Starting phenix.real_space_refine on Sun Mar 17 14:36:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9x_21129/03_2024/6v9x_21129_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9x_21129/03_2024/6v9x_21129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9x_21129/03_2024/6v9x_21129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9x_21129/03_2024/6v9x_21129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9x_21129/03_2024/6v9x_21129_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9x_21129/03_2024/6v9x_21129_updated.pdb" } resolution = 3.3 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 11856 2.51 5 N 3000 2.21 5 O 3100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A ARG 919": "NH1" <-> "NH2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A GLU 924": "OE1" <-> "OE2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A GLU 987": "OE1" <-> "OE2" Residue "A ARG 1050": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 632": "OE1" <-> "OE2" Residue "B GLU 668": "OE1" <-> "OE2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "B GLU 808": "OE1" <-> "OE2" Residue "B ARG 852": "NH1" <-> "NH2" Residue "B ARG 872": "NH1" <-> "NH2" Residue "B ARG 919": "NH1" <-> "NH2" Residue "B GLU 920": "OE1" <-> "OE2" Residue "B GLU 924": "OE1" <-> "OE2" Residue "B ARG 928": "NH1" <-> "NH2" Residue "B ARG 975": "NH1" <-> "NH2" Residue "B GLU 987": "OE1" <-> "OE2" Residue "B ARG 1050": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D GLU 594": "OE1" <-> "OE2" Residue "D PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 632": "OE1" <-> "OE2" Residue "D GLU 668": "OE1" <-> "OE2" Residue "D ARG 717": "NH1" <-> "NH2" Residue "D GLU 808": "OE1" <-> "OE2" Residue "D ARG 852": "NH1" <-> "NH2" Residue "D ARG 872": "NH1" <-> "NH2" Residue "D ARG 919": "NH1" <-> "NH2" Residue "D GLU 920": "OE1" <-> "OE2" Residue "D GLU 924": "OE1" <-> "OE2" Residue "D ARG 928": "NH1" <-> "NH2" Residue "D ARG 975": "NH1" <-> "NH2" Residue "D GLU 987": "OE1" <-> "OE2" Residue "D ARG 1050": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C GLU 594": "OE1" <-> "OE2" Residue "C PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 632": "OE1" <-> "OE2" Residue "C GLU 668": "OE1" <-> "OE2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C GLU 808": "OE1" <-> "OE2" Residue "C ARG 852": "NH1" <-> "NH2" Residue "C ARG 872": "NH1" <-> "NH2" Residue "C ARG 919": "NH1" <-> "NH2" Residue "C GLU 920": "OE1" <-> "OE2" Residue "C GLU 924": "OE1" <-> "OE2" Residue "C ARG 928": "NH1" <-> "NH2" Residue "C ARG 975": "NH1" <-> "NH2" Residue "C GLU 987": "OE1" <-> "OE2" Residue "C ARG 1050": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18084 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4521 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 20, 'TRANS': 550} Chain breaks: 3 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'YCM:plan-2': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 4521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4521 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 20, 'TRANS': 550} Chain breaks: 3 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'YCM:plan-2': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 4521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4521 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 20, 'TRANS': 550} Chain breaks: 3 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'YCM:plan-2': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 4521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4521 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 20, 'TRANS': 550} Chain breaks: 3 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'YCM:plan-2': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Time building chain proxies: 9.81, per 1000 atoms: 0.54 Number of scatterers: 18084 At special positions: 0 Unit cell: (117.913, 117.913, 141.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3100 8.00 N 3000 7.00 C 11856 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: 6.55 Conformation dependent library (CDL) restraints added in 3.7 seconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4376 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 0 sheets defined 65.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 448 through 455 Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 485 through 491 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 527 through 536 removed outlier: 3.529A pdb=" N THR A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 551 through 557 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 583 through 589 removed outlier: 3.717A pdb=" N ALA A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 623 through 629 Processing helix chain 'A' and resid 631 through 641 Processing helix chain 'A' and resid 667 through 669 No H-bonds generated for 'chain 'A' and resid 667 through 669' Processing helix chain 'A' and resid 684 through 691 Processing helix chain 'A' and resid 695 through 698 No H-bonds generated for 'chain 'A' and resid 695 through 698' Processing helix chain 'A' and resid 701 through 713 Processing helix chain 'A' and resid 715 through 739 removed outlier: 3.586A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 770 through 789 Processing helix chain 'A' and resid 804 through 822 removed outlier: 4.059A pdb=" N ILE A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) Proline residue: A 821 - end of helix Processing helix chain 'A' and resid 828 through 853 removed outlier: 3.685A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 853 " --> pdb=" O TYR A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 891 removed outlier: 3.529A pdb=" N ILE A 866 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 867 " --> pdb=" O GLU A 864 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 871 " --> pdb=" O LYS A 868 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR A 874 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 875 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 876 " --> pdb=" O SER A 873 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE A 877 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 878 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 881 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE A 884 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 885 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 887 " --> pdb=" O PHE A 884 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 913 Processing helix chain 'A' and resid 918 through 921 No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 923 through 927 Processing helix chain 'A' and resid 934 through 945 Processing helix chain 'A' and resid 947 through 989 removed outlier: 3.753A pdb=" N LEU A 952 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N HIS A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER A 972 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 998 removed outlier: 4.070A pdb=" N LYS A 997 " --> pdb=" O TRP A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1068 removed outlier: 3.597A pdb=" N LEU A1064 " --> pdb=" O LYS A1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 455 Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 485 through 491 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 517 through 522 Processing helix chain 'B' and resid 527 through 536 removed outlier: 3.530A pdb=" N THR B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 3.717A pdb=" N ALA B 587 " --> pdb=" O PHE B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 600 Processing helix chain 'B' and resid 605 through 609 Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 631 through 641 Processing helix chain 'B' and resid 667 through 669 No H-bonds generated for 'chain 'B' and resid 667 through 669' Processing helix chain 'B' and resid 684 through 691 Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 701 through 713 Processing helix chain 'B' and resid 715 through 739 removed outlier: 3.586A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 770 through 789 Processing helix chain 'B' and resid 804 through 822 removed outlier: 4.059A pdb=" N ILE B 816 " --> pdb=" O TYR B 812 " (cutoff:3.500A) Proline residue: B 821 - end of helix Processing helix chain 'B' and resid 828 through 853 removed outlier: 3.685A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE B 853 " --> pdb=" O TYR B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 891 removed outlier: 3.529A pdb=" N ILE B 866 " --> pdb=" O LEU B 863 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU B 867 " --> pdb=" O GLU B 864 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 871 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR B 874 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 875 " --> pdb=" O ARG B 872 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL B 876 " --> pdb=" O SER B 873 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE B 877 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 878 " --> pdb=" O VAL B 875 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 881 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE B 884 " --> pdb=" O LEU B 881 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY B 885 " --> pdb=" O LEU B 882 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 887 " --> pdb=" O PHE B 884 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 913 Processing helix chain 'B' and resid 918 through 921 No H-bonds generated for 'chain 'B' and resid 918 through 921' Processing helix chain 'B' and resid 923 through 927 Processing helix chain 'B' and resid 934 through 945 Processing helix chain 'B' and resid 947 through 989 removed outlier: 3.753A pdb=" N LEU B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER B 972 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 973 " --> pdb=" O LYS B 969 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 989 " --> pdb=" O SER B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 998 removed outlier: 4.070A pdb=" N LYS B 997 " --> pdb=" O TRP B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1068 removed outlier: 3.596A pdb=" N LEU B1064 " --> pdb=" O LYS B1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 Processing helix chain 'D' and resid 459 through 465 Processing helix chain 'D' and resid 485 through 491 Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 517 through 522 Processing helix chain 'D' and resid 527 through 536 removed outlier: 3.530A pdb=" N THR D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 551 through 557 Processing helix chain 'D' and resid 561 through 569 Processing helix chain 'D' and resid 583 through 589 removed outlier: 3.717A pdb=" N ALA D 587 " --> pdb=" O PHE D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 600 Processing helix chain 'D' and resid 605 through 609 Processing helix chain 'D' and resid 623 through 629 Processing helix chain 'D' and resid 631 through 641 Processing helix chain 'D' and resid 667 through 669 No H-bonds generated for 'chain 'D' and resid 667 through 669' Processing helix chain 'D' and resid 684 through 691 Processing helix chain 'D' and resid 695 through 698 No H-bonds generated for 'chain 'D' and resid 695 through 698' Processing helix chain 'D' and resid 701 through 713 Processing helix chain 'D' and resid 715 through 739 removed outlier: 3.585A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 770 through 789 Processing helix chain 'D' and resid 804 through 822 removed outlier: 4.059A pdb=" N ILE D 816 " --> pdb=" O TYR D 812 " (cutoff:3.500A) Proline residue: D 821 - end of helix Processing helix chain 'D' and resid 828 through 853 removed outlier: 3.684A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE D 853 " --> pdb=" O TYR D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 891 removed outlier: 3.529A pdb=" N ILE D 866 " --> pdb=" O LEU D 863 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU D 867 " --> pdb=" O GLU D 864 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 871 " --> pdb=" O LYS D 868 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR D 874 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 875 " --> pdb=" O ARG D 872 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL D 876 " --> pdb=" O SER D 873 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE D 877 " --> pdb=" O THR D 874 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 878 " --> pdb=" O VAL D 875 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 881 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE D 884 " --> pdb=" O LEU D 881 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY D 885 " --> pdb=" O LEU D 882 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 887 " --> pdb=" O PHE D 884 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE D 888 " --> pdb=" O GLY D 885 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 891 " --> pdb=" O PHE D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 913 Processing helix chain 'D' and resid 918 through 921 No H-bonds generated for 'chain 'D' and resid 918 through 921' Processing helix chain 'D' and resid 923 through 927 Processing helix chain 'D' and resid 934 through 945 Processing helix chain 'D' and resid 947 through 989 removed outlier: 3.753A pdb=" N LEU D 952 " --> pdb=" O VAL D 948 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D 955 " --> pdb=" O VAL D 951 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS D 970 " --> pdb=" O ASP D 966 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER D 972 " --> pdb=" O GLN D 968 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU D 973 " --> pdb=" O LYS D 969 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 989 " --> pdb=" O SER D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 998 removed outlier: 4.071A pdb=" N LYS D 997 " --> pdb=" O TRP D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1068 removed outlier: 3.597A pdb=" N LEU D1064 " --> pdb=" O LYS D1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 459 through 465 Processing helix chain 'C' and resid 485 through 491 Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 517 through 522 Processing helix chain 'C' and resid 527 through 536 removed outlier: 3.529A pdb=" N THR C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 551 through 557 Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 583 through 589 removed outlier: 3.717A pdb=" N ALA C 587 " --> pdb=" O PHE C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 600 Processing helix chain 'C' and resid 605 through 609 Processing helix chain 'C' and resid 623 through 629 Processing helix chain 'C' and resid 631 through 641 Processing helix chain 'C' and resid 667 through 669 No H-bonds generated for 'chain 'C' and resid 667 through 669' Processing helix chain 'C' and resid 684 through 691 Processing helix chain 'C' and resid 695 through 698 No H-bonds generated for 'chain 'C' and resid 695 through 698' Processing helix chain 'C' and resid 701 through 713 Processing helix chain 'C' and resid 715 through 739 removed outlier: 3.586A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 770 through 789 Processing helix chain 'C' and resid 804 through 822 removed outlier: 4.058A pdb=" N ILE C 816 " --> pdb=" O TYR C 812 " (cutoff:3.500A) Proline residue: C 821 - end of helix Processing helix chain 'C' and resid 828 through 853 removed outlier: 3.684A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE C 853 " --> pdb=" O TYR C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 891 removed outlier: 3.529A pdb=" N ILE C 866 " --> pdb=" O LEU C 863 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU C 867 " --> pdb=" O GLU C 864 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 871 " --> pdb=" O LYS C 868 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR C 874 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 875 " --> pdb=" O ARG C 872 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL C 876 " --> pdb=" O SER C 873 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE C 877 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 878 " --> pdb=" O VAL C 875 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 881 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE C 884 " --> pdb=" O LEU C 881 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY C 885 " --> pdb=" O LEU C 882 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 887 " --> pdb=" O PHE C 884 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 913 Processing helix chain 'C' and resid 918 through 921 No H-bonds generated for 'chain 'C' and resid 918 through 921' Processing helix chain 'C' and resid 923 through 927 Processing helix chain 'C' and resid 934 through 945 Processing helix chain 'C' and resid 947 through 989 removed outlier: 3.753A pdb=" N LEU C 952 " --> pdb=" O VAL C 948 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS C 970 " --> pdb=" O ASP C 966 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER C 972 " --> pdb=" O GLN C 968 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU C 973 " --> pdb=" O LYS C 969 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 998 removed outlier: 4.071A pdb=" N LYS C 997 " --> pdb=" O TRP C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1068 removed outlier: 3.597A pdb=" N LEU C1064 " --> pdb=" O LYS C1060 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2412 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: 5.27 Time building geometry restraints manager: 7.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2816 1.31 - 1.44: 4836 1.44 - 1.56: 10616 1.56 - 1.69: 8 1.69 - 1.82: 212 Bond restraints: 18488 Sorted by residual: bond pdb=" CE YCM C 621 " pdb=" NZ2 YCM C 621 " ideal model delta sigma weight residual 1.369 1.451 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" CE YCM B 621 " pdb=" NZ2 YCM B 621 " ideal model delta sigma weight residual 1.369 1.451 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CE YCM D 621 " pdb=" NZ2 YCM D 621 " ideal model delta sigma weight residual 1.369 1.451 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CE YCM A 621 " pdb=" NZ2 YCM A 621 " ideal model delta sigma weight residual 1.369 1.451 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" CE YCM D 621 " pdb=" OZ1 YCM D 621 " ideal model delta sigma weight residual 1.251 1.184 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 18483 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.86: 361 105.86 - 112.90: 10060 112.90 - 119.95: 6518 119.95 - 126.99: 7879 126.99 - 134.04: 238 Bond angle restraints: 25056 Sorted by residual: angle pdb=" N ILE C 803 " pdb=" CA ILE C 803 " pdb=" C ILE C 803 " ideal model delta sigma weight residual 113.53 107.12 6.41 9.80e-01 1.04e+00 4.28e+01 angle pdb=" N ILE D 803 " pdb=" CA ILE D 803 " pdb=" C ILE D 803 " ideal model delta sigma weight residual 113.53 107.14 6.39 9.80e-01 1.04e+00 4.25e+01 angle pdb=" N ILE B 803 " pdb=" CA ILE B 803 " pdb=" C ILE B 803 " ideal model delta sigma weight residual 113.53 107.16 6.37 9.80e-01 1.04e+00 4.23e+01 angle pdb=" N ILE A 803 " pdb=" CA ILE A 803 " pdb=" C ILE A 803 " ideal model delta sigma weight residual 113.53 107.16 6.37 9.80e-01 1.04e+00 4.23e+01 angle pdb=" CB GLU A 788 " pdb=" CG GLU A 788 " pdb=" CD GLU A 788 " ideal model delta sigma weight residual 112.60 119.46 -6.86 1.70e+00 3.46e-01 1.63e+01 ... (remaining 25051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 9684 16.77 - 33.53: 1057 33.53 - 50.30: 239 50.30 - 67.07: 56 67.07 - 83.83: 16 Dihedral angle restraints: 11052 sinusoidal: 4324 harmonic: 6728 Sorted by residual: dihedral pdb=" CA VAL C 948 " pdb=" C VAL C 948 " pdb=" N PRO C 949 " pdb=" CA PRO C 949 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA VAL D 948 " pdb=" C VAL D 948 " pdb=" N PRO D 949 " pdb=" CA PRO D 949 " ideal model delta harmonic sigma weight residual 180.00 153.21 26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA VAL A 948 " pdb=" C VAL A 948 " pdb=" N PRO A 949 " pdb=" CA PRO A 949 " ideal model delta harmonic sigma weight residual 180.00 153.23 26.77 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 11049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2309 0.055 - 0.110: 496 0.110 - 0.165: 107 0.165 - 0.220: 24 0.220 - 0.276: 4 Chirality restraints: 2940 Sorted by residual: chirality pdb=" CB ILE B 811 " pdb=" CA ILE B 811 " pdb=" CG1 ILE B 811 " pdb=" CG2 ILE B 811 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB ILE A 811 " pdb=" CA ILE A 811 " pdb=" CG1 ILE A 811 " pdb=" CG2 ILE A 811 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB ILE C 811 " pdb=" CA ILE C 811 " pdb=" CG1 ILE C 811 " pdb=" CG2 ILE C 811 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2937 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 820 " 0.051 5.00e-02 4.00e+02 7.74e-02 9.60e+00 pdb=" N PRO C 821 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 821 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 821 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 820 " 0.051 5.00e-02 4.00e+02 7.74e-02 9.59e+00 pdb=" N PRO B 821 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 821 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 821 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 820 " -0.051 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO A 821 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 821 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 821 " -0.044 5.00e-02 4.00e+02 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4988 2.80 - 3.33: 16273 3.33 - 3.85: 29113 3.85 - 4.38: 36080 4.38 - 4.90: 58924 Nonbonded interactions: 145378 Sorted by model distance: nonbonded pdb=" O ILE C 810 " pdb=" OG1 THR C 814 " model vdw 2.280 2.440 nonbonded pdb=" O ILE B 810 " pdb=" OG1 THR B 814 " model vdw 2.280 2.440 nonbonded pdb=" O ILE A 810 " pdb=" OG1 THR A 814 " model vdw 2.280 2.440 nonbonded pdb=" O ILE D 810 " pdb=" OG1 THR D 814 " model vdw 2.280 2.440 nonbonded pdb=" O VAL B 980 " pdb=" OG1 THR B 984 " model vdw 2.353 2.440 ... (remaining 145373 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.410 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 50.070 Find NCS groups from input model: 1.260 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: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 18488 Z= 0.309 Angle : 0.901 9.763 25056 Z= 0.472 Chirality : 0.051 0.276 2940 Planarity : 0.008 0.077 3084 Dihedral : 15.215 83.833 6676 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.24 % Allowed : 7.94 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.84 (0.11), residues: 2240 helix: -4.14 (0.06), residues: 1552 sheet: -0.83 (0.71), residues: 40 loop : -2.65 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 711 HIS 0.005 0.001 HIS D 614 PHE 0.016 0.002 PHE D 612 TYR 0.018 0.002 TYR C 842 ARG 0.003 0.000 ARG C 852 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 508 time to evaluate : 2.208 Fit side-chains revert: symmetry clash REVERT: A 481 HIS cc_start: 0.7945 (m90) cc_final: 0.7700 (m170) REVERT: A 483 MET cc_start: 0.8417 (mtt) cc_final: 0.8169 (mtt) REVERT: A 509 LEU cc_start: 0.8614 (mm) cc_final: 0.8332 (mt) REVERT: A 708 LEU cc_start: 0.8506 (tt) cc_final: 0.8202 (tp) REVERT: A 833 GLN cc_start: 0.7963 (mt0) cc_final: 0.7718 (tt0) REVERT: A 868 LYS cc_start: 0.6429 (tptt) cc_final: 0.6134 (tptt) REVERT: A 952 LEU cc_start: 0.8601 (tp) cc_final: 0.8384 (mt) REVERT: B 509 LEU cc_start: 0.8441 (mm) cc_final: 0.8212 (mt) REVERT: B 597 LEU cc_start: 0.8943 (mt) cc_final: 0.8717 (mt) REVERT: B 634 MET cc_start: 0.8492 (tpt) cc_final: 0.7848 (tpt) REVERT: B 720 MET cc_start: 0.7569 (tpp) cc_final: 0.7249 (mmm) REVERT: B 833 GLN cc_start: 0.7892 (mt0) cc_final: 0.7500 (tt0) REVERT: B 878 ILE cc_start: 0.8760 (tp) cc_final: 0.8553 (tp) REVERT: B 963 ASP cc_start: 0.7260 (m-30) cc_final: 0.7055 (m-30) REVERT: D 483 MET cc_start: 0.8231 (mtt) cc_final: 0.8008 (mtt) REVERT: D 808 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7395 (mt-10) REVERT: D 830 LEU cc_start: 0.8785 (tp) cc_final: 0.8135 (tp) REVERT: D 834 CYS cc_start: 0.8137 (m) cc_final: 0.7613 (m) REVERT: D 966 ASP cc_start: 0.8245 (m-30) cc_final: 0.7911 (m-30) REVERT: D 978 MET cc_start: 0.6949 (ptm) cc_final: 0.6622 (ptm) REVERT: D 987 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6700 (mt-10) REVERT: C 480 LEU cc_start: 0.8374 (pt) cc_final: 0.8142 (pt) REVERT: C 612 PHE cc_start: 0.7513 (p90) cc_final: 0.7247 (p90) REVERT: C 775 ILE cc_start: 0.9078 (pt) cc_final: 0.8754 (pt) REVERT: C 779 LEU cc_start: 0.8223 (tt) cc_final: 0.7780 (mm) REVERT: C 786 CYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7717 (m) REVERT: C 830 LEU cc_start: 0.8784 (tp) cc_final: 0.8068 (tp) REVERT: C 834 CYS cc_start: 0.8127 (m) cc_final: 0.7613 (m) REVERT: C 905 ILE cc_start: 0.8734 (tt) cc_final: 0.8507 (mt) REVERT: C 908 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8396 (m) REVERT: C 959 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7497 (mt) REVERT: C 966 ASP cc_start: 0.8263 (m-30) cc_final: 0.7914 (m-30) REVERT: C 974 LYS cc_start: 0.8217 (tptp) cc_final: 0.7722 (mtpp) REVERT: C 987 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6749 (mt-10) REVERT: C 1059 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7315 (mt-10) outliers start: 24 outliers final: 7 residues processed: 519 average time/residue: 0.2850 time to fit residues: 228.2138 Evaluate side-chains 358 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 348 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain B residue 786 CYS Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain C residue 786 CYS Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 0.0030 chunk 133 optimal weight: 0.0770 chunk 207 optimal weight: 1.9990 overall best weight: 0.5148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN A 481 HIS A 492 ASN A 579 GLN A 614 HIS A 700 HIS A 805 ASN A 855 ASN B 460 ASN B 492 ASN B 614 HIS B 700 HIS B 805 ASN B 855 ASN B1047 GLN D 460 ASN D 492 ASN D 619 ASN D 700 HIS D 805 ASN D 855 ASN C 460 ASN C 579 GLN C 614 HIS C 700 HIS C 739 ASN C 805 ASN C 855 ASN C1047 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18488 Z= 0.185 Angle : 0.595 10.943 25056 Z= 0.307 Chirality : 0.040 0.162 2940 Planarity : 0.006 0.063 3084 Dihedral : 5.784 56.039 2447 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.23 % Allowed : 13.17 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.15), residues: 2240 helix: -1.62 (0.11), residues: 1584 sheet: -1.04 (0.78), residues: 40 loop : -2.22 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 993 HIS 0.003 0.001 HIS C 614 PHE 0.017 0.001 PHE B 818 TYR 0.022 0.001 TYR C 812 ARG 0.006 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 387 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LEU cc_start: 0.8462 (mm) cc_final: 0.8244 (mt) REVERT: A 634 MET cc_start: 0.8379 (tpt) cc_final: 0.8023 (tpp) REVERT: A 708 LEU cc_start: 0.8212 (tt) cc_final: 0.7993 (tp) REVERT: A 721 MET cc_start: 0.7259 (tpp) cc_final: 0.7011 (mmm) REVERT: A 785 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.6347 (t80) REVERT: A 833 GLN cc_start: 0.7966 (mt0) cc_final: 0.7562 (tt0) REVERT: A 850 LEU cc_start: 0.8676 (tt) cc_final: 0.8442 (tp) REVERT: B 720 MET cc_start: 0.7810 (tpp) cc_final: 0.7360 (tpp) REVERT: B 774 MET cc_start: 0.8068 (ttm) cc_final: 0.7632 (mtp) REVERT: B 974 LYS cc_start: 0.8663 (tptp) cc_final: 0.8363 (tptm) REVERT: B 978 MET cc_start: 0.7701 (ptp) cc_final: 0.7493 (ptm) REVERT: D 483 MET cc_start: 0.8194 (mtt) cc_final: 0.7914 (mtt) REVERT: D 486 LEU cc_start: 0.8830 (tp) cc_final: 0.8571 (tp) REVERT: D 779 LEU cc_start: 0.8462 (tt) cc_final: 0.7768 (mt) REVERT: D 785 TYR cc_start: 0.6357 (OUTLIER) cc_final: 0.6104 (t80) REVERT: D 868 LYS cc_start: 0.6468 (tptt) cc_final: 0.5818 (tppt) REVERT: D 870 LEU cc_start: 0.8009 (tp) cc_final: 0.7732 (tt) REVERT: D 966 ASP cc_start: 0.8225 (m-30) cc_final: 0.7860 (m-30) REVERT: C 486 LEU cc_start: 0.8801 (tp) cc_final: 0.8491 (tp) REVERT: C 779 LEU cc_start: 0.8347 (tt) cc_final: 0.7836 (mm) outliers start: 43 outliers final: 21 residues processed: 407 average time/residue: 0.2743 time to fit residues: 177.1100 Evaluate side-chains 354 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 331 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 680 TYR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain B residue 1043 GLU Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 680 TYR Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 869 THR Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 986 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 476 ASN B 907 GLN B 954 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 ASN D 719 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18488 Z= 0.213 Angle : 0.570 8.783 25056 Z= 0.291 Chirality : 0.040 0.162 2940 Planarity : 0.005 0.060 3084 Dihedral : 4.712 42.511 2430 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.33 % Allowed : 14.94 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.17), residues: 2240 helix: -0.34 (0.12), residues: 1596 sheet: 0.08 (0.87), residues: 40 loop : -1.73 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 993 HIS 0.011 0.001 HIS C 970 PHE 0.018 0.001 PHE C 922 TYR 0.020 0.001 TYR A 714 ARG 0.003 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 345 time to evaluate : 1.937 Fit side-chains revert: symmetry clash REVERT: A 634 MET cc_start: 0.8381 (tpt) cc_final: 0.8127 (tpp) REVERT: A 708 LEU cc_start: 0.8317 (tt) cc_final: 0.8114 (tp) REVERT: A 785 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.6482 (t80) REVERT: A 842 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.6631 (t80) REVERT: A 850 LEU cc_start: 0.8788 (tt) cc_final: 0.8472 (tp) REVERT: A 868 LYS cc_start: 0.6451 (tptt) cc_final: 0.5745 (tppt) REVERT: B 597 LEU cc_start: 0.8899 (mt) cc_final: 0.8651 (mt) REVERT: B 720 MET cc_start: 0.7622 (tpp) cc_final: 0.7237 (tpp) REVERT: B 774 MET cc_start: 0.7929 (ttm) cc_final: 0.7672 (mtp) REVERT: B 1042 MET cc_start: 0.6406 (tpt) cc_final: 0.6163 (mmt) REVERT: D 483 MET cc_start: 0.8296 (mtt) cc_final: 0.8046 (mtt) REVERT: D 509 LEU cc_start: 0.8740 (mm) cc_final: 0.8527 (mt) REVERT: D 720 MET cc_start: 0.7866 (tpp) cc_final: 0.7623 (tpp) REVERT: D 779 LEU cc_start: 0.8559 (tt) cc_final: 0.8010 (mp) REVERT: D 785 TYR cc_start: 0.6540 (OUTLIER) cc_final: 0.6156 (t80) REVERT: D 808 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7523 (mm-30) REVERT: D 833 GLN cc_start: 0.8052 (mt0) cc_final: 0.7607 (tt0) REVERT: D 868 LYS cc_start: 0.6339 (tptt) cc_final: 0.5754 (tppt) REVERT: C 480 LEU cc_start: 0.8673 (pt) cc_final: 0.8452 (pp) REVERT: C 779 LEU cc_start: 0.8459 (tt) cc_final: 0.8026 (mp) REVERT: C 833 GLN cc_start: 0.8123 (mt0) cc_final: 0.7612 (tt0) REVERT: C 868 LYS cc_start: 0.6649 (tptt) cc_final: 0.6012 (tppt) REVERT: C 1042 MET cc_start: 0.6574 (tpt) cc_final: 0.6323 (mmt) outliers start: 45 outliers final: 23 residues processed: 373 average time/residue: 0.2564 time to fit residues: 154.0262 Evaluate side-chains 345 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 319 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain B residue 999 ASP Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 680 TYR Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 869 THR Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 986 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN D 719 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN C 494 HIS C 719 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18488 Z= 0.289 Angle : 0.599 7.501 25056 Z= 0.305 Chirality : 0.041 0.161 2940 Planarity : 0.005 0.060 3084 Dihedral : 4.593 35.055 2428 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.89 % Allowed : 15.61 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.18), residues: 2240 helix: 0.22 (0.13), residues: 1592 sheet: 0.53 (0.90), residues: 40 loop : -1.62 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 993 HIS 0.005 0.001 HIS C 970 PHE 0.022 0.002 PHE D 922 TYR 0.015 0.002 TYR C 840 ARG 0.004 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 319 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: A 634 MET cc_start: 0.8418 (tpt) cc_final: 0.8085 (tpp) REVERT: A 720 MET cc_start: 0.7919 (tpp) cc_final: 0.7650 (tpp) REVERT: A 785 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.6557 (t80) REVERT: A 842 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.6231 (t80) REVERT: B 693 ASN cc_start: 0.8279 (p0) cc_final: 0.7915 (p0) REVERT: B 774 MET cc_start: 0.7954 (ttm) cc_final: 0.7716 (mtp) REVERT: B 953 MET cc_start: 0.7035 (mmm) cc_final: 0.6780 (tpp) REVERT: D 486 LEU cc_start: 0.8819 (tp) cc_final: 0.8584 (tp) REVERT: D 779 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8127 (mp) REVERT: D 785 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.6091 (t80) REVERT: D 833 GLN cc_start: 0.8058 (mt0) cc_final: 0.7614 (tt0) REVERT: D 842 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7006 (t80) REVERT: D 868 LYS cc_start: 0.6251 (tptt) cc_final: 0.5689 (tppt) REVERT: D 1042 MET cc_start: 0.6701 (tpt) cc_final: 0.6483 (mmt) REVERT: C 612 PHE cc_start: 0.8116 (p90) cc_final: 0.7788 (p90) REVERT: C 720 MET cc_start: 0.7972 (tpp) cc_final: 0.7678 (tpp) REVERT: C 779 LEU cc_start: 0.8533 (tt) cc_final: 0.8058 (mp) REVERT: C 833 GLN cc_start: 0.8151 (mt0) cc_final: 0.7657 (tt0) REVERT: C 842 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.6515 (t80) REVERT: C 868 LYS cc_start: 0.6571 (tptt) cc_final: 0.5901 (tppt) outliers start: 75 outliers final: 41 residues processed: 367 average time/residue: 0.2481 time to fit residues: 144.9662 Evaluate side-chains 342 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 295 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 869 THR Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 917 ASN Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 981 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 719 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18488 Z= 0.228 Angle : 0.565 8.145 25056 Z= 0.285 Chirality : 0.040 0.175 2940 Planarity : 0.004 0.059 3084 Dihedral : 4.406 28.570 2428 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.53 % Allowed : 17.32 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.18), residues: 2240 helix: 0.55 (0.13), residues: 1608 sheet: 0.92 (0.94), residues: 40 loop : -1.36 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 993 HIS 0.005 0.001 HIS C 614 PHE 0.017 0.001 PHE B 922 TYR 0.023 0.001 TYR D 714 ARG 0.004 0.000 ARG B 852 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 313 time to evaluate : 1.672 Fit side-chains REVERT: A 634 MET cc_start: 0.8418 (tpt) cc_final: 0.8111 (tpp) REVERT: A 720 MET cc_start: 0.7913 (tpp) cc_final: 0.7695 (tpp) REVERT: A 785 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6639 (t80) REVERT: A 842 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6313 (t80) REVERT: A 868 LYS cc_start: 0.6754 (tptt) cc_final: 0.6126 (tppt) REVERT: A 1042 MET cc_start: 0.6819 (tpt) cc_final: 0.6573 (mmt) REVERT: B 774 MET cc_start: 0.7951 (ttm) cc_final: 0.7717 (mtp) REVERT: B 851 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8283 (tm-30) REVERT: B 953 MET cc_start: 0.7223 (mmm) cc_final: 0.6980 (tpp) REVERT: D 720 MET cc_start: 0.7889 (tpp) cc_final: 0.7681 (tpp) REVERT: D 779 LEU cc_start: 0.8691 (tt) cc_final: 0.8123 (mp) REVERT: D 785 TYR cc_start: 0.6402 (OUTLIER) cc_final: 0.6067 (t80) REVERT: D 842 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.6937 (t80) REVERT: D 868 LYS cc_start: 0.6160 (tptt) cc_final: 0.5603 (tppt) REVERT: C 708 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8227 (tp) REVERT: C 720 MET cc_start: 0.7990 (tpp) cc_final: 0.7693 (tpp) REVERT: C 779 LEU cc_start: 0.8597 (tt) cc_final: 0.8121 (mp) REVERT: C 842 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.6614 (t80) REVERT: C 868 LYS cc_start: 0.6538 (tptt) cc_final: 0.5876 (tppt) REVERT: C 953 MET cc_start: 0.6936 (mmm) cc_final: 0.6501 (tpp) REVERT: C 1073 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6964 (mm-30) outliers start: 68 outliers final: 39 residues processed: 358 average time/residue: 0.2458 time to fit residues: 140.2430 Evaluate side-chains 339 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 294 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 957 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 129 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 220 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1047 GLN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18488 Z= 0.195 Angle : 0.552 9.066 25056 Z= 0.279 Chirality : 0.040 0.176 2940 Planarity : 0.004 0.058 3084 Dihedral : 4.268 24.142 2428 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.05 % Allowed : 17.12 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.18), residues: 2240 helix: 0.77 (0.13), residues: 1624 sheet: 1.23 (0.98), residues: 40 loop : -1.29 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 993 HIS 0.015 0.001 HIS C 719 PHE 0.017 0.001 PHE A 612 TYR 0.023 0.001 TYR D 714 ARG 0.004 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 307 time to evaluate : 2.150 Fit side-chains revert: symmetry clash REVERT: A 634 MET cc_start: 0.8436 (tpt) cc_final: 0.8156 (tpp) REVERT: A 720 MET cc_start: 0.7902 (tpp) cc_final: 0.7684 (tpp) REVERT: A 842 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.6184 (t80) REVERT: A 868 LYS cc_start: 0.6681 (tptt) cc_final: 0.5999 (tppt) REVERT: A 953 MET cc_start: 0.7125 (mmt) cc_final: 0.6795 (tpp) REVERT: B 509 LEU cc_start: 0.8602 (mm) cc_final: 0.8385 (mt) REVERT: B 693 ASN cc_start: 0.8165 (p0) cc_final: 0.7785 (p0) REVERT: B 721 MET cc_start: 0.7290 (tpp) cc_final: 0.7036 (tpp) REVERT: B 774 MET cc_start: 0.7906 (ttm) cc_final: 0.7633 (mtp) REVERT: B 851 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8266 (tm-30) REVERT: B 953 MET cc_start: 0.7071 (mmm) cc_final: 0.6826 (tpp) REVERT: D 779 LEU cc_start: 0.8655 (tt) cc_final: 0.8099 (mp) REVERT: D 785 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.6229 (t80) REVERT: D 842 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7057 (t80) REVERT: D 868 LYS cc_start: 0.6108 (tptt) cc_final: 0.5479 (tppt) REVERT: C 612 PHE cc_start: 0.8112 (p90) cc_final: 0.7811 (p90) REVERT: C 708 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8239 (tp) REVERT: C 774 MET cc_start: 0.7577 (mtp) cc_final: 0.7344 (mtp) REVERT: C 779 LEU cc_start: 0.8590 (tt) cc_final: 0.8130 (mp) REVERT: C 842 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.6387 (t80) REVERT: C 868 LYS cc_start: 0.6494 (tptt) cc_final: 0.5857 (tppt) REVERT: C 953 MET cc_start: 0.6886 (mmm) cc_final: 0.6471 (tpp) REVERT: C 978 MET cc_start: 0.7799 (mpp) cc_final: 0.7519 (mtp) REVERT: C 1073 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6976 (mm-30) outliers start: 78 outliers final: 50 residues processed: 356 average time/residue: 0.2500 time to fit residues: 142.9617 Evaluate side-chains 348 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 293 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 869 THR Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 917 ASN Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 981 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 161 optimal weight: 0.4980 chunk 124 optimal weight: 0.1980 chunk 185 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1047 GLN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS C1047 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18488 Z= 0.175 Angle : 0.545 8.273 25056 Z= 0.275 Chirality : 0.039 0.182 2940 Planarity : 0.004 0.057 3084 Dihedral : 4.158 19.919 2428 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.68 % Allowed : 17.43 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.19), residues: 2240 helix: 0.99 (0.13), residues: 1616 sheet: 1.51 (1.01), residues: 40 loop : -1.20 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 993 HIS 0.013 0.001 HIS D 719 PHE 0.016 0.001 PHE B 859 TYR 0.021 0.001 TYR D 714 ARG 0.005 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 318 time to evaluate : 2.124 Fit side-chains revert: symmetry clash REVERT: A 509 LEU cc_start: 0.8582 (mm) cc_final: 0.8331 (mt) REVERT: A 634 MET cc_start: 0.8399 (tpt) cc_final: 0.8118 (tpp) REVERT: A 842 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.6144 (t80) REVERT: A 953 MET cc_start: 0.7121 (mmt) cc_final: 0.6797 (tpp) REVERT: A 1043 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6867 (tt0) REVERT: B 693 ASN cc_start: 0.8122 (p0) cc_final: 0.7741 (p0) REVERT: B 774 MET cc_start: 0.7907 (ttm) cc_final: 0.7687 (mtp) REVERT: B 851 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 953 MET cc_start: 0.7125 (mmm) cc_final: 0.6829 (tpp) REVERT: D 779 LEU cc_start: 0.8644 (tt) cc_final: 0.8101 (mp) REVERT: D 842 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7115 (t80) REVERT: D 868 LYS cc_start: 0.5921 (tptt) cc_final: 0.5417 (tppt) REVERT: C 612 PHE cc_start: 0.8111 (p90) cc_final: 0.7841 (p90) REVERT: C 708 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8214 (tp) REVERT: C 779 LEU cc_start: 0.8508 (tt) cc_final: 0.8081 (mp) REVERT: C 842 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.6296 (t80) REVERT: C 868 LYS cc_start: 0.6355 (tptt) cc_final: 0.5754 (tppt) REVERT: C 953 MET cc_start: 0.6953 (mmm) cc_final: 0.6510 (tpp) REVERT: C 978 MET cc_start: 0.7832 (mpp) cc_final: 0.7530 (mtp) outliers start: 71 outliers final: 52 residues processed: 360 average time/residue: 0.2451 time to fit residues: 142.2644 Evaluate side-chains 364 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 307 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 869 THR Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 917 ASN Chi-restraints excluded: chain D residue 923 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain C residue 986 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 139 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 20 optimal weight: 0.0570 chunk 172 optimal weight: 3.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1062 HIS ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18488 Z= 0.177 Angle : 0.558 10.499 25056 Z= 0.278 Chirality : 0.040 0.183 2940 Planarity : 0.004 0.056 3084 Dihedral : 4.097 18.861 2428 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.58 % Allowed : 18.10 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.19), residues: 2240 helix: 1.10 (0.13), residues: 1616 sheet: 1.57 (1.01), residues: 40 loop : -1.11 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 993 HIS 0.006 0.001 HIS C 614 PHE 0.018 0.001 PHE A 612 TYR 0.013 0.001 TYR C 785 ARG 0.006 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 315 time to evaluate : 1.769 Fit side-chains revert: symmetry clash REVERT: A 509 LEU cc_start: 0.8516 (mm) cc_final: 0.8255 (mt) REVERT: A 634 MET cc_start: 0.8398 (tpt) cc_final: 0.8112 (tpp) REVERT: A 842 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6035 (t80) REVERT: A 953 MET cc_start: 0.7110 (mmt) cc_final: 0.6831 (tpp) REVERT: A 1043 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6913 (tt0) REVERT: B 693 ASN cc_start: 0.8156 (p0) cc_final: 0.7779 (p0) REVERT: B 721 MET cc_start: 0.7204 (tpp) cc_final: 0.6967 (tpp) REVERT: B 851 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8274 (tm-30) REVERT: B 953 MET cc_start: 0.7089 (mmm) cc_final: 0.6830 (tpp) REVERT: D 779 LEU cc_start: 0.8719 (tt) cc_final: 0.8129 (mp) REVERT: D 842 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7034 (t80) REVERT: D 868 LYS cc_start: 0.5942 (tptt) cc_final: 0.5437 (tppt) REVERT: C 612 PHE cc_start: 0.8114 (p90) cc_final: 0.7856 (p90) REVERT: C 779 LEU cc_start: 0.8504 (tt) cc_final: 0.8080 (mp) REVERT: C 842 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.6271 (t80) REVERT: C 868 LYS cc_start: 0.6338 (tptt) cc_final: 0.5717 (tppt) REVERT: C 953 MET cc_start: 0.6929 (mmm) cc_final: 0.6504 (tpp) REVERT: C 978 MET cc_start: 0.7797 (mpp) cc_final: 0.7405 (mtp) REVERT: C 1073 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7042 (mm-30) outliers start: 69 outliers final: 57 residues processed: 355 average time/residue: 0.2391 time to fit residues: 138.3887 Evaluate side-chains 363 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 302 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 917 ASN Chi-restraints excluded: chain D residue 923 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 981 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.9980 chunk 210 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 185 optimal weight: 0.6980 chunk 193 optimal weight: 7.9990 chunk 134 optimal weight: 0.0030 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18488 Z= 0.178 Angle : 0.570 12.673 25056 Z= 0.282 Chirality : 0.040 0.184 2940 Planarity : 0.004 0.056 3084 Dihedral : 4.062 18.595 2428 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.73 % Allowed : 18.31 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.19), residues: 2240 helix: 1.16 (0.13), residues: 1616 sheet: 1.62 (1.02), residues: 40 loop : -1.09 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 993 HIS 0.006 0.001 HIS C 614 PHE 0.019 0.001 PHE D 859 TYR 0.023 0.001 TYR D 714 ARG 0.006 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 309 time to evaluate : 2.340 Fit side-chains revert: symmetry clash REVERT: A 509 LEU cc_start: 0.8521 (mm) cc_final: 0.8254 (mt) REVERT: A 634 MET cc_start: 0.8391 (tpt) cc_final: 0.8091 (tpp) REVERT: A 808 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7297 (mm-30) REVERT: A 842 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.6033 (t80) REVERT: A 953 MET cc_start: 0.7122 (mmt) cc_final: 0.6864 (tpp) REVERT: A 1043 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6837 (tt0) REVERT: B 693 ASN cc_start: 0.8133 (p0) cc_final: 0.7753 (p0) REVERT: B 721 MET cc_start: 0.7244 (tpp) cc_final: 0.6999 (tpp) REVERT: B 723 LEU cc_start: 0.8496 (tp) cc_final: 0.8259 (tp) REVERT: B 851 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8260 (tm-30) REVERT: B 953 MET cc_start: 0.7142 (mmm) cc_final: 0.6870 (tpp) REVERT: D 774 MET cc_start: 0.7191 (mtp) cc_final: 0.6921 (mtp) REVERT: D 779 LEU cc_start: 0.8716 (tt) cc_final: 0.8119 (mp) REVERT: D 842 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7124 (t80) REVERT: D 868 LYS cc_start: 0.6175 (tptt) cc_final: 0.5664 (tppt) REVERT: D 981 GLU cc_start: 0.7377 (pp20) cc_final: 0.7123 (pp20) REVERT: D 1047 GLN cc_start: 0.8210 (tt0) cc_final: 0.7962 (tt0) REVERT: C 612 PHE cc_start: 0.8125 (p90) cc_final: 0.7872 (p90) REVERT: C 774 MET cc_start: 0.7379 (mtp) cc_final: 0.7084 (mtp) REVERT: C 779 LEU cc_start: 0.8494 (tt) cc_final: 0.8049 (mp) REVERT: C 842 TYR cc_start: 0.7665 (OUTLIER) cc_final: 0.6257 (t80) REVERT: C 868 LYS cc_start: 0.6296 (tptt) cc_final: 0.5724 (tppt) REVERT: C 953 MET cc_start: 0.6929 (mmm) cc_final: 0.6483 (tpp) REVERT: C 978 MET cc_start: 0.7789 (mpp) cc_final: 0.7407 (mtp) REVERT: C 1073 GLU cc_start: 0.7251 (mm-30) cc_final: 0.7045 (mm-30) outliers start: 72 outliers final: 60 residues processed: 351 average time/residue: 0.2467 time to fit residues: 139.9887 Evaluate side-chains 368 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 304 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 869 THR Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 917 ASN Chi-restraints excluded: chain D residue 923 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 981 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 227 optimal weight: 0.0370 chunk 209 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 719 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS C1047 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18488 Z= 0.194 Angle : 0.573 10.665 25056 Z= 0.284 Chirality : 0.040 0.182 2940 Planarity : 0.004 0.056 3084 Dihedral : 4.046 17.753 2428 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.48 % Allowed : 18.46 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.19), residues: 2240 helix: 1.18 (0.13), residues: 1616 sheet: 1.60 (1.02), residues: 40 loop : -1.08 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 993 HIS 0.006 0.001 HIS C 614 PHE 0.018 0.001 PHE B 612 TYR 0.014 0.001 TYR C 785 ARG 0.006 0.000 ARG B 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 307 time to evaluate : 1.967 Fit side-chains revert: symmetry clash REVERT: A 509 LEU cc_start: 0.8667 (mm) cc_final: 0.8396 (mt) REVERT: A 634 MET cc_start: 0.8402 (tpt) cc_final: 0.8100 (tpp) REVERT: A 842 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.6139 (t80) REVERT: A 953 MET cc_start: 0.7136 (mmt) cc_final: 0.6911 (tpp) REVERT: B 693 ASN cc_start: 0.8142 (p0) cc_final: 0.7774 (p0) REVERT: B 723 LEU cc_start: 0.8505 (tp) cc_final: 0.8245 (tp) REVERT: B 851 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 868 LYS cc_start: 0.6639 (tptt) cc_final: 0.6108 (tppt) REVERT: B 953 MET cc_start: 0.7151 (mmm) cc_final: 0.6926 (tpp) REVERT: D 774 MET cc_start: 0.7170 (mtp) cc_final: 0.6919 (mtp) REVERT: D 779 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8055 (mp) REVERT: D 842 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.6935 (t80) REVERT: D 851 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8469 (tm-30) REVERT: D 863 LEU cc_start: 0.7160 (tt) cc_final: 0.6893 (tp) REVERT: D 868 LYS cc_start: 0.6214 (tptt) cc_final: 0.5711 (tppt) REVERT: C 612 PHE cc_start: 0.8141 (p90) cc_final: 0.7899 (p90) REVERT: C 779 LEU cc_start: 0.8490 (tt) cc_final: 0.8040 (mp) REVERT: C 842 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.6220 (t80) REVERT: C 868 LYS cc_start: 0.6325 (tptt) cc_final: 0.5770 (tppt) REVERT: C 953 MET cc_start: 0.6930 (mmm) cc_final: 0.6510 (tpp) REVERT: C 978 MET cc_start: 0.7777 (mpp) cc_final: 0.7383 (mtp) REVERT: C 1073 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7023 (mm-30) outliers start: 67 outliers final: 59 residues processed: 348 average time/residue: 0.2423 time to fit residues: 135.7481 Evaluate side-chains 363 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 300 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 869 THR Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 917 ASN Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 981 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 166 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 159 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.162169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135762 restraints weight = 26163.819| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.01 r_work: 0.3461 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18488 Z= 0.198 Angle : 0.583 11.727 25056 Z= 0.289 Chirality : 0.040 0.180 2940 Planarity : 0.004 0.056 3084 Dihedral : 4.044 17.288 2428 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.58 % Allowed : 18.57 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.19), residues: 2240 helix: 1.18 (0.13), residues: 1624 sheet: 1.60 (1.02), residues: 40 loop : -1.08 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 993 HIS 0.005 0.001 HIS C 614 PHE 0.017 0.001 PHE D 859 TYR 0.022 0.001 TYR D 714 ARG 0.005 0.000 ARG B 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3968.77 seconds wall clock time: 72 minutes 34.88 seconds (4354.88 seconds total)