Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 11 23:02:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk4_40179/10_2023/8gk4_40179_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk4_40179/10_2023/8gk4_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_40179/10_2023/8gk4_40179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk4_40179/10_2023/8gk4_40179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk4_40179/10_2023/8gk4_40179_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk4_40179/10_2023/8gk4_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 12.03, per 1000 atoms: 0.50 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: 9.67 Conformation dependent library (CDL) restraints added in 3.4 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: 5.52 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: 9.25 Time building geometry restraints manager: 10.32 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: 13217 14.11 - 28.22: 1066 28.22 - 42.33: 286 42.33 - 56.43: 55 56.43 - 70.54: 8 Dihedral angle restraints: 14632 sinusoidal: 5599 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 14629 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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.740 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 61.860 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.270 ------------------------------------------------------------------------------- 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 : 11.419 70.542 8792 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 *********************** 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 : 2.954 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 outliers start: 62 outliers final: 5 residues processed: 852 average time/residue: 0.3560 time to fit residues: 474.8311 Evaluate side-chains 400 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 395 time to evaluate : 2.776 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2151 time to fit residues: 5.8410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 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 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2959 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 9.438 33115 Z= 0.319 Chirality : 0.042 0.175 3942 Planarity : 0.005 0.066 4198 Dihedral : 4.540 48.759 3289 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.05 % Allowed : 14.81 % Favored : 82.14 % 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: 1.01 (0.15), residues: 3088 helix: 1.44 (0.12), residues: 1729 sheet: 0.14 (0.23), residues: 447 loop : -0.42 (0.19), residues: 912 *********************** 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 523 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 443 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 40 residues processed: 498 average time/residue: 0.3219 time to fit residues: 265.7030 Evaluate side-chains 383 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 343 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2283 time to fit residues: 20.7647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 233 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 281 optimal weight: 0.9980 chunk 303 optimal weight: 0.6980 chunk 250 optimal weight: 0.9980 chunk 278 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 225 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 C 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24373 Z= 0.204 Angle : 0.537 7.207 33115 Z= 0.282 Chirality : 0.041 0.197 3942 Planarity : 0.004 0.054 4198 Dihedral : 4.374 50.693 3289 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.06 % Allowed : 17.60 % Favored : 80.34 % 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: 1.31 (0.15), residues: 3088 helix: 1.71 (0.12), residues: 1729 sheet: 0.10 (0.22), residues: 469 loop : -0.25 (0.20), residues: 890 *********************** 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 436 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 382 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 25 residues processed: 422 average time/residue: 0.3024 time to fit residues: 212.9511 Evaluate side-chains 348 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 323 time to evaluate : 2.861 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2102 time to fit residues: 13.6629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 3.9990 chunk 211 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 298 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 267 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 293 ASN C 502 ASN C 679 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24373 Z= 0.185 Angle : 0.520 13.402 33115 Z= 0.269 Chirality : 0.041 0.269 3942 Planarity : 0.004 0.051 4198 Dihedral : 4.278 51.615 3289 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.60 % Allowed : 17.82 % Favored : 80.57 % 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: 1.47 (0.15), residues: 3088 helix: 1.86 (0.12), residues: 1715 sheet: 0.23 (0.23), residues: 444 loop : -0.22 (0.20), residues: 929 *********************** 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 409 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 367 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 22 residues processed: 396 average time/residue: 0.3113 time to fit residues: 207.1654 Evaluate side-chains 343 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 321 time to evaluate : 2.535 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2101 time to fit residues: 12.1591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 5.9990 chunk 169 optimal weight: 0.0370 chunk 4 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 152 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1464 ------------------------------------------------------------------------------- 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** C 293 ASN C 422 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24373 Z= 0.224 Angle : 0.527 11.193 33115 Z= 0.269 Chirality : 0.041 0.199 3942 Planarity : 0.004 0.045 4198 Dihedral : 4.252 52.148 3289 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.56 % Allowed : 18.74 % Favored : 79.69 % 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: 1.50 (0.15), residues: 3088 helix: 1.89 (0.12), residues: 1720 sheet: 0.27 (0.24), residues: 450 loop : -0.28 (0.20), residues: 918 *********************** 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 389 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 348 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 24 residues processed: 375 average time/residue: 0.3080 time to fit residues: 193.4662 Evaluate side-chains 339 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 315 time to evaluate : 2.712 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2175 time to fit residues: 13.4960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 C 422 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4235 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= 0.289 Angle : 0.551 9.854 33115 Z= 0.284 Chirality : 0.042 0.182 3942 Planarity : 0.004 0.044 4198 Dihedral : 4.331 52.871 3289 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.18 % Allowed : 19.47 % Favored : 79.35 % 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: 1.47 (0.15), residues: 3088 helix: 1.91 (0.12), residues: 1716 sheet: 0.17 (0.23), residues: 461 loop : -0.32 (0.20), residues: 911 *********************** 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 356 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 325 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 347 average time/residue: 0.3017 time to fit residues: 176.3378 Evaluate side-chains 316 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 302 time to evaluate : 2.570 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2172 time to fit residues: 9.4610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 170 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 169 optimal weight: 0.0370 chunk 251 optimal weight: 0.3980 chunk 166 optimal weight: 5.9990 chunk 297 optimal weight: 0.6980 chunk 186 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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: 0.7256 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24373 Z= 0.163 Angle : 0.510 10.651 33115 Z= 0.261 Chirality : 0.040 0.163 3942 Planarity : 0.004 0.043 4198 Dihedral : 4.216 51.742 3289 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.65 % Allowed : 20.00 % Favored : 79.35 % 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: 2.00 (0.12), residues: 1719 sheet: 0.24 (0.24), residues: 450 loop : -0.33 (0.20), residues: 919 *********************** 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 370 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 353 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 364 average time/residue: 0.3150 time to fit residues: 192.2015 Evaluate side-chains 316 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 310 time to evaluate : 2.650 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2176 time to fit residues: 6.0941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 471 GLN ** 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: 0.7274 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24373 Z= 0.190 Angle : 0.518 11.557 33115 Z= 0.266 Chirality : 0.041 0.164 3942 Planarity : 0.004 0.044 4198 Dihedral : 4.182 51.873 3289 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.73 % Allowed : 20.73 % Favored : 78.55 % 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: 1.62 (0.15), residues: 3088 helix: 2.05 (0.12), residues: 1720 sheet: 0.27 (0.24), residues: 453 loop : -0.35 (0.20), residues: 915 *********************** 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 341 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 322 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 335 average time/residue: 0.3046 time to fit residues: 171.9690 Evaluate side-chains 317 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 308 time to evaluate : 2.691 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2174 time to fit residues: 7.3683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.7980 chunk 285 optimal weight: 0.9990 chunk 260 optimal weight: 0.6980 chunk 277 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 250 optimal weight: 0.5980 chunk 262 optimal weight: 0.0570 chunk 276 optimal weight: 7.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 ASN B 214 GLN B 471 GLN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24373 Z= 0.169 Angle : 0.525 11.655 33115 Z= 0.267 Chirality : 0.040 0.244 3942 Planarity : 0.004 0.043 4198 Dihedral : 4.124 51.709 3289 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.23 % Allowed : 21.18 % Favored : 78.59 % 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: 1.62 (0.15), residues: 3088 helix: 2.05 (0.12), residues: 1718 sheet: 0.30 (0.24), residues: 453 loop : -0.35 (0.20), residues: 917 *********************** 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 347 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 341 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 345 average time/residue: 0.3040 time to fit residues: 177.8957 Evaluate side-chains 317 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 315 time to evaluate : 2.688 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2202 time to fit residues: 4.5019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.0670 chunk 293 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 307 optimal weight: 0.7980 chunk 283 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 189 optimal weight: 0.0570 chunk 150 optimal weight: 0.7980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 ASN B 214 GLN B 661 ASN ** B 680 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24373 Z= 0.163 Angle : 0.519 11.956 33115 Z= 0.265 Chirality : 0.040 0.223 3942 Planarity : 0.004 0.043 4198 Dihedral : 4.088 51.804 3289 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.27 % Allowed : 21.45 % Favored : 78.28 % 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: 1.65 (0.15), residues: 3088 helix: 2.08 (0.12), residues: 1716 sheet: 0.29 (0.24), residues: 450 loop : -0.32 (0.20), residues: 922 ********************** 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 333 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 326 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 329 average time/residue: 0.3247 time to fit residues: 178.6419 Evaluate side-chains 316 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 313 time to evaluate : 3.192 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2406 time to fit residues: 5.1518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 75 optimal weight: 0.1980 chunk 226 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.094228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.077563 restraints weight = 48847.081| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.50 r_work: 0.2983 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4753 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= 0.203 Angle : 0.534 12.188 33115 Z= 0.272 Chirality : 0.041 0.183 3942 Planarity : 0.004 0.044 4198 Dihedral : 4.109 52.526 3289 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.15 % Allowed : 21.72 % Favored : 78.13 % 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: 1.65 (0.15), residues: 3088 helix: 2.08 (0.12), residues: 1719 sheet: 0.32 (0.24), residues: 455 loop : -0.34 (0.20), residues: 914 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5157.91 seconds wall clock time: 94 minutes 31.52 seconds (5671.52 seconds total)