Starting phenix.real_space_refine on Mon May 13 04:52:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk4_40179/05_2024/8gk4_40179_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk4_40179/05_2024/8gk4_40179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk4_40179/05_2024/8gk4_40179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk4_40179/05_2024/8gk4_40179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk4_40179/05_2024/8gk4_40179_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk4_40179/05_2024/8gk4_40179_trim_updated.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 84 5.16 5 Cl 2 4.86 5 C 15509 2.51 5 N 3854 2.21 5 O 4462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 701": "NH1" <-> "NH2" Residue "B ARG 947": "NH1" <-> "NH2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 802": "NH1" <-> "NH2" Residue "C TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 956": "OE1" <-> "OE2" Residue "C PHE 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 23911 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 7956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7956 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 989} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 7970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7970 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7985 Unusual residues: {'CLM': 1} Classifications: {'peptide': 1031, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 41, 'TRANS': 989, None: 1} Not linked: pdbres="ASP C1031 " pdbres="CLM C1101 " Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 12.49, per 1000 atoms: 0.52 Number of scatterers: 23911 At special positions: 0 Unit cell: (119.84, 119.84, 150.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 84 16.00 O 4462 8.00 N 3854 7.00 C 15509 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: 9.99 Conformation dependent library (CDL) restraints added in 4.1 seconds 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 24 sheets defined 54.7% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.07 Creating SS restraints... Processing helix chain 'B' and resid 2 through 8 removed outlier: 4.095A 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 60 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 100 through 117 removed outlier: 4.399A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 151 through 160 removed outlier: 3.678A pdb=" N LEU B 160 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 168 removed outlier: 3.510A pdb=" N LEU B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) 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: 3.827A pdb=" N ASN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 360 removed outlier: 3.946A pdb=" N ALA B 336 " --> pdb=" O PHE B 333 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 360 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 387 Proline residue: B 369 - end of helix removed outlier: 3.732A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 393 through 421 removed outlier: 4.386A pdb=" N GLY B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 459 removed outlier: 4.744A 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 498 removed outlier: 3.713A pdb=" N PHE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 509 through 533 removed outlier: 3.981A pdb=" N SER B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 555 Processing helix chain 'B' and resid 581 through 597 Processing helix chain 'B' and resid 638 through 653 removed outlier: 4.583A pdb=" N ALA B 651 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP B 652 " --> pdb=" O GLN B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 702 Processing helix chain 'B' and resid 726 through 731 Processing helix chain 'B' and resid 736 through 746 Processing helix chain 'B' and resid 778 through 780 No H-bonds generated for 'chain 'B' and resid 778 through 780' 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 845 Processing helix chain 'B' and resid 856 through 861 Processing helix chain 'B' and resid 868 through 885 removed outlier: 4.583A pdb=" N VAL B 872 " --> pdb=" O ALA B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 913 removed outlier: 3.707A pdb=" N THR B 897 " --> pdb=" O ALA B 894 " (cutoff:3.500A) Proline residue: B 900 - end of helix removed outlier: 3.550A pdb=" N ILE B 907 " --> pdb=" O PHE B 904 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL B 910 " --> pdb=" O ILE B 907 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 913 " --> pdb=" O VAL B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 948 removed outlier: 3.709A pdb=" N LEU B 926 " --> pdb=" O GLN B 922 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 927 " --> pdb=" O THR B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 984 removed outlier: 4.278A pdb=" N ARG B 967 " --> pdb=" O LYS B 963 " (cutoff:3.500A) Proline residue: B 968 - end of helix Proline residue: B 982 - end of helix Processing helix chain 'B' and resid 991 through 1009 Processing helix chain 'B' and resid 1011 through 1030 Proline residue: B1017 - end of helix Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.599A 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 124 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.629A pdb=" N LEU A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 162 through 166' Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 201 through 211 Processing helix chain 'A' and resid 244 through 249 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: 4.019A pdb=" N ASN A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 360 Processing helix chain 'A' and resid 363 through 386 removed outlier: 3.946A pdb=" N ILE A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.577A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Proline residue: A 374 - end of helix removed outlier: 3.533A pdb=" N ALA A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 removed outlier: 4.286A pdb=" N GLY A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 460 removed outlier: 4.915A pdb=" N SER A 442 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix removed outlier: 3.514A pdb=" N PHE A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Proline residue: A 457 - end of helix removed outlier: 4.133A pdb=" N PHE A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 488 removed outlier: 3.639A 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: 3.559A pdb=" N SER A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 555 removed outlier: 3.527A pdb=" N VAL A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 597 Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 686 through 702 removed outlier: 3.760A pdb=" N GLN A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'A' and resid 736 through 746 Processing helix chain 'A' and resid 757 through 759 No H-bonds generated for 'chain 'A' and resid 757 through 759' Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.830A pdb=" N LEU A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 797 No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 830 through 844 Processing helix chain 'A' and resid 855 through 862 Processing helix chain 'A' and resid 865 through 886 removed outlier: 3.846A pdb=" N TYR A 869 " --> pdb=" O ALA A 866 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 870 " --> pdb=" O GLY A 867 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 873 " --> pdb=" O ALA A 870 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 874 " --> pdb=" O PHE A 871 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 878 " --> pdb=" O MET A 875 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 882 " --> pdb=" O PHE A 879 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 883 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 886 " --> pdb=" O ALA A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 913 removed outlier: 4.307A pdb=" N LEU A 893 " --> pdb=" O TRP A 889 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 4.250A 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: 3.855A pdb=" N GLY A 930 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 984 removed outlier: 3.537A pdb=" N ALA A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.842A 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 1009 Processing helix chain 'A' and resid 1011 through 1031 Proline residue: A1017 - end of helix Processing helix chain 'C' and resid 2 through 8 removed outlier: 3.861A pdb=" N PHE C 6 " --> pdb=" O PHE C 2 " (cutoff:3.500A) 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: 3.771A pdb=" N ALA C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.581A pdb=" N LYS C 196 " --> pdb=" O ASP C 192 " (cutoff:3.500A) 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 317 removed outlier: 3.625A pdb=" N LYS C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 359 Processing helix chain 'C' and resid 363 through 387 removed outlier: 4.064A pdb=" N ILE C 367 " --> pdb=" O PHE C 363 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Proline residue: C 369 - end of helix Proline residue: C 374 - end of helix Processing helix chain 'C' and resid 393 through 423 removed outlier: 3.945A pdb=" N GLY C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 460 removed outlier: 4.721A pdb=" N SER C 442 " --> pdb=" O ASN C 438 " (cutoff:3.500A) Proline residue: C 443 - end of helix removed outlier: 3.614A pdb=" N CYS C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Proline residue: C 457 - end of helix Processing helix chain 'C' and resid 463 through 488 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 removed outlier: 3.534A pdb=" N LEU C 540 " --> pdb=" O ILE C 536 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 597 removed outlier: 3.542A pdb=" N GLN C 597 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 649 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 Processing helix chain 'C' and resid 776 through 781 removed outlier: 3.920A 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 removed outlier: 3.626A pdb=" N VAL C 878 " --> pdb=" O GLY C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 913 Proline residue: C 900 - end of helix removed outlier: 3.990A pdb=" N GLY C 905 " --> pdb=" O ALA C 902 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 906 " --> pdb=" O VAL C 903 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 913 " --> pdb=" O VAL C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 948 removed outlier: 3.557A pdb=" N LEU C 927 " --> pdb=" O THR C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 985 removed outlier: 4.337A pdb=" N ARG C 967 " --> pdb=" O LYS C 963 " (cutoff:3.500A) Proline residue: C 968 - end of helix Proline residue: C 982 - end of helix removed outlier: 3.687A pdb=" N PHE C 985 " --> pdb=" O LEU C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1030 removed outlier: 3.781A pdb=" N ALA C1012 " --> pdb=" O ALA C1008 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE C1013 " --> pdb=" O SER C1009 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE C1014 " --> pdb=" O THR C1010 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C1015 " --> pdb=" O LEU C1011 " (cutoff:3.500A) Proline residue: C1017 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= B, first strand: chain 'B' and resid 322 through 325 removed outlier: 3.733A pdb=" N GLU B 138 " --> pdb=" O ILE B 292 " (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 280 through 282 removed outlier: 6.898A pdb=" N ILE B 627 " --> pdb=" O SER B 602 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER B 604 " --> pdb=" O PHE B 625 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE B 625 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER B 606 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 623 " --> pdb=" O SER B 606 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE B 608 " --> pdb=" O ALA B 621 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ALA B 621 " --> pdb=" O ILE B 608 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 817 through 819 Processing sheet with id= F, first strand: chain 'B' and resid 718 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: 6.860A pdb=" N LEU B 261 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 128 through 132 removed outlier: 4.065A pdb=" N THR A 43 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 322 through 325 removed outlier: 6.788A pdb=" N ILE A 292 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A 139 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE A 290 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER A 141 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL A 288 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 267 through 273 Processing sheet with id= M, first strand: chain 'A' and resid 279 through 282 removed outlier: 6.760A pdb=" N ILE A 627 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 604 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE A 625 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A 606 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 623 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE A 608 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA A 621 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.575A pdb=" N ALA A 818 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU A 675 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 717 through 724 Processing sheet with id= P, first strand: chain 'A' and resid 783 through 785 Processing sheet with id= Q, first strand: chain 'C' and resid 128 through 131 removed outlier: 12.348A pdb=" N ASP C 808 " --> pdb=" O LEU C 819 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N LEU C 819 " --> pdb=" O ASP C 808 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS C 810 " --> pdb=" O ALA C 817 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 322 through 325 removed outlier: 6.987A pdb=" N ILE C 292 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL C 139 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE C 290 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER C 141 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 288 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR C 143 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA C 286 " --> pdb=" O TYR C 143 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 267 through 269 removed outlier: 3.715A pdb=" N ASN C 753 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE C 766 " --> pdb=" O TYR C 751 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TYR C 751 " --> pdb=" O ILE C 766 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 216 through 220 Processing sheet with id= U, first strand: chain 'C' and resid 279 through 282 removed outlier: 6.829A pdb=" N ILE C 627 " --> pdb=" O SER C 602 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER C 604 " --> pdb=" O PHE C 625 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE C 625 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER C 606 " --> pdb=" O ALA C 623 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA C 623 " --> pdb=" O SER C 606 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE C 608 " --> pdb=" O ALA C 621 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA C 621 " --> pdb=" O ILE C 608 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 718 through 724 Processing sheet with id= W, first strand: chain 'C' and resid 783 through 785 Processing sheet with id= X, first strand: chain 'C' and resid 251 through 254 removed outlier: 6.920A pdb=" N LEU C 261 " --> pdb=" O LEU C 252 " (cutoff:3.500A) 1334 hydrogen bonds defined for protein. 3732 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: 8.86 Time building geometry restraints manager: 10.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7415 1.33 - 1.45: 3126 1.45 - 1.57: 13668 1.57 - 1.69: 0 1.69 - 1.81: 164 Bond restraints: 24373 Sorted by residual: bond pdb=" N9 CLM C1101 " pdb=" O9A CLM C1101 " ideal model delta sigma weight residual 1.209 1.399 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" CA SER C 84 " pdb=" C SER C 84 " ideal model delta sigma weight residual 1.520 1.482 0.038 1.02e-02 9.61e+03 1.37e+01 bond pdb=" C ILE A 792 " pdb=" N PRO A 793 " ideal model delta sigma weight residual 1.332 1.375 -0.043 1.33e-02 5.65e+03 1.04e+01 bond pdb=" CA ILE C 456 " pdb=" C ILE C 456 " ideal model delta sigma weight residual 1.520 1.546 -0.027 8.80e-03 1.29e+04 9.10e+00 bond pdb=" CA VAL B 899 " pdb=" C VAL B 899 " ideal model delta sigma weight residual 1.520 1.546 -0.026 8.80e-03 1.29e+04 8.97e+00 ... (remaining 24368 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.78: 582 105.78 - 113.64: 13551 113.64 - 121.49: 14863 121.49 - 129.35: 4020 129.35 - 137.21: 99 Bond angle restraints: 33115 Sorted by residual: angle pdb=" N ASP A 652 " pdb=" CA ASP A 652 " pdb=" C ASP A 652 " ideal model delta sigma weight residual 111.82 100.93 10.89 1.16e+00 7.43e-01 8.82e+01 angle pdb=" N ILE C 178 " pdb=" CA ILE C 178 " pdb=" C ILE C 178 " ideal model delta sigma weight residual 110.62 119.78 -9.16 1.02e+00 9.61e-01 8.07e+01 angle pdb=" N VAL A 752 " pdb=" CA VAL A 752 " pdb=" C VAL A 752 " ideal model delta sigma weight residual 110.42 117.49 -7.07 9.40e-01 1.13e+00 5.65e+01 angle pdb=" N GLY C 874 " pdb=" CA GLY C 874 " pdb=" C GLY C 874 " ideal model delta sigma weight residual 115.32 105.55 9.77 1.31e+00 5.83e-01 5.56e+01 angle pdb=" N ILE A 162 " pdb=" CA ILE A 162 " pdb=" C ILE A 162 " ideal model delta sigma weight residual 110.62 118.22 -7.60 1.02e+00 9.61e-01 5.56e+01 ... (remaining 33110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 13225 14.11 - 28.22: 1068 28.22 - 42.33: 286 42.33 - 56.43: 57 56.43 - 70.54: 8 Dihedral angle restraints: 14644 sinusoidal: 5611 harmonic: 9033 Sorted by residual: dihedral pdb=" N TYR C 50 " pdb=" C TYR C 50 " pdb=" CA TYR C 50 " pdb=" CB TYR C 50 " ideal model delta harmonic sigma weight residual 122.80 112.44 10.36 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" C PHE C 740 " pdb=" N PHE C 740 " pdb=" CA PHE C 740 " pdb=" CB PHE C 740 " ideal model delta harmonic sigma weight residual -122.60 -132.60 10.00 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" C PHE C1015 " pdb=" N PHE C1015 " pdb=" CA PHE C1015 " pdb=" CB PHE C1015 " ideal model delta harmonic sigma weight residual -122.60 -132.47 9.87 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 14641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3080 0.097 - 0.194: 717 0.194 - 0.290: 124 0.290 - 0.387: 17 0.387 - 0.484: 4 Chirality restraints: 3942 Sorted by residual: 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 2.03 0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CA PHE C1015 " pdb=" N PHE C1015 " pdb=" C PHE C1015 " pdb=" CB PHE C1015 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CA PHE C 740 " pdb=" N PHE C 740 " pdb=" C PHE C 740 " pdb=" CB PHE C 740 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.35e+00 ... (remaining 3939 not shown) Planarity restraints: 4198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 891 " 0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO A 892 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 892 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 892 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 456 " 0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO C 457 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 457 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 457 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 442 " -0.052 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO A 443 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 443 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 443 " -0.044 5.00e-02 4.00e+02 ... (remaining 4195 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 8142 2.84 - 3.35: 25144 3.35 - 3.87: 41497 3.87 - 4.38: 50754 4.38 - 4.90: 79823 Nonbonded interactions: 205360 Sorted by model distance: nonbonded pdb=" CB LEU B 948 " pdb=" NZ LYS B 949 " model vdw 2.324 3.520 nonbonded pdb=" O LEU C 699 " pdb=" OG1 THR C 702 " model vdw 2.448 2.440 nonbonded pdb=" N ALA B 707 " pdb=" O ASP B 823 " model vdw 2.450 2.520 nonbonded pdb=" O ASN B 362 " pdb=" OG SER B 365 " model vdw 2.455 2.440 nonbonded pdb=" O THR B 491 " pdb=" OG SER B 495 " model vdw 2.460 2.440 ... (remaining 205355 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 501 or (resid 502 through 503 and (name N or nam \ e CA or name C or name O or name CB )) or resid 504 through 652 or (resid 653 an \ d (name N or name CA or name C or name O or name CB )) or resid 654 through 831 \ or (resid 832 through 833 and (name N or name CA or name C or name O or name CB \ )) or resid 834 through 838 or (resid 839 and (name N or name CA or name C or na \ me O or name CB )) or resid 840 through 863 or (resid 864 and (name N or name CA \ or name C or name O or name CB )) or resid 865 through 1031)) selection = (chain 'B' and (resid 1 through 255 or (resid 256 and (name N or name CA or name \ C or name O or name CB )) or resid 257 or (resid 258 and (name N or name CA or \ name C or name O or name CB )) or resid 259 through 831 or (resid 832 through 83 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 834 through \ 838 or (resid 839 and (name N or name CA or name C or name O or name CB )) or re \ sid 840 through 1031)) selection = (chain 'C' and (resid 1 through 255 or (resid 256 and (name N or name CA or name \ C or name O or name CB )) or resid 257 or (resid 258 and (name N or name CA or \ name C or name O or name CB )) or resid 259 through 501 or (resid 502 through 50 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 504 through \ 652 or (resid 653 and (name N or name CA or name C or name O or name CB )) or re \ sid 654 through 863 or (resid 864 and (name N or name CA or name C or name O or \ name CB )) or resid 865 through 1031)) } 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: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.230 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 63.080 Find NCS groups from input model: 1.730 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 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 : 0.007 0.190 24373 Z= 0.461 Angle : 1.280 12.208 33115 Z= 0.893 Chirality : 0.085 0.484 3942 Planarity : 0.007 0.084 4198 Dihedral : 11.440 70.542 8804 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.43 % Favored : 97.54 % Rotamer: Outliers : 2.37 % Allowed : 7.10 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.46 (0.15), residues: 3088 helix: 0.83 (0.13), residues: 1738 sheet: 0.42 (0.24), residues: 426 loop : -0.59 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 853 HIS 0.005 0.002 HIS A 582 PHE 0.020 0.002 PHE A 755 TYR 0.018 0.002 TYR C 783 ARG 0.004 0.001 ARG C 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 807 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 THR cc_start: 0.7294 (m) cc_final: 0.6774 (p) outliers start: 62 outliers final: 5 residues processed: 852 average time/residue: 0.3581 time to fit residues: 477.5107 Evaluate side-chains 401 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 396 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 450 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: 6.9990 chunk 129 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 242 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 180 optimal weight: 7.9990 chunk 280 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 214 GLN B 245 GLN B 275 GLN B 299 ASN B 312 GLN B 325 GLN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN B 935 ASN A 214 GLN A 320 GLN A 597 GLN C 108 ASN C 308 ASN C 312 GLN C 502 ASN C 582 HIS C 592 ASN C 679 GLN C 691 GLN C 761 ASN C 795 ASN C 922 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24373 Z= 0.220 Angle : 0.592 9.554 33115 Z= 0.319 Chirality : 0.043 0.183 3942 Planarity : 0.005 0.066 4198 Dihedral : 4.787 50.079 3307 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.09 % Allowed : 14.81 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.04 (0.15), residues: 3088 helix: 1.48 (0.12), residues: 1729 sheet: 0.19 (0.23), residues: 444 loop : -0.45 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 853 HIS 0.006 0.001 HIS C 582 PHE 0.025 0.002 PHE A 509 TYR 0.040 0.002 TYR A 649 ARG 0.006 0.001 ARG B 802 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 443 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.7736 (ttp) cc_final: 0.7434 (ttp) REVERT: A 211 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7354 (mp10) outliers start: 81 outliers final: 41 residues processed: 499 average time/residue: 0.3179 time to fit residues: 262.4576 Evaluate side-chains 383 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 341 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1028 GLU 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: 1.9990 chunk 233 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 303 optimal weight: 3.9990 chunk 250 optimal weight: 0.6980 chunk 278 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 225 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 763 GLN B 776 GLN C 45 GLN C 293 ASN C 679 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24373 Z= 0.289 Angle : 0.570 7.822 33115 Z= 0.300 Chirality : 0.042 0.178 3942 Planarity : 0.005 0.054 4198 Dihedral : 4.741 55.896 3304 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.70 % Allowed : 16.98 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.27 (0.15), residues: 3088 helix: 1.66 (0.12), residues: 1730 sheet: 0.02 (0.22), residues: 456 loop : -0.19 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 631 HIS 0.002 0.001 HIS C 582 PHE 0.044 0.002 PHE B 516 TYR 0.023 0.002 TYR A 649 ARG 0.004 0.001 ARG B 534 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 356 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7406 (mp10) outliers start: 97 outliers final: 53 residues processed: 432 average time/residue: 0.3332 time to fit residues: 242.7932 Evaluate side-chains 371 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 317 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 1025 ASN Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 959 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 298 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN B 416 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN C 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24373 Z= 0.238 Angle : 0.536 11.982 33115 Z= 0.278 Chirality : 0.041 0.300 3942 Planarity : 0.004 0.050 4198 Dihedral : 4.622 56.318 3302 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.36 % Allowed : 17.82 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.38 (0.15), residues: 3088 helix: 1.82 (0.12), residues: 1720 sheet: 0.08 (0.23), residues: 447 loop : -0.29 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 631 HIS 0.002 0.001 HIS B 995 PHE 0.018 0.001 PHE B 516 TYR 0.020 0.001 TYR A 649 ARG 0.003 0.000 ARG B 802 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 352 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.7658 (ttp) cc_final: 0.7376 (ttp) REVERT: C 649 TYR cc_start: 0.5624 (m-80) cc_final: 0.5400 (m-80) outliers start: 88 outliers final: 62 residues processed: 421 average time/residue: 0.3037 time to fit residues: 214.2005 Evaluate side-chains 376 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 314 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 754 ASP Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 460 PHE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 0.0980 chunk 169 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 471 GLN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1027 ASN C 293 ASN C 502 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24373 Z= 0.265 Angle : 0.543 9.435 33115 Z= 0.280 Chirality : 0.042 0.248 3942 Planarity : 0.004 0.045 4198 Dihedral : 4.639 57.599 3302 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.78 % Allowed : 18.28 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.43 (0.15), residues: 3088 helix: 1.87 (0.12), residues: 1717 sheet: 0.12 (0.23), residues: 457 loop : -0.30 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 631 HIS 0.002 0.001 HIS B 995 PHE 0.018 0.001 PHE C 318 TYR 0.025 0.001 TYR A 649 ARG 0.004 0.000 ARG A 888 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 340 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.7747 (ttp) cc_final: 0.7457 (ttp) REVERT: C 490 LEU cc_start: 0.7638 (tt) cc_final: 0.7297 (tt) REVERT: C 649 TYR cc_start: 0.5688 (m-80) cc_final: 0.5425 (m-80) outliers start: 99 outliers final: 70 residues processed: 417 average time/residue: 0.3104 time to fit residues: 219.8424 Evaluate side-chains 379 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 309 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 754 ASP Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 460 PHE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 502 ASN Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 0.9990 chunk 268 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 471 GLN B 661 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24373 Z= 0.215 Angle : 0.518 8.354 33115 Z= 0.268 Chirality : 0.041 0.151 3942 Planarity : 0.004 0.044 4198 Dihedral : 4.581 59.020 3302 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.47 % Allowed : 19.08 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.49 (0.15), residues: 3088 helix: 1.94 (0.12), residues: 1722 sheet: 0.15 (0.23), residues: 459 loop : -0.34 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 889 HIS 0.002 0.001 HIS C 422 PHE 0.019 0.001 PHE B 485 TYR 0.019 0.001 TYR A 649 ARG 0.003 0.000 ARG C 501 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 336 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.7663 (ttp) cc_final: 0.7378 (ttp) REVERT: C 649 TYR cc_start: 0.5691 (m-80) cc_final: 0.5417 (m-80) outliers start: 91 outliers final: 76 residues processed: 403 average time/residue: 0.3327 time to fit residues: 227.7356 Evaluate side-chains 384 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 308 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 754 ASP Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 773 ARG Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 460 PHE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 169 optimal weight: 0.2980 chunk 251 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 297 optimal weight: 0.6980 chunk 186 optimal weight: 0.9980 chunk 181 optimal weight: 0.0370 chunk 137 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 471 GLN B 661 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24373 Z= 0.159 Angle : 0.507 9.216 33115 Z= 0.261 Chirality : 0.040 0.160 3942 Planarity : 0.004 0.043 4198 Dihedral : 4.489 58.908 3302 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.98 % Allowed : 19.66 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.56 (0.15), residues: 3088 helix: 2.02 (0.12), residues: 1716 sheet: 0.20 (0.24), residues: 451 loop : -0.35 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 889 HIS 0.002 0.001 HIS B 582 PHE 0.025 0.001 PHE C 318 TYR 0.024 0.001 TYR B 357 ARG 0.003 0.000 ARG C 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 344 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.7566 (ttp) cc_final: 0.7274 (ttp) REVERT: C 88 MET cc_start: 0.7693 (tmm) cc_final: 0.7461 (tmm) REVERT: C 649 TYR cc_start: 0.5611 (m-80) cc_final: 0.5345 (m-80) outliers start: 78 outliers final: 62 residues processed: 398 average time/residue: 0.3071 time to fit residues: 206.3412 Evaluate side-chains 377 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 315 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 754 ASP Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 chunk 89 optimal weight: 0.0870 chunk 58 optimal weight: 0.0170 chunk 57 optimal weight: 6.9990 chunk 189 optimal weight: 0.0370 chunk 202 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 234 optimal weight: 0.9990 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 GLN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 471 GLN B 661 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24373 Z= 0.149 Angle : 0.504 9.628 33115 Z= 0.258 Chirality : 0.040 0.163 3942 Planarity : 0.004 0.043 4198 Dihedral : 4.345 57.866 3302 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.79 % Allowed : 20.11 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.64 (0.15), residues: 3088 helix: 2.05 (0.12), residues: 1717 sheet: 0.33 (0.24), residues: 455 loop : -0.33 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP B 853 HIS 0.002 0.001 HIS B 582 PHE 0.023 0.001 PHE C 318 TYR 0.017 0.001 TYR B 649 ARG 0.002 0.000 ARG C 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 349 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.7445 (ppp) cc_final: 0.7062 (ptm) REVERT: C 88 MET cc_start: 0.7677 (tmm) cc_final: 0.7451 (tmm) REVERT: C 649 TYR cc_start: 0.5570 (m-80) cc_final: 0.5302 (m-80) outliers start: 73 outliers final: 60 residues processed: 397 average time/residue: 0.3231 time to fit residues: 219.8958 Evaluate side-chains 383 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 323 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 754 ASP Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 773 ARG Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 2.9990 chunk 285 optimal weight: 0.8980 chunk 260 optimal weight: 0.7980 chunk 277 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 250 optimal weight: 0.9980 chunk 262 optimal weight: 0.9980 chunk 276 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 661 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24373 Z= 0.195 Angle : 0.529 10.387 33115 Z= 0.269 Chirality : 0.040 0.159 3942 Planarity : 0.004 0.043 4198 Dihedral : 4.308 54.119 3302 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.71 % Allowed : 20.42 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.63 (0.15), residues: 3088 helix: 2.06 (0.12), residues: 1719 sheet: 0.27 (0.24), residues: 452 loop : -0.33 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 889 HIS 0.002 0.001 HIS B 582 PHE 0.023 0.001 PHE C 318 TYR 0.022 0.001 TYR B 357 ARG 0.002 0.000 ARG B 802 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 331 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.7446 (ppp) cc_final: 0.7056 (ptm) REVERT: C 88 MET cc_start: 0.7698 (tmm) cc_final: 0.7484 (tmm) REVERT: C 649 TYR cc_start: 0.5634 (m-80) cc_final: 0.5355 (m-80) outliers start: 71 outliers final: 59 residues processed: 378 average time/residue: 0.3039 time to fit residues: 195.3136 Evaluate side-chains 378 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 319 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 754 ASP Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 495 SER Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 788 ASP Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.0000 chunk 293 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 307 optimal weight: 0.7980 chunk 283 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 189 optimal weight: 0.0980 chunk 150 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 ASN B 214 GLN B 661 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24373 Z= 0.162 Angle : 0.518 11.202 33115 Z= 0.263 Chirality : 0.040 0.164 3942 Planarity : 0.004 0.043 4198 Dihedral : 4.202 48.560 3302 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.44 % Allowed : 20.76 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 3088 helix: 2.04 (0.12), residues: 1721 sheet: 0.33 (0.24), residues: 454 loop : -0.37 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 889 HIS 0.002 0.001 HIS B 582 PHE 0.021 0.001 PHE C 318 TYR 0.019 0.001 TYR B1021 ARG 0.002 0.000 ARG B 802 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 335 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.7368 (ppp) cc_final: 0.7048 (ptm) REVERT: C 88 MET cc_start: 0.7690 (tmm) cc_final: 0.7468 (tmm) REVERT: C 649 TYR cc_start: 0.5570 (m-80) cc_final: 0.5301 (m-80) outliers start: 64 outliers final: 60 residues processed: 378 average time/residue: 0.3188 time to fit residues: 203.7991 Evaluate side-chains 385 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 325 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 754 ASP Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2591 > 50: distance: 5 - 24: 5.951 distance: 9 - 36: 29.374 distance: 15 - 44: 14.897 distance: 20 - 23: 4.067 distance: 21 - 22: 6.105 distance: 21 - 24: 4.099 distance: 24 - 25: 3.837 distance: 25 - 26: 7.086 distance: 25 - 28: 11.019 distance: 26 - 27: 15.910 distance: 26 - 36: 20.932 distance: 27 - 64: 3.976 distance: 28 - 29: 8.806 distance: 29 - 30: 13.862 distance: 29 - 31: 11.778 distance: 30 - 32: 8.829 distance: 31 - 33: 10.119 distance: 32 - 34: 12.084 distance: 33 - 34: 16.113 distance: 34 - 35: 8.229 distance: 36 - 37: 34.740 distance: 37 - 38: 6.676 distance: 37 - 40: 25.636 distance: 38 - 39: 5.584 distance: 38 - 44: 10.116 distance: 40 - 41: 38.014 distance: 41 - 42: 27.204 distance: 41 - 43: 23.819 distance: 44 - 45: 4.638 distance: 45 - 46: 5.126 distance: 45 - 48: 8.425 distance: 46 - 55: 4.128 distance: 49 - 50: 4.366 distance: 49 - 51: 9.591 distance: 50 - 52: 3.930 distance: 51 - 53: 6.087 distance: 52 - 54: 8.645 distance: 53 - 54: 6.096 distance: 55 - 56: 3.236 distance: 56 - 57: 5.785 distance: 56 - 59: 9.226 distance: 57 - 58: 3.348 distance: 59 - 60: 7.122 distance: 60 - 61: 11.050 distance: 61 - 62: 10.299 distance: 62 - 63: 7.738 distance: 64 - 65: 4.360 distance: 65 - 66: 7.268 distance: 65 - 68: 9.513 distance: 66 - 67: 3.693 distance: 66 - 72: 6.915 distance: 68 - 69: 11.938 distance: 68 - 70: 11.556 distance: 69 - 71: 10.623 distance: 72 - 73: 6.625 distance: 73 - 74: 5.393 distance: 73 - 76: 6.128 distance: 74 - 75: 4.504 distance: 74 - 79: 5.729 distance: 76 - 77: 14.616 distance: 76 - 78: 28.027 distance: 79 - 80: 5.990 distance: 79 - 85: 10.047 distance: 80 - 81: 3.505 distance: 80 - 83: 11.940 distance: 81 - 82: 6.418 distance: 81 - 86: 3.741 distance: 83 - 84: 7.690 distance: 84 - 85: 12.948 distance: 86 - 87: 4.474 distance: 87 - 88: 6.702 distance: 87 - 90: 9.272 distance: 88 - 89: 15.746 distance: 88 - 92: 10.149 distance: 90 - 91: 6.160 distance: 92 - 93: 8.933 distance: 93 - 96: 6.349 distance: 94 - 95: 16.762 distance: 94 - 98: 4.384 distance: 96 - 97: 8.768