 773 and (name N or name CA or name C or name O or name \ CB )) or resid 774 through 775 or (resid 776 and (name N or name CA or name C o \ r name O or name CB )) or resid 777 through 944 or (resid 945 and (name N or nam \ e CA or name C or name O or name CB )) or resid 946 through 955 or (resid 956 th \ rough 958 and (name N or name CA or name C or name O or name CB )) or resid 959 \ through 964 or (resid 965 and (name N or name CA or name C or name O or name CB \ )) or resid 966 through 1032)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.970 Check model and map are aligned: 0.340 Set scattering table: 0.190 Process input model: 66.210 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.373 24363 Z= 0.586 Angle : 1.371 15.194 33108 Z= 0.958 Chirality : 0.093 0.445 3946 Planarity : 0.008 0.090 4196 Dihedral : 12.136 89.104 8786 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.73 % Rotamer: Outliers : 2.75 % Allowed : 7.57 % Favored : 89.68 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 2.44 % 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 (0.15), residues: 3090 helix: 0.84 (0.13), residues: 1745 sheet: -0.10 (0.23), residues: 482 loop : -0.54 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 188 HIS 0.005 0.002 HIS C 582 PHE 0.020 0.002 PHE C 955 TYR 0.017 0.002 TYR A 276 ARG 0.005 0.001 ARG A 994 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 657 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 LEU cc_start: 0.8699 (mt) cc_final: 0.8474 (mt) REVERT: B 311 MET cc_start: 0.8365 (mmm) cc_final: 0.8035 (mmm) REVERT: B 357 TYR cc_start: 0.8050 (t80) cc_final: 0.7680 (t80) REVERT: B 407 VAL cc_start: 0.9283 (t) cc_final: 0.9062 (p) REVERT: B 449 LEU cc_start: 0.9321 (mt) cc_final: 0.9106 (mm) REVERT: B 498 PHE cc_start: 0.7442 (p90) cc_final: 0.6949 (p90) REVERT: B 904 PHE cc_start: 0.7270 (t80) cc_final: 0.6624 (t80) REVERT: B 916 ASP cc_start: 0.7670 (p0) cc_final: 0.7412 (p0) REVERT: B 944 MET cc_start: 0.8191 (mmm) cc_final: 0.7878 (mmm) REVERT: B 1027 ASN cc_start: 0.8362 (t0) cc_final: 0.8101 (t0) REVERT: A 808 ASP cc_start: 0.7803 (p0) cc_final: 0.7552 (p0) REVERT: C 626 PHE cc_start: 0.7716 (m-80) cc_final: 0.7461 (m-80) outliers start: 72 outliers final: 15 residues processed: 705 average time/residue: 0.3560 time to fit residues: 391.0312 Evaluate side-chains 336 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 321 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 561 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 chunk 280 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 295 GLN B 392 ASN B 438 ASN B 469 GLN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN B 765 ASN B 821 GLN B 832 GLN B 843 GLN B 859 GLN B 960 ASN B1027 ASN A 87 GLN A 202 ASN A 255 ASN A 293 ASN A 312 GLN A 325 GLN A 426 ASN A 514 ASN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN A 741 ASN A 795 ASN C 45 GLN C 302 ASN C 308 ASN C 312 GLN C 325 GLN C 362 ASN C 422 HIS C 469 GLN C 511 GLN C 694 ASN C 708 ASN C 765 ASN C 843 GLN C 922 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24363 Z= 0.224 Angle : 0.605 10.470 33108 Z= 0.324 Chirality : 0.043 0.188 3946 Planarity : 0.005 0.055 4196 Dihedral : 5.357 55.323 3321 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.45 % Allowed : 13.46 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.16 (0.15), residues: 3090 helix: 1.51 (0.12), residues: 1726 sheet: -0.00 (0.24), residues: 463 loop : -0.10 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 853 HIS 0.009 0.001 HIS C 422 PHE 0.026 0.002 PHE C1019 TYR 0.019 0.001 TYR B 858 ARG 0.006 0.001 ARG C 785 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 389 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8626 (mp) REVERT: B 385 TYR cc_start: 0.8797 (t80) cc_final: 0.8580 (t80) REVERT: B 736 MET cc_start: 0.7983 (ttm) cc_final: 0.7675 (ttt) REVERT: B 916 ASP cc_start: 0.7428 (p0) cc_final: 0.7204 (p0) REVERT: B 1015 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6695 (t80) REVERT: B 1027 ASN cc_start: 0.8492 (t0) cc_final: 0.8165 (t0) REVERT: A 18 ILE cc_start: 0.9246 (mt) cc_final: 0.9023 (mm) REVERT: A 34 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7655 (mt-10) REVERT: A 808 ASP cc_start: 0.7696 (p0) cc_final: 0.7444 (p0) REVERT: C 76 MET cc_start: 0.8424 (ttp) cc_final: 0.8145 (ptm) REVERT: C 918 ASP cc_start: 0.7587 (p0) cc_final: 0.6954 (p0) REVERT: C 971 MET cc_start: 0.9249 (mtp) cc_final: 0.8877 (mtm) outliers start: 64 outliers final: 33 residues processed: 434 average time/residue: 0.3255 time to fit residues: 232.9991 Evaluate side-chains 350 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 315 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 1015 PHE Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 916 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 233 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 281 optimal weight: 2.9990 chunk 303 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 225 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 765 ASN B 832 GLN A 594 ASN A 774 ASN C 469 GLN C 679 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24363 Z= 0.226 Angle : 0.549 7.675 33108 Z= 0.287 Chirality : 0.042 0.190 3946 Planarity : 0.004 0.047 4196 Dihedral : 5.043 59.732 3309 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.79 % Allowed : 14.37 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.47 (0.15), residues: 3090 helix: 1.83 (0.12), residues: 1732 sheet: -0.02 (0.24), residues: 451 loop : -0.05 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 853 HIS 0.004 0.001 HIS B 582 PHE 0.030 0.002 PHE C 464 TYR 0.035 0.001 TYR B 858 ARG 0.005 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 337 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8748 (mm) REVERT: B 351 LEU cc_start: 0.8732 (mt) cc_final: 0.8529 (tp) REVERT: B 357 TYR cc_start: 0.8093 (t80) cc_final: 0.7209 (t80) REVERT: B 368 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8595 (mp) REVERT: B 385 TYR cc_start: 0.8737 (t80) cc_final: 0.8221 (t80) REVERT: B 407 VAL cc_start: 0.9024 (t) cc_final: 0.8801 (p) REVERT: B 736 MET cc_start: 0.7998 (ttm) cc_final: 0.7786 (ttt) REVERT: B 1027 ASN cc_start: 0.8521 (t0) cc_final: 0.8174 (t0) REVERT: A 18 ILE cc_start: 0.9249 (mt) cc_final: 0.8984 (mm) REVERT: A 34 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7699 (mt-10) REVERT: A 808 ASP cc_start: 0.7739 (p0) cc_final: 0.7466 (p0) REVERT: C 76 MET cc_start: 0.8445 (ttp) cc_final: 0.8138 (ptm) REVERT: C 294 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8898 (tt) outliers start: 73 outliers final: 42 residues processed: 390 average time/residue: 0.3128 time to fit residues: 202.8179 Evaluate side-chains 333 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 288 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 906 SER Chi-restraints excluded: chain C residue 916 ASP Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 134 optimal weight: 0.0020 chunk 188 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 267 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 GLN B 765 ASN A 182 ASN A 277 ASN C 469 GLN C 843 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24363 Z= 0.163 Angle : 0.513 7.470 33108 Z= 0.264 Chirality : 0.041 0.196 3946 Planarity : 0.004 0.041 4196 Dihedral : 4.862 57.255 3309 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.75 % Allowed : 15.75 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.61 (0.15), residues: 3090 helix: 1.98 (0.12), residues: 1727 sheet: -0.02 (0.24), residues: 454 loop : -0.03 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 853 HIS 0.003 0.001 HIS B 582 PHE 0.030 0.001 PHE C 464 TYR 0.014 0.001 TYR B 78 ARG 0.003 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 354 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8697 (mm) REVERT: B 368 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8566 (mp) REVERT: B 385 TYR cc_start: 0.8657 (t80) cc_final: 0.8162 (t80) REVERT: B 976 PHE cc_start: 0.8353 (t80) cc_final: 0.7905 (t80) REVERT: B 1005 MET cc_start: 0.8064 (tmm) cc_final: 0.7646 (ttm) REVERT: B 1027 ASN cc_start: 0.8560 (t0) cc_final: 0.8237 (t0) REVERT: A 34 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7600 (mt-10) REVERT: A 808 ASP cc_start: 0.7636 (p0) cc_final: 0.7359 (p0) REVERT: C 76 MET cc_start: 0.8347 (ttp) cc_final: 0.8057 (ptm) REVERT: C 294 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8810 (tt) outliers start: 72 outliers final: 43 residues processed: 402 average time/residue: 0.3178 time to fit residues: 212.3107 Evaluate side-chains 357 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 311 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 906 SER Chi-restraints excluded: chain C residue 916 ASP Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 222 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 254 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 268 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 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 679 GLN C 108 ASN C 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24363 Z= 0.165 Angle : 0.505 7.578 33108 Z= 0.258 Chirality : 0.041 0.211 3946 Planarity : 0.004 0.039 4196 Dihedral : 4.713 54.783 3307 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.94 % Allowed : 16.13 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.71 (0.15), residues: 3090 helix: 2.05 (0.12), residues: 1737 sheet: -0.00 (0.24), residues: 445 loop : 0.04 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 853 HIS 0.003 0.001 HIS B 582 PHE 0.029 0.001 PHE C 464 TYR 0.020 0.001 TYR B 858 ARG 0.004 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 350 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8679 (mm) REVERT: B 357 TYR cc_start: 0.8277 (t80) cc_final: 0.7556 (t80) REVERT: B 385 TYR cc_start: 0.8665 (t80) cc_final: 0.8249 (t80) REVERT: B 540 LEU cc_start: 0.8951 (mt) cc_final: 0.8608 (tt) REVERT: B 1027 ASN cc_start: 0.8564 (t0) cc_final: 0.8260 (t0) REVERT: A 34 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 891 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.6811 (mmm) REVERT: C 76 MET cc_start: 0.8357 (ttp) cc_final: 0.8044 (ptm) REVERT: C 690 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8168 (tp40) outliers start: 77 outliers final: 52 residues processed: 403 average time/residue: 0.3090 time to fit residues: 206.8181 Evaluate side-chains 365 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 310 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 906 SER Chi-restraints excluded: chain C residue 916 ASP Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 298 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 24 optimal weight: 0.0270 chunk 98 optimal weight: 8.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN C 843 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24363 Z= 0.191 Angle : 0.516 9.627 33108 Z= 0.262 Chirality : 0.041 0.237 3946 Planarity : 0.004 0.039 4196 Dihedral : 4.662 53.371 3307 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.64 % Allowed : 17.01 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.15), residues: 3090 helix: 2.09 (0.12), residues: 1736 sheet: -0.01 (0.24), residues: 456 loop : 0.06 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 853 HIS 0.003 0.001 HIS B 582 PHE 0.028 0.001 PHE B 542 TYR 0.016 0.001 TYR B 551 ARG 0.005 0.000 ARG C 785 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 330 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8696 (mm) REVERT: B 357 TYR cc_start: 0.8313 (t80) cc_final: 0.7569 (t80) REVERT: B 385 TYR cc_start: 0.8654 (t80) cc_final: 0.8279 (t80) REVERT: B 540 LEU cc_start: 0.8884 (mt) cc_final: 0.8552 (tt) REVERT: B 1027 ASN cc_start: 0.8604 (t0) cc_final: 0.8294 (t0) REVERT: A 34 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 696 MET cc_start: 0.8312 (tmm) cc_final: 0.8049 (tmm) REVERT: C 76 MET cc_start: 0.8376 (ttp) cc_final: 0.8072 (ptm) outliers start: 69 outliers final: 53 residues processed: 376 average time/residue: 0.3148 time to fit residues: 197.9318 Evaluate side-chains 361 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 307 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 906 SER Chi-restraints excluded: chain C residue 916 ASP Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 251 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 297 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN C 426 ASN C 843 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24363 Z= 0.166 Angle : 0.509 7.715 33108 Z= 0.258 Chirality : 0.041 0.251 3946 Planarity : 0.003 0.039 4196 Dihedral : 4.517 53.526 3305 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.87 % Allowed : 17.43 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.78 (0.15), residues: 3090 helix: 2.10 (0.12), residues: 1738 sheet: 0.02 (0.24), residues: 455 loop : 0.07 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 853 HIS 0.003 0.001 HIS B 582 PHE 0.030 0.001 PHE B 542 TYR 0.019 0.001 TYR B 78 ARG 0.004 0.000 ARG C 785 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 325 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8672 (mm) REVERT: B 357 TYR cc_start: 0.8314 (t80) cc_final: 0.7590 (t80) REVERT: B 385 TYR cc_start: 0.8656 (t80) cc_final: 0.8332 (t80) REVERT: B 540 LEU cc_start: 0.9017 (mt) cc_final: 0.8641 (tt) REVERT: B 791 MET cc_start: 0.8564 (mmm) cc_final: 0.8358 (mmm) REVERT: B 1027 ASN cc_start: 0.8611 (t0) cc_final: 0.8306 (t0) REVERT: A 34 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 696 MET cc_start: 0.8306 (tmm) cc_final: 0.8046 (tmm) REVERT: A 891 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.6828 (mmm) REVERT: C 76 MET cc_start: 0.8365 (ttp) cc_final: 0.8073 (ptm) outliers start: 75 outliers final: 60 residues processed: 370 average time/residue: 0.3017 time to fit residues: 187.8078 Evaluate side-chains 371 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 309 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 906 SER Chi-restraints excluded: chain C residue 916 ASP Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 189 optimal weight: 0.1980 chunk 202 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN C 843 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24363 Z= 0.188 Angle : 0.515 7.736 33108 Z= 0.261 Chirality : 0.041 0.262 3946 Planarity : 0.003 0.040 4196 Dihedral : 4.475 53.849 3304 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.94 % Allowed : 17.58 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.15), residues: 3090 helix: 2.13 (0.12), residues: 1737 sheet: -0.03 (0.24), residues: 457 loop : 0.10 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 853 HIS 0.003 0.001 HIS B 582 PHE 0.031 0.001 PHE B 542 TYR 0.017 0.001 TYR B 78 ARG 0.005 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 323 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8676 (mm) REVERT: B 357 TYR cc_start: 0.8289 (t80) cc_final: 0.7516 (t80) REVERT: B 385 TYR cc_start: 0.8663 (t80) cc_final: 0.8347 (t80) REVERT: B 540 LEU cc_start: 0.8969 (mt) cc_final: 0.8598 (tt) REVERT: B 548 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.6404 (t80) REVERT: B 791 MET cc_start: 0.8571 (mmm) cc_final: 0.8367 (mmm) REVERT: B 944 MET cc_start: 0.8174 (mtp) cc_final: 0.7966 (mtp) REVERT: B 1005 MET cc_start: 0.8071 (tmm) cc_final: 0.7576 (mtp) REVERT: B 1027 ASN cc_start: 0.8612 (t0) cc_final: 0.8313 (t0) REVERT: A 163 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8551 (mp) REVERT: A 237 MET cc_start: 0.8596 (ppp) cc_final: 0.8396 (ppp) REVERT: A 696 MET cc_start: 0.8328 (tmm) cc_final: 0.8069 (tmm) REVERT: C 76 MET cc_start: 0.8387 (ttp) cc_final: 0.8104 (ptm) outliers start: 77 outliers final: 64 residues processed: 372 average time/residue: 0.3042 time to fit residues: 190.6872 Evaluate side-chains 365 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 298 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 548 PHE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 460 PHE Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 906 SER Chi-restraints excluded: chain C residue 916 ASP Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.4980 chunk 285 optimal weight: 0.9990 chunk 260 optimal weight: 7.9990 chunk 277 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 250 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN C 108 ASN C 843 GLN C 922 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24363 Z= 0.211 Angle : 0.537 11.611 33108 Z= 0.270 Chirality : 0.041 0.299 3946 Planarity : 0.003 0.040 4196 Dihedral : 4.459 53.891 3303 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.10 % Allowed : 17.74 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.15), residues: 3090 helix: 2.07 (0.12), residues: 1744 sheet: -0.01 (0.24), residues: 456 loop : 0.08 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 853 HIS 0.003 0.001 HIS B 582 PHE 0.033 0.001 PHE B 542 TYR 0.017 0.001 TYR B 530 ARG 0.004 0.000 ARG C 785 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 314 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8679 (mm) REVERT: B 353 LEU cc_start: 0.8304 (pp) cc_final: 0.8049 (mm) REVERT: B 357 TYR cc_start: 0.8145 (t80) cc_final: 0.7470 (t80) REVERT: B 385 TYR cc_start: 0.8640 (t80) cc_final: 0.8314 (t80) REVERT: B 540 LEU cc_start: 0.8923 (mt) cc_final: 0.8570 (tt) REVERT: B 548 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6443 (t80) REVERT: B 944 MET cc_start: 0.8198 (mtp) cc_final: 0.7983 (mtp) REVERT: B 1027 ASN cc_start: 0.8615 (t0) cc_final: 0.8318 (t0) REVERT: A 163 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8556 (mp) REVERT: A 696 MET cc_start: 0.8364 (tmm) cc_final: 0.8104 (tmm) REVERT: C 76 MET cc_start: 0.8410 (ttp) cc_final: 0.8135 (ptm) outliers start: 81 outliers final: 65 residues processed: 367 average time/residue: 0.3140 time to fit residues: 193.8357 Evaluate side-chains 373 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 305 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 548 PHE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 906 SER Chi-restraints excluded: chain C residue 916 ASP Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 204 optimal weight: 0.4980 chunk 307 optimal weight: 0.9990 chunk 283 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 843 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24363 Z= 0.196 Angle : 0.544 10.303 33108 Z= 0.273 Chirality : 0.041 0.309 3946 Planarity : 0.004 0.068 4196 Dihedral : 4.447 53.844 3303 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.87 % Allowed : 17.93 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.76 (0.15), residues: 3090 helix: 2.08 (0.12), residues: 1740 sheet: -0.02 (0.24), residues: 458 loop : 0.09 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 853 HIS 0.003 0.001 HIS B 582 PHE 0.044 0.001 PHE B 976 TYR 0.019 0.001 TYR B 78 ARG 0.029 0.000 ARG B 534 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 310 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8665 (mm) REVERT: B 353 LEU cc_start: 0.8255 (pp) cc_final: 0.7999 (mm) REVERT: B 357 TYR cc_start: 0.8130 (t80) cc_final: 0.7410 (t80) REVERT: B 385 TYR cc_start: 0.8614 (t80) cc_final: 0.8296 (t80) REVERT: B 548 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.6438 (t80) REVERT: B 944 MET cc_start: 0.8197 (mtp) cc_final: 0.7986 (mtp) REVERT: B 1027 ASN cc_start: 0.8615 (t0) cc_final: 0.8316 (t0) REVERT: A 696 MET cc_start: 0.8373 (tmm) cc_final: 0.8129 (tmm) REVERT: A 891 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.6732 (mmm) REVERT: C 76 MET cc_start: 0.8401 (ttp) cc_final: 0.8128 (ptm) outliers start: 75 outliers final: 64 residues processed: 360 average time/residue: 0.2998 time to fit residues: 180.9323 Evaluate side-chains 364 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 297 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 548 PHE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 821 GLN Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 906 SER Chi-restraints excluded: chain C residue 916 ASP Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 36 optimal weight: 0.0170 chunk 68 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 252 optimal weight: 0.8980 chunk 31 optimal weight: 0.0570 chunk 45 optimal weight: 0.9980 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN C 843 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076473 restraints weight = 52059.567| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.65 r_work: 0.2936 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24363 Z= 0.160 Angle : 0.543 11.443 33108 Z= 0.271 Chirality : 0.041 0.295 3946 Planarity : 0.004 0.067 4196 Dihedral : 4.387 55.232 3303 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.52 % Allowed : 18.39 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.77 (0.15), residues: 3090 helix: 2.06 (0.12), residues: 1744 sheet: -0.04 (0.25), residues: 449 loop : 0.16 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 853 HIS 0.003 0.001 HIS B 582 PHE 0.033 0.001 PHE B 542 TYR 0.018 0.001 TYR B 78 ARG 0.014 0.000 ARG B 534 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5360.57 seconds wall clock time: 98 minutes 19.39 seconds (5899.39 seconds total)