Starting phenix.real_space_refine on Fri Jul 3 22:24:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ea8_31040/07_2026/7ea8_31040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ea8_31040/07_2026/7ea8_31040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ea8_31040/07_2026/7ea8_31040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ea8_31040/07_2026/7ea8_31040.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ea8_31040/07_2026/7ea8_31040.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ea8_31040/07_2026/7ea8_31040.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ea8_31040/07_2026/7ea8_31040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ea8_31040/07_2026/7ea8_31040.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4902 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 244 5.49 5 S 33 5.16 5 C 7305 2.51 5 N 2401 2.21 5 O 2879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12865 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1993 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} Chain: "A" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 818 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 799 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 771 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "I" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2485 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "J" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2517 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 542 SG CYS L1516 43.708 62.969 53.053 1.00 45.67 S ATOM 643 SG CYS L1529 40.601 58.945 52.919 1.00 46.92 S ATOM 672 SG CYS L1533 40.198 62.627 55.544 1.00 53.00 S ATOM 717 SG CYS L1539 40.330 62.668 51.612 1.00 47.82 S ATOM 416 SG CYS L1499 43.510 60.073 56.178 1.00 47.21 S ATOM 431 SG CYS L1501 46.699 61.864 55.722 1.00 51.47 S ATOM 542 SG CYS L1516 43.708 62.969 53.053 1.00 45.67 S ATOM 569 SG CYS L1520 45.259 58.912 52.403 1.00 43.65 S ATOM 1863 SG CYS L1678 39.772 46.170 17.879 1.00 67.56 S ATOM 1909 SG CYS L1685 43.414 44.340 16.211 1.00 57.15 S Time building chain proxies: 2.03, per 1000 atoms: 0.16 Number of scatterers: 12865 At special positions: 0 Unit cell: (132, 88, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 33 16.00 P 244 15.00 O 2879 8.00 N 2401 7.00 C 7305 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 Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 428.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L1801 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1539 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1516 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1533 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1529 " pdb=" ZN L1802 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1520 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1499 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1516 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1501 " pdb=" ZN L1803 " pdb="ZN ZN L1803 " - pdb=" SG CYS L1678 " pdb="ZN ZN L1803 " - pdb=" SG CYS L1685 " Number of angles added : 12 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 57.7% alpha, 4.6% beta 121 base pairs and 214 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'L' and resid 1520 through 1525 removed outlier: 3.660A pdb=" N LEU L1524 " --> pdb=" O CYS L1520 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU L1525 " --> pdb=" O LEU L1521 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1520 through 1525' Processing helix chain 'L' and resid 1535 through 1539 removed outlier: 4.046A pdb=" N CYS L1539 " --> pdb=" O GLY L1536 " (cutoff:3.500A) Processing helix chain 'L' and resid 1585 through 1597 removed outlier: 4.080A pdb=" N PHE L1589 " --> pdb=" O ASP L1585 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS L1590 " --> pdb=" O HIS L1586 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA L1591 " --> pdb=" O LYS L1587 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS L1594 " --> pdb=" O LYS L1590 " (cutoff:3.500A) Processing helix chain 'L' and resid 1598 through 1600 No H-bonds generated for 'chain 'L' and resid 1598 through 1600' Processing helix chain 'L' and resid 1622 through 1626 removed outlier: 3.531A pdb=" N ARG L1625 " --> pdb=" O ASN L1622 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE L1626 " --> pdb=" O CYS L1623 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1622 through 1626' Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.597A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.657A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.849A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.748A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.738A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.996A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.706A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.815A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.659A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.905A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 122 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.792A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.044A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU E 94 " --> pdb=" O GLY E 90 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.718A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.026A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.978A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.912A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.718A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR H 83 " --> pdb=" O ARG H 79 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.613A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR H 122 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 1556 through 1558 removed outlier: 4.337A pdb=" N GLU L1558 " --> pdb=" O GLY L1561 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 1575 through 1578 removed outlier: 6.954A pdb=" N PHE L1650 " --> pdb=" O VAL L1576 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLU L1578 " --> pdb=" O VAL L1648 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL L1648 " --> pdb=" O GLU L1578 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 1582 through 1583 Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.068A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.322A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.110A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.904A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.302A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 392 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 314 hydrogen bonds 628 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 214 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.22 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: 2951 1.34 - 1.46: 4033 1.46 - 1.58: 6070 1.58 - 1.70: 486 1.70 - 1.82: 49 Bond restraints: 13589 Sorted by residual: bond pdb=" C5' DA I 39 " pdb=" C4' DA I 39 " ideal model delta sigma weight residual 1.512 1.538 -0.026 7.00e-03 2.04e+04 1.33e+01 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DC I 12 " pdb=" C2' DC I 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT I 104 " pdb=" C2' DT I 104 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG I 94 " pdb=" C2' DG I 94 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 ... (remaining 13584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 18193 1.70 - 3.39: 1109 3.39 - 5.09: 54 5.09 - 6.79: 14 6.79 - 8.48: 5 Bond angle restraints: 19375 Sorted by residual: angle pdb=" O5' DA I 39 " pdb=" C5' DA I 39 " pdb=" C4' DA I 39 " ideal model delta sigma weight residual 109.40 113.25 -3.85 8.00e-01 1.56e+00 2.31e+01 angle pdb=" N3 DT J 42 " pdb=" C4 DT J 42 " pdb=" O4 DT J 42 " ideal model delta sigma weight residual 119.90 122.70 -2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT I 35 " pdb=" C4 DT I 35 " pdb=" O4 DT I 35 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.96e+01 ... (remaining 19370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.88: 6124 27.88 - 55.77: 1292 55.77 - 83.65: 111 83.65 - 111.53: 0 111.53 - 139.41: 3 Dihedral angle restraints: 7530 sinusoidal: 4686 harmonic: 2844 Sorted by residual: dihedral pdb=" CA TYR L1666 " pdb=" C TYR L1666 " pdb=" N GLN L1667 " pdb=" CA GLN L1667 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA GLU L1478 " pdb=" C GLU L1478 " pdb=" N ASN L1479 " pdb=" CA ASN L1479 " ideal model delta harmonic sigma weight residual -180.00 -159.36 -20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 80.59 139.41 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 7527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1609 0.052 - 0.104: 489 0.104 - 0.156: 69 0.156 - 0.208: 5 0.208 - 0.260: 1 Chirality restraints: 2173 Sorted by residual: chirality pdb=" CB ILE A 119 " pdb=" CA ILE A 119 " pdb=" CG1 ILE A 119 " pdb=" CG2 ILE A 119 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE L1494 " pdb=" CA ILE L1494 " pdb=" CG1 ILE L1494 " pdb=" CG2 ILE L1494 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CG LEU E 61 " pdb=" CB LEU E 61 " pdb=" CD1 LEU E 61 " pdb=" CD2 LEU E 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 2170 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO H 103 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO C 80 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO D 103 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.028 5.00e-02 4.00e+02 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3109 2.82 - 3.34: 10018 3.34 - 3.86: 22773 3.86 - 4.38: 26823 4.38 - 4.90: 39763 Nonbonded interactions: 102486 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.306 3.040 nonbonded pdb=" ND2 ASN L1634 " pdb=" O GLU L1661 " model vdw 2.379 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.381 3.120 nonbonded pdb=" O LEU A 103 " pdb=" OG1 THR A 107 " model vdw 2.382 3.040 nonbonded pdb=" O GLU L1578 " pdb=" ND2 ASN L1622 " model vdw 2.387 3.120 ... (remaining 102481 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 39 through 76 or resid 78 through 133)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 35 through 123) selection = chain 'H' } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.650 Find NCS groups from input model: 0.130 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 : 0.011 0.487 13600 Z= 0.600 Angle : 0.900 27.780 19387 Z= 0.675 Chirality : 0.048 0.260 2173 Planarity : 0.006 0.051 1621 Dihedral : 24.015 139.413 5700 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.21), residues: 964 helix: -1.58 (0.17), residues: 540 sheet: -2.04 (0.90), residues: 31 loop : -2.88 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 116 TYR 0.024 0.002 TYR H 42 PHE 0.021 0.002 PHE L1664 TRP 0.014 0.002 TRP L1640 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.50 (13589) covalent geometry : angle 0.82927 / 0.67 (19375) hydrogen bonds : bond 0.10867 / 7.23 ( 706) hydrogen bonds : angle 4.47227 / 3.00 ( 1783) metal coordination : bond 0.35222 / 21.15 ( 10) metal coordination : angle 14.08458 / 7.21 ( 12) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: L 1486 LYS cc_start: 0.4525 (pmtt) cc_final: 0.4282 (mmtt) REVERT: L 1599 ASN cc_start: 0.4018 (m-40) cc_final: 0.3671 (t0) REVERT: B 68 ASP cc_start: 0.7662 (m-30) cc_final: 0.7440 (m-30) REVERT: C 75 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8335 (mmtt) REVERT: D 62 MET cc_start: 0.8493 (mmm) cc_final: 0.8249 (mmm) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1912 time to fit residues: 56.7676 Evaluate side-chains 157 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 50.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1548 GLN L1601 ASN A 39 HIS A 68 GLN B 93 GLN C 68 ASN F 27 GLN H 47 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.188446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.143649 restraints weight = 14099.746| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.19 r_work: 0.3151 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13600 Z= 0.242 Angle : 0.729 12.828 19387 Z= 0.408 Chirality : 0.048 0.190 2173 Planarity : 0.006 0.049 1621 Dihedral : 29.110 148.705 3741 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.45 % Allowed : 8.44 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.25), residues: 964 helix: 0.39 (0.22), residues: 547 sheet: -1.65 (0.86), residues: 31 loop : -2.87 (0.25), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 55 TYR 0.017 0.003 TYR L1596 PHE 0.023 0.003 PHE C 25 TRP 0.010 0.003 TRP L1562 HIS 0.008 0.002 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.24 (13589) covalent geometry : angle 0.71167 / 0.41 (19375) hydrogen bonds : bond 0.08243 / 5.35 ( 706) hydrogen bonds : angle 3.24169 / 2.15 ( 1783) metal coordination : bond 0.01908 / 1.28 ( 10) metal coordination : angle 6.45584 / 3.43 ( 12) Misc. bond : bond 0.00066 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: L 1477 GLU cc_start: 0.5016 (tp30) cc_final: 0.4770 (tm-30) REVERT: L 1479 ASN cc_start: 0.7272 (m-40) cc_final: 0.6957 (m-40) REVERT: A 115 LYS cc_start: 0.7774 (mttp) cc_final: 0.7474 (mtmm) REVERT: C 75 LYS cc_start: 0.8933 (mmtp) cc_final: 0.8655 (mmtt) REVERT: C 104 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7966 (mt0) REVERT: G 36 LYS cc_start: 0.8405 (tttt) cc_final: 0.7785 (mmtm) REVERT: H 47 GLN cc_start: 0.8203 (mt0) cc_final: 0.7931 (mt0) outliers start: 12 outliers final: 4 residues processed: 157 average time/residue: 0.1951 time to fit residues: 39.0906 Evaluate side-chains 141 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 73 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 8.9990 chunk 94 optimal weight: 50.0000 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 117 optimal weight: 50.0000 chunk 28 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1545 GLN E 68 GLN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.192843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148385 restraints weight = 14214.085| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.19 r_work: 0.3221 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13600 Z= 0.131 Angle : 0.575 9.804 19387 Z= 0.337 Chirality : 0.042 0.183 2173 Planarity : 0.004 0.043 1621 Dihedral : 29.125 149.124 3741 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.45 % Allowed : 8.08 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.27), residues: 964 helix: 1.48 (0.23), residues: 550 sheet: -1.71 (0.95), residues: 28 loop : -2.57 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 81 TYR 0.013 0.001 TYR L1596 PHE 0.037 0.001 PHE L1589 TRP 0.006 0.001 TRP L1562 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.13 (13589) covalent geometry : angle 0.56315 / 0.34 (19375) hydrogen bonds : bond 0.05552 / 3.62 ( 706) hydrogen bonds : angle 2.85090 / 1.90 ( 1783) metal coordination : bond 0.00900 / 0.45 ( 10) metal coordination : angle 4.77098 / 2.56 ( 12) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: L 1465 LYS cc_start: 0.3936 (ttpt) cc_final: 0.3095 (mtmt) REVERT: L 1514 ILE cc_start: 0.6040 (OUTLIER) cc_final: 0.5711 (pp) REVERT: L 1545 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: L 1547 LYS cc_start: 0.8119 (mmmm) cc_final: 0.7903 (mmmm) REVERT: A 115 LYS cc_start: 0.7366 (mttp) cc_final: 0.7074 (mtmm) REVERT: C 75 LYS cc_start: 0.8937 (mmtp) cc_final: 0.8723 (mmtt) REVERT: C 89 ASN cc_start: 0.8678 (m-40) cc_final: 0.8466 (m-40) REVERT: G 36 LYS cc_start: 0.8325 (tttt) cc_final: 0.7729 (mmtm) outliers start: 12 outliers final: 5 residues processed: 150 average time/residue: 0.1705 time to fit residues: 33.6557 Evaluate side-chains 145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1514 ILE Chi-restraints excluded: chain L residue 1545 GLN Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 50.0000 chunk 87 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1545 GLN L1599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.191765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.148098 restraints weight = 14232.448| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.07 r_work: 0.3207 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13600 Z= 0.143 Angle : 0.567 7.192 19387 Z= 0.333 Chirality : 0.042 0.173 2173 Planarity : 0.004 0.042 1621 Dihedral : 29.157 149.186 3741 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.09 % Allowed : 9.53 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 964 helix: 1.89 (0.23), residues: 549 sheet: -1.52 (0.94), residues: 28 loop : -2.50 (0.26), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L1546 TYR 0.009 0.001 TYR C 57 PHE 0.012 0.002 PHE L1589 TRP 0.008 0.001 TRP L1562 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (13589) covalent geometry : angle 0.55879 / 0.33 (19375) hydrogen bonds : bond 0.05742 / 3.75 ( 706) hydrogen bonds : angle 2.81268 / 1.86 ( 1783) metal coordination : bond 0.00550 / 0.28 ( 10) metal coordination : angle 3.87652 / 2.05 ( 12) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.413 Fit side-chains REVERT: L 1477 GLU cc_start: 0.4877 (tp30) cc_final: 0.4604 (tm-30) REVERT: L 1514 ILE cc_start: 0.6062 (OUTLIER) cc_final: 0.5724 (pp) REVERT: A 115 LYS cc_start: 0.7516 (mttp) cc_final: 0.7196 (mtmm) REVERT: C 89 ASN cc_start: 0.8735 (m-40) cc_final: 0.8526 (m-40) REVERT: G 36 LYS cc_start: 0.8331 (tttt) cc_final: 0.7732 (mmtm) outliers start: 9 outliers final: 6 residues processed: 145 average time/residue: 0.1710 time to fit residues: 32.4900 Evaluate side-chains 143 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1514 ILE Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 115 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1541 ASN L1643 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.191012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.147566 restraints weight = 14289.247| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.07 r_work: 0.3204 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13600 Z= 0.146 Angle : 0.571 6.888 19387 Z= 0.332 Chirality : 0.042 0.174 2173 Planarity : 0.004 0.041 1621 Dihedral : 29.181 150.194 3741 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.45 % Allowed : 10.13 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.28), residues: 964 helix: 2.12 (0.23), residues: 543 sheet: -1.22 (0.99), residues: 28 loop : -2.44 (0.26), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 81 TYR 0.008 0.001 TYR C 57 PHE 0.015 0.002 PHE C 25 TRP 0.011 0.002 TRP L1562 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (13589) covalent geometry : angle 0.56499 / 0.33 (19375) hydrogen bonds : bond 0.05839 / 3.80 ( 706) hydrogen bonds : angle 2.80533 / 1.85 ( 1783) metal coordination : bond 0.00468 / 0.24 ( 10) metal coordination : angle 3.25494 / 1.70 ( 12) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.373 Fit side-chains REVERT: L 1514 ILE cc_start: 0.5840 (OUTLIER) cc_final: 0.5463 (pp) REVERT: A 73 GLU cc_start: 0.8131 (tt0) cc_final: 0.7883 (tt0) REVERT: A 115 LYS cc_start: 0.7543 (mttp) cc_final: 0.7255 (mtmm) REVERT: G 36 LYS cc_start: 0.8361 (tttt) cc_final: 0.7755 (mmtm) outliers start: 12 outliers final: 9 residues processed: 146 average time/residue: 0.1724 time to fit residues: 33.0344 Evaluate side-chains 146 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1514 ILE Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain L residue 1643 ASN Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 77 optimal weight: 0.0870 chunk 89 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1548 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.191487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.149689 restraints weight = 14148.995| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.24 r_work: 0.3160 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13600 Z= 0.136 Angle : 0.556 6.633 19387 Z= 0.327 Chirality : 0.041 0.173 2173 Planarity : 0.004 0.040 1621 Dihedral : 29.183 150.448 3741 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.84 % Allowed : 11.10 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.28), residues: 964 helix: 2.30 (0.23), residues: 541 sheet: -1.09 (1.00), residues: 28 loop : -2.35 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L1459 TYR 0.007 0.001 TYR C 57 PHE 0.015 0.001 PHE L1589 TRP 0.010 0.001 TRP L1562 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (13589) covalent geometry : angle 0.55090 / 0.33 (19375) hydrogen bonds : bond 0.05535 / 3.61 ( 706) hydrogen bonds : angle 2.75852 / 1.82 ( 1783) metal coordination : bond 0.00419 / 0.22 ( 10) metal coordination : angle 2.94008 / 1.54 ( 12) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.375 Fit side-chains REVERT: L 1544 PHE cc_start: 0.7260 (m-10) cc_final: 0.7034 (m-10) REVERT: L 1606 PHE cc_start: 0.6719 (m-10) cc_final: 0.6333 (m-80) REVERT: L 1627 MET cc_start: 0.6032 (mmm) cc_final: 0.5693 (mmm) REVERT: A 73 GLU cc_start: 0.8288 (tt0) cc_final: 0.8054 (tt0) REVERT: A 115 LYS cc_start: 0.7480 (mttp) cc_final: 0.7195 (mtmm) REVERT: D 42 TYR cc_start: 0.8416 (t80) cc_final: 0.8043 (t80) REVERT: G 64 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7708 (tp30) outliers start: 7 outliers final: 4 residues processed: 147 average time/residue: 0.1723 time to fit residues: 33.2298 Evaluate side-chains 145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain G residue 64 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 115 optimal weight: 20.0000 chunk 117 optimal weight: 50.0000 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 52 optimal weight: 0.2980 chunk 66 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1466 GLN L1548 GLN L1643 ASN E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.188068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.144332 restraints weight = 14103.685| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.20 r_work: 0.3149 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13600 Z= 0.186 Angle : 0.615 8.182 19387 Z= 0.354 Chirality : 0.044 0.169 2173 Planarity : 0.004 0.042 1621 Dihedral : 29.209 150.397 3741 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.09 % Allowed : 11.10 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.28), residues: 964 helix: 2.10 (0.23), residues: 541 sheet: -1.10 (0.97), residues: 28 loop : -2.41 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 35 TYR 0.010 0.001 TYR D 121 PHE 0.020 0.003 PHE A 84 TRP 0.017 0.002 TRP L1562 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (13589) covalent geometry : angle 0.61032 / 0.35 (19375) hydrogen bonds : bond 0.06816 / 4.44 ( 706) hydrogen bonds : angle 2.89993 / 1.91 ( 1783) metal coordination : bond 0.00440 / 0.24 ( 10) metal coordination : angle 2.96358 / 1.51 ( 12) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: L 1582 GLU cc_start: 0.6107 (mt-10) cc_final: 0.5481 (tp30) REVERT: L 1606 PHE cc_start: 0.6672 (m-10) cc_final: 0.6308 (m-80) REVERT: L 1627 MET cc_start: 0.5735 (mmm) cc_final: 0.5394 (mmm) REVERT: A 115 LYS cc_start: 0.7767 (mttp) cc_final: 0.7482 (mtmm) REVERT: D 42 TYR cc_start: 0.8390 (t80) cc_final: 0.8022 (t80) REVERT: G 64 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7619 (tp30) outliers start: 9 outliers final: 7 residues processed: 149 average time/residue: 0.1783 time to fit residues: 34.6898 Evaluate side-chains 151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 50 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.185374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.140169 restraints weight = 14027.814| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.03 r_work: 0.3129 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13600 Z= 0.222 Angle : 0.667 7.157 19387 Z= 0.376 Chirality : 0.047 0.179 2173 Planarity : 0.005 0.044 1621 Dihedral : 29.298 151.036 3741 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.21 % Allowed : 11.34 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.27), residues: 964 helix: 1.73 (0.23), residues: 548 sheet: -1.15 (0.96), residues: 28 loop : -2.51 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 35 TYR 0.013 0.002 TYR D 121 PHE 0.026 0.003 PHE A 84 TRP 0.017 0.003 TRP L1562 HIS 0.007 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 (13589) covalent geometry : angle 0.66320 / 0.38 (19375) hydrogen bonds : bond 0.07963 / 5.17 ( 706) hydrogen bonds : angle 3.06436 / 2.02 ( 1783) metal coordination : bond 0.00461 / 0.25 ( 10) metal coordination : angle 3.03680 / 1.53 ( 12) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: L 1582 GLU cc_start: 0.6124 (mt-10) cc_final: 0.5587 (tp30) REVERT: L 1606 PHE cc_start: 0.6620 (m-10) cc_final: 0.6295 (m-80) REVERT: L 1627 MET cc_start: 0.5927 (mmm) cc_final: 0.5599 (mmm) REVERT: L 1638 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: A 115 LYS cc_start: 0.7927 (mttp) cc_final: 0.7550 (mtmm) REVERT: D 42 TYR cc_start: 0.8394 (t80) cc_final: 0.7991 (t80) REVERT: G 64 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7599 (tp30) outliers start: 10 outliers final: 8 residues processed: 156 average time/residue: 0.1734 time to fit residues: 35.3536 Evaluate side-chains 157 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain L residue 1638 GLN Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 45 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.187107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.142159 restraints weight = 14127.539| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.10 r_work: 0.3138 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13600 Z= 0.162 Angle : 0.621 7.255 19387 Z= 0.356 Chirality : 0.045 0.176 2173 Planarity : 0.004 0.044 1621 Dihedral : 29.275 151.174 3741 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.21 % Allowed : 12.06 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.28), residues: 964 helix: 1.94 (0.23), residues: 546 sheet: -0.88 (0.91), residues: 33 loop : -2.40 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 35 TYR 0.012 0.002 TYR L1666 PHE 0.015 0.002 PHE L1589 TRP 0.010 0.002 TRP L1562 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (13589) covalent geometry : angle 0.61752 / 0.36 (19375) hydrogen bonds : bond 0.06958 / 4.53 ( 706) hydrogen bonds : angle 2.97923 / 1.97 ( 1783) metal coordination : bond 0.00394 / 0.21 ( 10) metal coordination : angle 2.56000 / 1.28 ( 12) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: L 1582 GLU cc_start: 0.6219 (mt-10) cc_final: 0.5598 (tp30) REVERT: L 1606 PHE cc_start: 0.6670 (m-10) cc_final: 0.6328 (m-80) REVERT: L 1627 MET cc_start: 0.5942 (mmm) cc_final: 0.5579 (mmm) REVERT: A 115 LYS cc_start: 0.7839 (mttp) cc_final: 0.7468 (mtmm) REVERT: D 42 TYR cc_start: 0.8349 (t80) cc_final: 0.7965 (t80) outliers start: 10 outliers final: 8 residues processed: 151 average time/residue: 0.1662 time to fit residues: 32.8753 Evaluate side-chains 152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 50.0000 chunk 117 optimal weight: 50.0000 chunk 79 optimal weight: 0.0470 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.187006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.141757 restraints weight = 14125.186| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.06 r_work: 0.3152 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13600 Z= 0.175 Angle : 0.613 7.289 19387 Z= 0.352 Chirality : 0.044 0.173 2173 Planarity : 0.004 0.044 1621 Dihedral : 29.282 150.899 3741 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.97 % Allowed : 12.18 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.28), residues: 964 helix: 1.95 (0.23), residues: 546 sheet: -0.86 (0.92), residues: 33 loop : -2.37 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 35 TYR 0.010 0.001 TYR D 121 PHE 0.016 0.002 PHE L1589 TRP 0.009 0.002 TRP L1562 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (13589) covalent geometry : angle 0.60959 / 0.35 (19375) hydrogen bonds : bond 0.06913 / 4.50 ( 706) hydrogen bonds : angle 2.96518 / 1.96 ( 1783) metal coordination : bond 0.00369 / 0.20 ( 10) metal coordination : angle 2.48449 / 1.26 ( 12) Misc. bond : bond 0.00002 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: L 1582 GLU cc_start: 0.6228 (mt-10) cc_final: 0.5674 (tp30) REVERT: L 1606 PHE cc_start: 0.6615 (m-10) cc_final: 0.6300 (m-80) REVERT: L 1627 MET cc_start: 0.5950 (mmm) cc_final: 0.5592 (mmm) REVERT: L 1638 GLN cc_start: 0.8195 (mt0) cc_final: 0.7945 (mt0) REVERT: A 115 LYS cc_start: 0.7827 (mttp) cc_final: 0.7468 (mtmm) REVERT: D 42 TYR cc_start: 0.8351 (t80) cc_final: 0.7971 (t80) outliers start: 8 outliers final: 8 residues processed: 153 average time/residue: 0.1689 time to fit residues: 34.1046 Evaluate side-chains 154 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 0.0470 chunk 117 optimal weight: 50.0000 chunk 96 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.188173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143937 restraints weight = 14148.046| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.22 r_work: 0.3121 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13600 Z= 0.139 Angle : 0.590 7.433 19387 Z= 0.342 Chirality : 0.043 0.176 2173 Planarity : 0.004 0.044 1621 Dihedral : 29.257 150.299 3741 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.84 % Allowed : 12.55 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.28), residues: 964 helix: 2.13 (0.23), residues: 546 sheet: -0.80 (0.92), residues: 33 loop : -2.28 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 35 TYR 0.008 0.001 TYR C 57 PHE 0.015 0.002 PHE L1589 TRP 0.009 0.002 TRP L1562 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (13589) covalent geometry : angle 0.58711 / 0.34 (19375) hydrogen bonds : bond 0.06286 / 4.09 ( 706) hydrogen bonds : angle 2.96462 / 1.96 ( 1783) metal coordination : bond 0.00341 / 0.17 ( 10) metal coordination : angle 2.38037 / 1.20 ( 12) Misc. bond : bond 0.00017 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2834.72 seconds wall clock time: 49 minutes 17.20 seconds (2957.20 seconds total)