Starting phenix.real_space_refine on Tue Mar 11 15:29:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bco_44432/03_2025/9bco_44432.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bco_44432/03_2025/9bco_44432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bco_44432/03_2025/9bco_44432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bco_44432/03_2025/9bco_44432.map" model { file = "/net/cci-nas-00/data/ceres_data/9bco_44432/03_2025/9bco_44432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bco_44432/03_2025/9bco_44432.cif" } resolution = 4.4 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= 0.002 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 9 5.16 5 C 3782 2.51 5 N 1170 2.21 5 O 1197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6164 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3054 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 328} Link IDs: {'PTRANS': 21, 'TRANS': 499} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1142 Unresolved non-hydrogen angles: 1450 Unresolved non-hydrogen dihedrals: 906 Unresolved non-hydrogen chiralities: 126 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 10, 'GLU:plan': 38, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 619 Chain: "B" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3048 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 316} Link IDs: {'PTRANS': 21, 'TRANS': 495} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1116 Unresolved non-hydrogen angles: 1417 Unresolved non-hydrogen dihedrals: 886 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 17, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 10, 'GLU:plan': 35, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 599 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.71, per 1000 atoms: 0.76 Number of scatterers: 6164 At special positions: 0 Unit cell: (78.048, 109.484, 128.996, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 P 6 15.00 O 1197 8.00 N 1170 7.00 C 3782 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM 6126 O3A ATP A1101 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.1 seconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1944 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 8 sheets defined 46.0% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 545 through 557 Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'A' and resid 600 through 620 Processing helix chain 'A' and resid 659 through 666 removed outlier: 3.556A pdb=" N THR A 662 " --> pdb=" O GLN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 703 Processing helix chain 'A' and resid 715 through 726 removed outlier: 4.088A pdb=" N GLY A 726 " --> pdb=" O ARG A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 753 removed outlier: 3.655A pdb=" N GLY A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 753 " --> pdb=" O GLN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 773 Processing helix chain 'A' and resid 774 through 776 No H-bonds generated for 'chain 'A' and resid 774 through 776' Processing helix chain 'A' and resid 781 through 818 removed outlier: 4.537A pdb=" N LEU A 785 " --> pdb=" O LEU A 781 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 817 " --> pdb=" O ALA A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.580A pdb=" N ALA A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 861 removed outlier: 4.446A pdb=" N THR A 861 " --> pdb=" O SER A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 881 Processing helix chain 'A' and resid 907 through 924 removed outlier: 3.500A pdb=" N CYS A 911 " --> pdb=" O ARG A 907 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 975 Processing helix chain 'A' and resid 985 through 996 removed outlier: 3.502A pdb=" N GLY A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 483 Processing helix chain 'B' and resid 545 through 558 removed outlier: 3.895A pdb=" N VAL B 558 " --> pdb=" O HIS B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 600 through 620 removed outlier: 3.752A pdb=" N HIS B 619 " --> pdb=" O MET B 615 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN B 620 " --> pdb=" O LEU B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 660 through 667 removed outlier: 4.327A pdb=" N LYS B 667 " --> pdb=" O VAL B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 676 Processing helix chain 'B' and resid 685 through 702 removed outlier: 3.928A pdb=" N LEU B 702 " --> pdb=" O GLN B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 725 Processing helix chain 'B' and resid 741 through 752 removed outlier: 3.595A pdb=" N TRP B 752 " --> pdb=" O MET B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 773 Processing helix chain 'B' and resid 779 through 821 removed outlier: 3.749A pdb=" N ASN B 783 " --> pdb=" O ASN B 779 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 831 removed outlier: 3.649A pdb=" N ARG B 831 " --> pdb=" O GLU B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 860 Processing helix chain 'B' and resid 861 through 880 removed outlier: 3.768A pdb=" N THR B 867 " --> pdb=" O MET B 863 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 879 " --> pdb=" O CYS B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 926 removed outlier: 4.053A pdb=" N VAL B 913 " --> pdb=" O HIS B 909 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 914 " --> pdb=" O ALA B 910 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU B 921 " --> pdb=" O ALA B 917 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP B 922 " --> pdb=" O LEU B 918 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER B 926 " --> pdb=" O ASP B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 976 removed outlier: 4.047A pdb=" N ASN B 976 " --> pdb=" O ARG B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 995 removed outlier: 3.764A pdb=" N VAL B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 524 through 527 removed outlier: 3.673A pdb=" N LYS A 535 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N CYS A 577 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA A 569 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 579 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 635 through 636 Processing sheet with id=AA3, first strand: chain 'A' and resid 886 through 889 removed outlier: 4.645A pdb=" N LYS A 887 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 898 " --> pdb=" O LYS A 887 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 847 " --> pdb=" O GLY A 942 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 949 through 953 Processing sheet with id=AA5, first strand: chain 'A' and resid 999 through 1008 removed outlier: 7.543A pdb=" N LEU A1000 " --> pdb=" O LEU A1020 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A1020 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU A1002 " --> pdb=" O TRP A1018 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TRP A1018 " --> pdb=" O LEU A1002 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 525 through 526 removed outlier: 7.070A pdb=" N LEU B 579 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 838 through 839 Processing sheet with id=AA8, first strand: chain 'B' and resid 886 through 891 removed outlier: 7.972A pdb=" N MET B 896 " --> pdb=" O VAL B 888 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR B 890 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA B 894 " --> pdb=" O THR B 890 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B 848 " --> pdb=" O TYR B 895 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 897 " --> pdb=" O TYR B 846 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 849 " --> pdb=" O ARG B 940 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG B 940 " --> pdb=" O ASP B 849 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N THR B 945 " --> pdb=" O SER B 985 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY B1012 " --> pdb=" O GLU B1007 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU B1007 " --> pdb=" O GLY B1012 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N VAL B1014 " --> pdb=" O ASP B1005 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B1005 " --> pdb=" O VAL B1014 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR B1016 " --> pdb=" O ARG B1003 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1065 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: 1.76 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2209 1.34 - 1.45: 621 1.45 - 1.57: 3412 1.57 - 1.69: 10 1.69 - 1.81: 15 Bond restraints: 6267 Sorted by residual: bond pdb=" C4 ATP B1101 " pdb=" C5 ATP B1101 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.61e+01 bond pdb=" C4 ATP A1101 " pdb=" C5 ATP A1101 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.25e+01 bond pdb=" C5 ATP B1101 " pdb=" C6 ATP B1101 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.28e+01 bond pdb=" C5 ATP A1101 " pdb=" C6 ATP A1101 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.99e+01 bond pdb=" C5 ATP B1101 " pdb=" N7 ATP B1101 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.31e+01 ... (remaining 6262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.71: 8641 4.71 - 9.41: 23 9.41 - 14.12: 0 14.12 - 18.82: 1 18.82 - 23.53: 3 Bond angle restraints: 8668 Sorted by residual: angle pdb=" PB ATP A1101 " pdb=" O3B ATP A1101 " pdb=" PG ATP A1101 " ideal model delta sigma weight residual 139.87 116.34 23.53 1.00e+00 1.00e+00 5.53e+02 angle pdb=" PB ATP B1101 " pdb=" O3B ATP B1101 " pdb=" PG ATP B1101 " ideal model delta sigma weight residual 139.87 119.21 20.66 1.00e+00 1.00e+00 4.27e+02 angle pdb=" PA ATP A1101 " pdb=" O3A ATP A1101 " pdb=" PB ATP A1101 " ideal model delta sigma weight residual 136.83 117.74 19.09 1.00e+00 1.00e+00 3.64e+02 angle pdb=" PA ATP B1101 " pdb=" O3A ATP B1101 " pdb=" PB ATP B1101 " ideal model delta sigma weight residual 136.83 121.07 15.76 1.00e+00 1.00e+00 2.48e+02 angle pdb=" C5 ATP B1101 " pdb=" C4 ATP B1101 " pdb=" N3 ATP B1101 " ideal model delta sigma weight residual 126.80 119.08 7.72 1.00e+00 1.00e+00 5.96e+01 ... (remaining 8663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3513 17.99 - 35.98: 132 35.98 - 53.96: 35 53.96 - 71.95: 11 71.95 - 89.94: 5 Dihedral angle restraints: 3696 sinusoidal: 702 harmonic: 2994 Sorted by residual: dihedral pdb=" CA ILE B 644 " pdb=" C ILE B 644 " pdb=" N THR B 645 " pdb=" CA THR B 645 " ideal model delta harmonic sigma weight residual 180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ARG B 759 " pdb=" C ARG B 759 " pdb=" N PRO B 760 " pdb=" CA PRO B 760 " ideal model delta harmonic sigma weight residual -180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA GLY B 529 " pdb=" C GLY B 529 " pdb=" N ASN B 530 " pdb=" CA ASN B 530 " ideal model delta harmonic sigma weight residual 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 3693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 918 0.076 - 0.152: 107 0.152 - 0.228: 6 0.228 - 0.303: 1 0.303 - 0.379: 2 Chirality restraints: 1034 Sorted by residual: chirality pdb=" CA THR A1016 " pdb=" N THR A1016 " pdb=" C THR A1016 " pdb=" CB THR A1016 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA HIS A 944 " pdb=" N HIS A 944 " pdb=" C HIS A 944 " pdb=" CB HIS A 944 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA VAL B 682 " pdb=" N VAL B 682 " pdb=" C VAL B 682 " pdb=" CB VAL B 682 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1031 not shown) Planarity restraints: 1208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 572 " -0.060 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO A 573 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 573 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 573 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 772 " 0.019 2.00e-02 2.50e+03 1.84e-02 5.92e+00 pdb=" CG PHE B 772 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 772 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 772 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 772 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 772 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 772 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 484 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO B 485 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.031 5.00e-02 4.00e+02 ... (remaining 1205 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 124 2.66 - 3.22: 6433 3.22 - 3.78: 8702 3.78 - 4.34: 9848 4.34 - 4.90: 15368 Nonbonded interactions: 40475 Sorted by model distance: nonbonded pdb=" OD1 ASN A 633 " pdb=" O1G ATP A1101 " model vdw 2.105 3.040 nonbonded pdb=" NZ LYS A 535 " pdb=" O3A ATP A1101 " model vdw 2.184 3.120 nonbonded pdb=" ND2 ASN B 633 " pdb=" O2B ATP B1101 " model vdw 2.212 3.120 nonbonded pdb=" O ASN A 628 " pdb=" OD1 ASN A 628 " model vdw 2.232 3.040 nonbonded pdb=" O ASN A 773 " pdb=" N SER A 777 " model vdw 2.285 3.120 ... (remaining 40470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 469 through 482 or (resid 483 through 484 and (name N or n \ ame CA or name C or name O or name CB )) or resid 485 through 486 or (resid 523 \ through 525 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 6 through 530 or (resid 531 through 533 and (name N or name CA or name C or name \ O or name CB )) or resid 534 through 537 or (resid 538 and (name N or name CA o \ r name C or name O or name CB )) or resid 539 through 541 or (resid 542 through \ 549 and (name N or name CA or name C or name O or name CB )) or resid 550 throug \ h 558 or (resid 559 through 561 and (name N or name CA or name C or name O or na \ me CB )) or resid 562 through 565 or (resid 566 through 567 and (name N or name \ CA or name C or name O or name CB )) or (resid 568 through 572 and (name N or na \ me CA or name C or name O or name CB )) or resid 573 through 587 or (resid 588 t \ hrough 600 and (name N or name CA or name C or name O or name CB )) or resid 601 \ through 615 or (resid 616 and (name N or name CA or name C or name O or name CB \ )) or resid 617 through 619 or (resid 620 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 621 through 625 and (name N or name CA or name C o \ r name O or name CB )) or resid 626 through 629 or (resid 630 and (name N or nam \ e CA or name C or name O or name CB )) or resid 631 through 638 or (resid 639 an \ d (name N or name CA or name C or name O or name CB )) or resid 640 through 641 \ or (resid 642 through 646 and (name N or name CA or name C or name O or name CB \ )) or resid 647 through 651 or (resid 652 through 653 and (name N or name CA or \ name C or name O or name CB )) or resid 654 through 655 or (resid 656 and (name \ N or name CA or name C or name O or name CB )) or resid 657 through 662 or (resi \ d 663 through 668 and (name N or name CA or name C or name O or name CB )) or re \ sid 669 through 678 or (resid 679 and (name N or name CA or name C or name O or \ name CB )) or resid 680 through 682 or (resid 683 and (name N or name CA or name \ C or name O or name CB )) or resid 684 or (resid 685 and (name N or name CA or \ name C or name O or name CB )) or resid 686 through 694 or (resid 695 through 70 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 705 through \ 707 or (resid 708 and (name N or name CA or name C or name O or name CB )) or re \ sid 709 through 714 or (resid 715 and (name N or name CA or name C or name O or \ name CB )) or resid 716 through 783 or (resid 784 through 787 and (name N or nam \ e CA or name C or name O or name CB )) or resid 788 through 794 or (resid 795 th \ rough 801 and (name N or name CA or name C or name O or name CB )) or resid 802 \ through 803 or (resid 804 through 805 and (name N or name CA or name C or name O \ or name CB )) or resid 806 or (resid 807 through 808 and (name N or name CA or \ name C or name O or name CB )) or resid 809 through 819 or (resid 820 through 82 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 822 through \ 858 or (resid 859 through 861 and (name N or name CA or name C or name O or name \ CB )) or resid 862 through 869 or (resid 870 through 891 and (name N or name CA \ or name C or name O or name CB )) or resid 892 or (resid 893 through 899 and (n \ ame N or name CA or name C or name O or name CB )) or resid 900 through 915 or ( \ resid 916 through 932 and (name N or name CA or name C or name O or name CB )) o \ r resid 933 through 1021 or resid 1101)) selection = (chain 'B' and ((resid 469 through 478 and (name N or name CA or name C or name \ O or name CB )) or resid 479 through 526 or (resid 527 through 528 and (name N o \ r name CA or name C or name O or name CB )) or resid 529 through 535 or (resid 5 \ 36 through 538 and (name N or name CA or name C or name O or name CB )) or resid \ 539 through 557 or (resid 558 through 561 and (name N or name CA or name C or n \ ame O or name CB )) or resid 562 through 563 or (resid 564 and (name N or name C \ A or name C or name O or name CB )) or resid 565 through 589 or (resid 590 throu \ gh 600 and (name N or name CA or name C or name O or name CB )) or resid 601 thr \ ough 603 or (resid 604 and (name N or name CA or name C or name O or name CB )) \ or resid 605 through 608 or (resid 609 through 613 and (name N or name CA or nam \ e C or name O or name CB )) or resid 614 through 618 or (resid 619 through 620 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 621 through 62 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 626 through \ 628 or (resid 629 through 630 and (name N or name CA or name C or name O or name \ CB )) or resid 631 or (resid 632 and (name N or name CA or name C or name O or \ name CB )) or resid 633 or (resid 634 through 635 and (name N or name CA or name \ C or name O or name CB )) or resid 636 through 640 or (resid 641 through 646 an \ d (name N or name CA or name C or name O or name CB )) or resid 647 through 654 \ or (resid 655 through 656 and (name N or name CA or name C or name O or name CB \ )) or resid 657 through 666 or (resid 667 through 668 and (name N or name CA or \ name C or name O or name CB )) or resid 669 or (resid 670 through 671 and (name \ N or name CA or name C or name O or name CB )) or resid 672 through 698 or (resi \ d 699 through 704 and (name N or name CA or name C or name O or name CB )) or re \ sid 705 or (resid 706 and (name N or name CA or name C or name O or name CB )) o \ r resid 707 through 712 or (resid 713 through 715 and (name N or name CA or name \ C or name O or name CB )) or resid 716 through 730 or (resid 731 through 732 an \ d (name N or name CA or name C or name O or name CB )) or resid 733 or (resid 73 \ 4 through 743 and (name N or name CA or name C or name O or name CB )) or resid \ 744 through 746 or (resid 747 through 748 and (name N or name CA or name C or na \ me O or name CB )) or resid 749 or (resid 750 through 751 and (name N or name CA \ or name C or name O or name CB )) or resid 752 through 753 or (resid 754 and (n \ ame N or name CA or name C or name O or name CB )) or resid 755 through 756 or ( \ resid 757 through 759 and (name N or name CA or name C or name O or name CB )) o \ r resid 760 through 762 or (resid 763 through 787 and (name N or name CA or name \ C or name O or name CB )) or resid 788 through 792 or (resid 793 through 801 an \ d (name N or name CA or name C or name O or name CB )) or resid 802 through 809 \ or (resid 810 through 821 and (name N or name CA or name C or name O or name CB \ )) or resid 822 through 856 or (resid 857 through 861 and (name N or name CA or \ name C or name O or name CB )) or resid 862 through 870 or (resid 871 through 89 \ 1 and (name N or name CA or name C or name O or name CB )) or (resid 892 through \ 899 and (name N or name CA or name C or name O or name CB )) or resid 900 throu \ gh 908 or (resid 909 through 932 and (name N or name CA or name C or name O or n \ ame CB )) or resid 933 through 946 or (resid 947 through 950 and (name N or name \ CA or name C or name O or name CB )) or (resid 951 through 976 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 977 through 995 and (name N o \ r name CA or name C or name O or name CB )) or resid 996 through 997 or (resid 9 \ 98 through 1003 and (name N or name CA or name C or name O or name CB )) or resi \ d 1004 through 1021 or resid 1101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.740 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 0.075 6267 Z= 0.363 Angle : 0.876 23.527 8668 Z= 0.663 Chirality : 0.048 0.379 1034 Planarity : 0.005 0.089 1208 Dihedral : 12.776 89.939 1752 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.10 % 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: -1.99 (0.25), residues: 1030 helix: 0.14 (0.24), residues: 437 sheet: -1.51 (0.45), residues: 129 loop : -2.77 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 480 HIS 0.007 0.002 HIS A 708 PHE 0.043 0.003 PHE B 772 TYR 0.014 0.002 TYR A 605 ARG 0.008 0.001 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 809 GLU cc_start: 0.8515 (tp30) cc_final: 0.8251 (tp30) REVERT: A 870 ASN cc_start: 0.8958 (t0) cc_final: 0.8308 (m110) REVERT: B 634 CYS cc_start: 0.6137 (p) cc_final: 0.5810 (p) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2075 time to fit residues: 28.3114 Evaluate side-chains 65 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 ASN A 633 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.120918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.099570 restraints weight = 23606.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101099 restraints weight = 17539.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.102343 restraints weight = 13992.506| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6267 Z= 0.213 Angle : 0.565 5.965 8668 Z= 0.320 Chirality : 0.043 0.151 1034 Planarity : 0.005 0.057 1208 Dihedral : 11.014 86.579 1137 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.38 % Allowed : 3.42 % Favored : 96.20 % 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 (0.26), residues: 1030 helix: 1.31 (0.25), residues: 437 sheet: -0.54 (0.50), residues: 107 loop : -2.46 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 480 HIS 0.005 0.001 HIS B 562 PHE 0.038 0.003 PHE B 772 TYR 0.016 0.002 TYR A 605 ARG 0.008 0.001 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 870 ASN cc_start: 0.9044 (t0) cc_final: 0.8405 (m-40) REVERT: B 634 CYS cc_start: 0.6724 (p) cc_final: 0.6391 (p) REVERT: B 647 TYR cc_start: 0.7791 (p90) cc_final: 0.7512 (p90) REVERT: B 757 GLN cc_start: 0.8122 (pp30) cc_final: 0.7761 (pp30) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1800 time to fit residues: 22.6350 Evaluate side-chains 64 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 80 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 85 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.122778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.101113 restraints weight = 23245.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.102767 restraints weight = 17278.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.103864 restraints weight = 13668.457| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6267 Z= 0.146 Angle : 0.490 5.554 8668 Z= 0.271 Chirality : 0.041 0.122 1034 Planarity : 0.004 0.052 1208 Dihedral : 10.053 82.055 1137 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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: -0.08 (0.27), residues: 1030 helix: 1.97 (0.25), residues: 442 sheet: -0.27 (0.53), residues: 97 loop : -2.04 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 601 HIS 0.003 0.001 HIS A 708 PHE 0.020 0.002 PHE B 772 TYR 0.013 0.001 TYR A 582 ARG 0.003 0.001 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 870 ASN cc_start: 0.8992 (t0) cc_final: 0.8396 (m-40) REVERT: B 634 CYS cc_start: 0.6562 (p) cc_final: 0.6146 (p) REVERT: B 647 TYR cc_start: 0.7942 (p90) cc_final: 0.7705 (p90) REVERT: B 757 GLN cc_start: 0.7910 (pp30) cc_final: 0.7472 (pp30) REVERT: B 763 GLN cc_start: 0.8362 (mp10) cc_final: 0.8145 (mp10) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1801 time to fit residues: 21.5708 Evaluate side-chains 68 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 6 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 32 optimal weight: 0.0670 chunk 64 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.120676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.099001 restraints weight = 23481.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.100645 restraints weight = 17425.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101891 restraints weight = 13760.121| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6267 Z= 0.165 Angle : 0.485 5.522 8668 Z= 0.269 Chirality : 0.041 0.135 1034 Planarity : 0.004 0.048 1208 Dihedral : 9.721 89.641 1137 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % 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: 0.18 (0.27), residues: 1030 helix: 2.17 (0.25), residues: 443 sheet: -0.02 (0.57), residues: 91 loop : -1.90 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 601 HIS 0.004 0.001 HIS B 562 PHE 0.019 0.002 PHE B 707 TYR 0.015 0.001 TYR A 605 ARG 0.004 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 870 ASN cc_start: 0.8964 (t0) cc_final: 0.8389 (m110) REVERT: B 634 CYS cc_start: 0.6618 (p) cc_final: 0.6361 (p) REVERT: B 647 TYR cc_start: 0.7964 (p90) cc_final: 0.7733 (p90) REVERT: B 757 GLN cc_start: 0.7863 (pp30) cc_final: 0.7527 (pp30) REVERT: B 763 GLN cc_start: 0.8413 (mp10) cc_final: 0.8178 (mp10) REVERT: B 802 ARG cc_start: 0.8960 (mmp80) cc_final: 0.8733 (mmp80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1695 time to fit residues: 18.1644 Evaluate side-chains 64 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 8 optimal weight: 0.0010 chunk 68 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 73 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.123085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101527 restraints weight = 23474.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.103205 restraints weight = 17533.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.104400 restraints weight = 13878.615| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6267 Z= 0.131 Angle : 0.475 7.463 8668 Z= 0.256 Chirality : 0.041 0.178 1034 Planarity : 0.004 0.047 1208 Dihedral : 9.175 87.694 1137 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: 0.47 (0.28), residues: 1030 helix: 2.48 (0.25), residues: 446 sheet: -0.41 (0.53), residues: 106 loop : -1.76 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 601 HIS 0.002 0.001 HIS A 626 PHE 0.018 0.002 PHE A 603 TYR 0.021 0.001 TYR A 605 ARG 0.004 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 790 GLN cc_start: 0.7749 (tp40) cc_final: 0.7539 (tp40) REVERT: A 870 ASN cc_start: 0.8954 (t0) cc_final: 0.8399 (m110) REVERT: B 634 CYS cc_start: 0.6520 (p) cc_final: 0.6236 (p) REVERT: B 763 GLN cc_start: 0.8403 (mp10) cc_final: 0.8138 (mp10) REVERT: B 802 ARG cc_start: 0.8948 (mmp80) cc_final: 0.8726 (mmp80) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1942 time to fit residues: 22.0688 Evaluate side-chains 68 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.119220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.097985 restraints weight = 23152.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.099521 restraints weight = 17532.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.100684 restraints weight = 14025.059| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6267 Z= 0.191 Angle : 0.505 7.353 8668 Z= 0.278 Chirality : 0.041 0.149 1034 Planarity : 0.004 0.046 1208 Dihedral : 8.930 72.696 1137 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: 0.37 (0.27), residues: 1030 helix: 2.33 (0.25), residues: 447 sheet: -0.36 (0.53), residues: 102 loop : -1.76 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 480 HIS 0.006 0.001 HIS B 562 PHE 0.020 0.002 PHE B 707 TYR 0.019 0.002 TYR A 605 ARG 0.003 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 870 ASN cc_start: 0.8998 (t0) cc_final: 0.8417 (m-40) REVERT: B 475 LEU cc_start: 0.6957 (mm) cc_final: 0.6750 (tt) REVERT: B 763 GLN cc_start: 0.8369 (mp10) cc_final: 0.8076 (mp10) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1788 time to fit residues: 19.1985 Evaluate side-chains 67 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 5 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 68 optimal weight: 0.3980 chunk 72 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 42 optimal weight: 0.0040 chunk 32 optimal weight: 0.0470 chunk 17 optimal weight: 0.0370 overall best weight: 0.2368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.123238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101849 restraints weight = 22635.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.103471 restraints weight = 17010.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.104624 restraints weight = 13572.289| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6267 Z= 0.128 Angle : 0.475 9.245 8668 Z= 0.250 Chirality : 0.040 0.138 1034 Planarity : 0.004 0.045 1208 Dihedral : 8.028 55.854 1137 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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: 0.58 (0.28), residues: 1030 helix: 2.58 (0.25), residues: 450 sheet: -0.61 (0.51), residues: 111 loop : -1.67 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 752 HIS 0.003 0.001 HIS A 626 PHE 0.026 0.002 PHE A 550 TYR 0.017 0.001 TYR A 605 ARG 0.003 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 752 TRP cc_start: 0.7280 (m-10) cc_final: 0.6953 (m-10) REVERT: A 790 GLN cc_start: 0.7757 (tp40) cc_final: 0.7528 (tp40) REVERT: A 870 ASN cc_start: 0.8999 (t0) cc_final: 0.8423 (m-40) REVERT: A 876 PHE cc_start: 0.7759 (m-80) cc_final: 0.7526 (m-80) REVERT: B 763 GLN cc_start: 0.8300 (mp10) cc_final: 0.8011 (mp10) REVERT: B 802 ARG cc_start: 0.8988 (mmp80) cc_final: 0.8738 (mmp80) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1715 time to fit residues: 19.9447 Evaluate side-chains 69 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 23 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 83 optimal weight: 0.0040 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.119052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097660 restraints weight = 23157.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.099216 restraints weight = 17680.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.100326 restraints weight = 14207.811| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6267 Z= 0.196 Angle : 0.528 10.506 8668 Z= 0.280 Chirality : 0.042 0.161 1034 Planarity : 0.004 0.044 1208 Dihedral : 8.013 70.044 1137 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: 0.53 (0.28), residues: 1030 helix: 2.52 (0.25), residues: 451 sheet: -0.44 (0.52), residues: 107 loop : -1.74 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 480 HIS 0.005 0.001 HIS B 562 PHE 0.020 0.002 PHE A 550 TYR 0.021 0.002 TYR A 605 ARG 0.003 0.001 ARG B 750 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 605 TYR cc_start: 0.7577 (m-80) cc_final: 0.7344 (m-80) REVERT: A 752 TRP cc_start: 0.7360 (m-10) cc_final: 0.7090 (m-10) REVERT: A 790 GLN cc_start: 0.7939 (tp40) cc_final: 0.7672 (tp40) REVERT: A 870 ASN cc_start: 0.8980 (t0) cc_final: 0.8428 (m-40) REVERT: A 876 PHE cc_start: 0.7765 (m-80) cc_final: 0.7516 (m-80) REVERT: B 763 GLN cc_start: 0.8341 (mp10) cc_final: 0.8021 (mp10) REVERT: B 802 ARG cc_start: 0.8926 (mmp80) cc_final: 0.8706 (mmp80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1766 time to fit residues: 19.0966 Evaluate side-chains 68 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 99 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 102 optimal weight: 40.0000 chunk 92 optimal weight: 0.0060 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.0370 chunk 83 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 66 optimal weight: 0.0470 overall best weight: 0.2972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.123305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.101794 restraints weight = 22944.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.103468 restraints weight = 17284.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.104728 restraints weight = 13760.049| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6267 Z= 0.123 Angle : 0.485 10.478 8668 Z= 0.251 Chirality : 0.040 0.130 1034 Planarity : 0.003 0.045 1208 Dihedral : 7.088 85.118 1137 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.82 (0.28), residues: 1030 helix: 2.82 (0.25), residues: 450 sheet: -0.57 (0.48), residues: 129 loop : -1.61 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 752 HIS 0.001 0.000 HIS B 619 PHE 0.024 0.001 PHE B 707 TYR 0.016 0.001 TYR A 605 ARG 0.004 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 790 GLN cc_start: 0.7764 (tp40) cc_final: 0.7529 (tp40) REVERT: A 870 ASN cc_start: 0.8985 (t0) cc_final: 0.8392 (m-40) REVERT: A 876 PHE cc_start: 0.7792 (m-80) cc_final: 0.7567 (m-80) REVERT: B 647 TYR cc_start: 0.8027 (p90) cc_final: 0.7602 (p90) REVERT: B 763 GLN cc_start: 0.8243 (mp10) cc_final: 0.7914 (mp10) REVERT: B 802 ARG cc_start: 0.8917 (mmp80) cc_final: 0.8654 (mmp80) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1765 time to fit residues: 20.6099 Evaluate side-chains 70 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 75 optimal weight: 20.0000 chunk 101 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 99 optimal weight: 0.1980 chunk 102 optimal weight: 0.0370 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.122718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.101491 restraints weight = 23025.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.103135 restraints weight = 17211.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104314 restraints weight = 13695.992| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6267 Z= 0.127 Angle : 0.494 11.781 8668 Z= 0.252 Chirality : 0.040 0.127 1034 Planarity : 0.003 0.045 1208 Dihedral : 6.537 70.450 1137 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.92 (0.28), residues: 1030 helix: 2.87 (0.25), residues: 451 sheet: -0.54 (0.48), residues: 129 loop : -1.51 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 480 HIS 0.002 0.001 HIS B 562 PHE 0.031 0.001 PHE A 550 TYR 0.023 0.001 TYR A 605 ARG 0.004 0.000 ARG B 750 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 790 GLN cc_start: 0.7765 (tp40) cc_final: 0.7546 (tp40) REVERT: A 870 ASN cc_start: 0.8966 (t0) cc_final: 0.8422 (m-40) REVERT: A 876 PHE cc_start: 0.7759 (m-80) cc_final: 0.7534 (m-80) REVERT: B 763 GLN cc_start: 0.8268 (mp10) cc_final: 0.7973 (mp10) REVERT: B 802 ARG cc_start: 0.8910 (mmp80) cc_final: 0.8665 (mmp80) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1751 time to fit residues: 19.2208 Evaluate side-chains 69 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 73 optimal weight: 0.5980 chunk 21 optimal weight: 0.0670 chunk 67 optimal weight: 0.1980 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 51 optimal weight: 30.0000 chunk 77 optimal weight: 0.1980 chunk 39 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.2518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.124597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.103307 restraints weight = 23206.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.105028 restraints weight = 17294.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.106284 restraints weight = 13673.124| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6267 Z= 0.120 Angle : 0.485 10.739 8668 Z= 0.245 Chirality : 0.040 0.129 1034 Planarity : 0.004 0.045 1208 Dihedral : 6.309 69.418 1137 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.02 (0.28), residues: 1030 helix: 2.96 (0.25), residues: 457 sheet: -0.51 (0.48), residues: 129 loop : -1.52 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 752 HIS 0.002 0.000 HIS A 626 PHE 0.023 0.001 PHE B 731 TYR 0.023 0.001 TYR A 605 ARG 0.003 0.000 ARG A 683 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.32 seconds wall clock time: 36 minutes 8.04 seconds (2168.04 seconds total)