Starting phenix.real_space_refine on Wed Sep 25 18:26:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7g_22698/09_2024/7k7g_22698.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7g_22698/09_2024/7k7g_22698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7g_22698/09_2024/7k7g_22698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7g_22698/09_2024/7k7g_22698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7g_22698/09_2024/7k7g_22698.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7g_22698/09_2024/7k7g_22698.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 246 5.49 5 S 10 5.16 5 C 6198 2.51 5 N 2071 2.21 5 O 2571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11098 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 741 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 749 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 741 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 772 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2522 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "J" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2521 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "M" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 336 Classifications: {'peptide': 43} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 40} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10831 SG CYS M 14 63.870 26.104 96.501 1.00380.11 S ATOM 10850 SG CYS M 17 62.190 27.132 94.952 1.00375.25 S ATOM 10910 SG CYS M 24 63.976 25.849 92.055 1.00349.57 S ATOM 10958 SG CYS M 30 66.711 27.538 93.702 1.00397.98 S ATOM 10831 SG CYS M 14 63.870 26.104 96.501 1.00380.11 S ATOM 10976 SG CYS M 33 66.258 27.313 98.467 1.00424.58 S ATOM 11049 SG CYS M 42 67.639 24.000 98.551 1.00431.44 S Time building chain proxies: 6.78, per 1000 atoms: 0.61 Number of scatterers: 11098 At special positions: 0 Unit cell: (83.74, 126.14, 128.26, 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 2 29.99 S 10 16.00 P 246 15.00 O 2571 8.00 N 2071 7.00 C 6198 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=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 770.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 701 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 14 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 17 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 30 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 24 " pdb=" ZN M 702 " pdb="ZN ZN M 702 " - pdb=" SG CYS M 33 " pdb="ZN ZN M 702 " - pdb=" SG CYS M 14 " pdb="ZN ZN M 702 " - pdb=" SG CYS M 42 " Number of angles added : 6 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1436 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 67.6% alpha, 2.1% beta 109 base pairs and 208 stacking pairs defined. Time for finding SS restraints: 5.69 Creating SS restraints... Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.643A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.818A pdb=" N ILE A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.569A pdb=" N ILE A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.561A pdb=" N GLN B 28 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 43 Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.651A pdb=" N GLU B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.785A pdb=" N ARG B 93 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 28 through 38 removed outlier: 3.905A pdb=" N ARG C 37 " --> pdb=" O HIS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 75 removed outlier: 3.796A pdb=" N ALA C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 removed outlier: 3.566A pdb=" N ALA C 88 " --> pdb=" O HIS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'D' and resid 41 through 53 removed outlier: 3.699A pdb=" N LYS D 50 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 88 Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.572A pdb=" N ILE D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 127 removed outlier: 3.909A pdb=" N SER D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA D 121 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 122 " --> pdb=" O GLY D 118 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.642A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.818A pdb=" N ILE E 90 " --> pdb=" O GLN E 86 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.569A pdb=" N ILE E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 removed outlier: 3.562A pdb=" N GLN F 28 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 30 " --> pdb=" O ILE F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 43 Processing helix chain 'F' and resid 49 through 77 removed outlier: 4.652A pdb=" N GLU F 53 " --> pdb=" O GLY F 49 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA F 77 " --> pdb=" O TYR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.785A pdb=" N ARG F 93 " --> pdb=" O TYR F 89 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 28 through 38 removed outlier: 3.505A pdb=" N ARG G 37 " --> pdb=" O HIS G 33 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 74 removed outlier: 3.603A pdb=" N ALA G 62 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 removed outlier: 3.664A pdb=" N LEU G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 53 removed outlier: 3.699A pdb=" N LYS H 50 " --> pdb=" O TYR H 46 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN H 51 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 88 Processing helix chain 'H' and resid 94 through 106 removed outlier: 3.572A pdb=" N ILE H 98 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 127 removed outlier: 3.908A pdb=" N SER H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU H 117 " --> pdb=" O HIS H 113 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL H 122 " --> pdb=" O GLY H 118 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 20 Processing helix chain 'M' and resid 38 through 43 removed outlier: 4.214A pdb=" N CYS M 42 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.182A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 removed outlier: 6.622A pdb=" N THR B 97 " --> pdb=" O THR G 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 44 through 45 removed outlier: 7.810A pdb=" N ARG C 44 " --> pdb=" O ILE D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AA6, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.280A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA8, first strand: chain 'G' and resid 44 through 45 removed outlier: 7.616A pdb=" N ARG G 44 " --> pdb=" O ILE H 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 337 hydrogen bonds defined for protein. 1005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 262 hydrogen bonds 502 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 208 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1658 1.33 - 1.45: 4068 1.45 - 1.57: 5550 1.57 - 1.69: 489 1.69 - 1.81: 14 Bond restraints: 11779 Sorted by residual: bond pdb=" C3' DT J 173 " pdb=" O3' DT J 173 " ideal model delta sigma weight residual 1.422 1.494 -0.072 3.00e-02 1.11e+03 5.74e+00 bond pdb=" C3' DT J 225 " pdb=" O3' DT J 225 " ideal model delta sigma weight residual 1.422 1.487 -0.065 3.00e-02 1.11e+03 4.74e+00 bond pdb=" C3' DA I 119 " pdb=" O3' DA I 119 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.77e+00 bond pdb=" C3' DT J 172 " pdb=" O3' DT J 172 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.46e+00 bond pdb=" C VAL G 109 " pdb=" N LEU G 110 " ideal model delta sigma weight residual 1.330 1.355 -0.024 1.37e-02 5.33e+03 3.12e+00 ... (remaining 11774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 16065 2.14 - 4.28: 786 4.28 - 6.42: 68 6.42 - 8.56: 14 8.56 - 10.70: 12 Bond angle restraints: 16945 Sorted by residual: angle pdb=" C ASP G 93 " pdb=" N GLU G 94 " pdb=" CA GLU G 94 " ideal model delta sigma weight residual 121.54 130.42 -8.88 1.91e+00 2.74e-01 2.16e+01 angle pdb=" C VAL M 22 " pdb=" N LYS M 23 " pdb=" CA LYS M 23 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" N GLY B 95 " pdb=" CA GLY B 95 " pdb=" C GLY B 95 " ideal model delta sigma weight residual 115.67 108.99 6.68 1.59e+00 3.96e-01 1.76e+01 angle pdb=" N GLY F 95 " pdb=" CA GLY F 95 " pdb=" C GLY F 95 " ideal model delta sigma weight residual 115.67 109.01 6.66 1.59e+00 3.96e-01 1.76e+01 angle pdb=" C VAL G 109 " pdb=" N LEU G 110 " pdb=" CA LEU G 110 " ideal model delta sigma weight residual 120.60 126.89 -6.29 1.53e+00 4.27e-01 1.69e+01 ... (remaining 16940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.31: 4920 32.31 - 64.61: 1531 64.61 - 96.91: 79 96.91 - 129.22: 2 129.22 - 161.52: 2 Dihedral angle restraints: 6534 sinusoidal: 4315 harmonic: 2219 Sorted by residual: dihedral pdb=" CA ASP A 82 " pdb=" C ASP A 82 " pdb=" N LEU A 83 " pdb=" CA LEU A 83 " ideal model delta harmonic sigma weight residual 180.00 -155.29 -24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ASP E 82 " pdb=" C ASP E 82 " pdb=" N LEU E 83 " pdb=" CA LEU E 83 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ARG E 64 " pdb=" C ARG E 64 " pdb=" N LYS E 65 " pdb=" CA LYS E 65 " ideal model delta harmonic sigma weight residual -180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 6531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1518 0.063 - 0.126: 359 0.126 - 0.189: 50 0.189 - 0.252: 6 0.252 - 0.315: 5 Chirality restraints: 1938 Sorted by residual: chirality pdb=" C1' DT J 173 " pdb=" O4' DT J 173 " pdb=" C2' DT J 173 " pdb=" N1 DT J 173 " both_signs ideal model delta sigma weight residual False 2.47 2.15 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CG LEU E 127 " pdb=" CB LEU E 127 " pdb=" CD1 LEU E 127 " pdb=" CD2 LEU E 127 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CG LEU A 127 " pdb=" CB LEU A 127 " pdb=" CD1 LEU A 127 " pdb=" CD2 LEU A 127 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1935 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 38 " -0.048 2.00e-02 2.50e+03 2.06e-02 1.17e+01 pdb=" N9 DA I 38 " 0.036 2.00e-02 2.50e+03 pdb=" C8 DA I 38 " 0.023 2.00e-02 2.50e+03 pdb=" N7 DA I 38 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DA I 38 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 38 " -0.007 2.00e-02 2.50e+03 pdb=" N6 DA I 38 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DA I 38 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 38 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 38 " 0.012 2.00e-02 2.50e+03 pdb=" C4 DA I 38 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 67 " 0.043 2.00e-02 2.50e+03 1.96e-02 9.65e+00 pdb=" N1 DT I 67 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DT I 67 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT I 67 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT I 67 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 67 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 67 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DT I 67 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 67 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT I 67 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 227 " -0.040 2.00e-02 2.50e+03 2.05e-02 9.43e+00 pdb=" N1 DC J 227 " 0.033 2.00e-02 2.50e+03 pdb=" C2 DC J 227 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DC J 227 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DC J 227 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC J 227 " -0.025 2.00e-02 2.50e+03 pdb=" N4 DC J 227 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DC J 227 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DC J 227 " 0.014 2.00e-02 2.50e+03 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2294 2.78 - 3.31: 9640 3.31 - 3.84: 22729 3.84 - 4.37: 24369 4.37 - 4.90: 34765 Nonbonded interactions: 93797 Sorted by model distance: nonbonded pdb=" O6 DG I 111 " pdb=" O4 DT J 181 " model vdw 2.251 2.432 nonbonded pdb=" OH TYR E 100 " pdb=" OE2 GLU E 134 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR A 100 " pdb=" OE2 GLU A 134 " model vdw 2.268 3.040 nonbonded pdb=" N2 DG I 98 " pdb=" O2 DC J 195 " model vdw 2.273 2.496 nonbonded pdb=" NH2 ARG E 70 " pdb=" OP1 DA I 90 " model vdw 2.283 3.120 ... (remaining 93792 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 19 through 115) } ncs_group { reference = chain 'D' 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 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: 0.920 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.830 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 0.008 0.072 11779 Z= 0.410 Angle : 1.029 10.698 16945 Z= 0.603 Chirality : 0.056 0.315 1938 Planarity : 0.006 0.048 1293 Dihedral : 29.994 161.524 5098 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.83 (0.27), residues: 748 helix: -0.63 (0.21), residues: 499 sheet: None (None), residues: 0 loop : -2.27 (0.32), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS A 114 PHE 0.027 0.004 PHE E 105 TYR 0.016 0.003 TYR B 52 ARG 0.011 0.001 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8375 (pm20) REVERT: A 53 ARG cc_start: 0.6995 (ttt180) cc_final: 0.6754 (mmm160) REVERT: A 103 SER cc_start: 0.9557 (t) cc_final: 0.9237 (p) REVERT: A 124 ASP cc_start: 0.8942 (m-30) cc_final: 0.8458 (m-30) REVERT: B 76 HIS cc_start: 0.8290 (t70) cc_final: 0.7843 (t70) REVERT: C 103 THR cc_start: 0.8727 (m) cc_final: 0.8235 (p) REVERT: E 74 GLU cc_start: 0.8302 (tp30) cc_final: 0.7957 (tt0) REVERT: G 40 ASN cc_start: 0.8805 (m-40) cc_final: 0.7724 (t0) REVERT: G 66 GLU cc_start: 0.8396 (tt0) cc_final: 0.8156 (tp30) REVERT: G 73 ARG cc_start: 0.8147 (ttp-170) cc_final: 0.7798 (tpt90) REVERT: G 90 ARG cc_start: 0.9243 (mmt-90) cc_final: 0.8898 (mmm-85) REVERT: G 94 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7763 (mm-30) REVERT: G 106 GLN cc_start: 0.8231 (mt0) cc_final: 0.7666 (mp10) REVERT: H 38 LYS cc_start: 0.6277 (mtpp) cc_final: 0.6031 (ttmm) REVERT: H 99 GLN cc_start: 0.8901 (tt0) cc_final: 0.8621 (tm-30) REVERT: H 103 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7832 (ptp90) REVERT: H 125 TYR cc_start: 0.8422 (t80) cc_final: 0.8219 (t80) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.3078 time to fit residues: 62.1290 Evaluate side-chains 74 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN G 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11779 Z= 0.243 Angle : 0.686 7.250 16945 Z= 0.404 Chirality : 0.040 0.225 1938 Planarity : 0.005 0.052 1293 Dihedral : 32.229 162.051 3592 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.31 % Allowed : 8.82 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.49 (0.29), residues: 748 helix: 0.60 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -2.29 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 114 PHE 0.024 0.002 PHE A 105 TYR 0.017 0.002 TYR B 99 ARG 0.010 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.9031 (m-30) cc_final: 0.8608 (m-30) REVERT: B 97 THR cc_start: 0.8704 (m) cc_final: 0.8391 (p) REVERT: D 63 MET cc_start: 0.8991 (mtp) cc_final: 0.8595 (mtt) REVERT: D 72 ASP cc_start: 0.9179 (t0) cc_final: 0.8881 (t0) REVERT: E 74 GLU cc_start: 0.8359 (tp30) cc_final: 0.7957 (tt0) REVERT: F 85 LEU cc_start: 0.9272 (tp) cc_final: 0.8975 (tp) REVERT: G 66 GLU cc_start: 0.8511 (tt0) cc_final: 0.8224 (tp30) REVERT: G 73 ARG cc_start: 0.8372 (ttp-170) cc_final: 0.7918 (tpt90) REVERT: G 106 GLN cc_start: 0.8269 (mt0) cc_final: 0.7777 (mp10) REVERT: H 38 LYS cc_start: 0.5864 (mtpp) cc_final: 0.5571 (mtmm) REVERT: H 99 GLN cc_start: 0.8883 (tt0) cc_final: 0.8564 (tm-30) REVERT: H 103 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7787 (ttm-80) outliers start: 2 outliers final: 0 residues processed: 105 average time/residue: 0.2538 time to fit residues: 36.5993 Evaluate side-chains 60 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11779 Z= 0.302 Angle : 0.705 7.793 16945 Z= 0.411 Chirality : 0.041 0.214 1938 Planarity : 0.005 0.050 1293 Dihedral : 32.268 161.480 3592 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.15 % Allowed : 6.97 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.10 (0.30), residues: 748 helix: 0.95 (0.23), residues: 507 sheet: None (None), residues: 0 loop : -2.30 (0.34), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS A 114 PHE 0.022 0.002 PHE A 105 TYR 0.017 0.002 TYR F 52 ARG 0.005 0.001 ARG H 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.9131 (m-30) cc_final: 0.8746 (m-30) REVERT: B 97 THR cc_start: 0.8894 (m) cc_final: 0.8495 (p) REVERT: D 72 ASP cc_start: 0.9179 (t0) cc_final: 0.8925 (t0) REVERT: E 74 GLU cc_start: 0.8457 (tp30) cc_final: 0.8003 (tt0) REVERT: F 28 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8658 (mm-40) REVERT: G 66 GLU cc_start: 0.8584 (tt0) cc_final: 0.8368 (tp30) REVERT: G 73 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.7924 (tpt90) REVERT: G 106 GLN cc_start: 0.8274 (mt0) cc_final: 0.7871 (mm-40) REVERT: H 38 LYS cc_start: 0.6219 (mtpp) cc_final: 0.5878 (mtmm) REVERT: H 125 TYR cc_start: 0.8705 (t80) cc_final: 0.8454 (t80) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.3073 time to fit residues: 38.6979 Evaluate side-chains 59 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.0670 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN E 86 GLN G 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11779 Z= 0.192 Angle : 0.633 7.481 16945 Z= 0.369 Chirality : 0.037 0.194 1938 Planarity : 0.004 0.040 1293 Dihedral : 31.914 159.847 3592 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.22 (0.30), residues: 748 helix: 1.23 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -2.33 (0.33), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 114 PHE 0.012 0.001 PHE E 105 TYR 0.013 0.001 TYR F 52 ARG 0.004 0.000 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.9105 (m-30) cc_final: 0.8660 (m-30) REVERT: B 85 LEU cc_start: 0.9620 (mp) cc_final: 0.9390 (mp) REVERT: B 97 THR cc_start: 0.8740 (m) cc_final: 0.8395 (p) REVERT: G 40 ASN cc_start: 0.8890 (m110) cc_final: 0.8201 (t0) REVERT: G 58 GLU cc_start: 0.9090 (tt0) cc_final: 0.8687 (mt-10) REVERT: G 73 ARG cc_start: 0.8306 (ttp-170) cc_final: 0.7981 (tpt90) REVERT: G 74 ASP cc_start: 0.8581 (p0) cc_final: 0.8277 (p0) REVERT: G 106 GLN cc_start: 0.8141 (mt0) cc_final: 0.7822 (mp10) REVERT: H 38 LYS cc_start: 0.6178 (mtpp) cc_final: 0.5826 (mtmm) REVERT: H 63 MET cc_start: 0.8888 (tpp) cc_final: 0.8679 (tpp) REVERT: H 125 TYR cc_start: 0.8697 (t80) cc_final: 0.8478 (t80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2848 time to fit residues: 35.6152 Evaluate side-chains 63 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN C 40 ASN H 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 11779 Z= 0.443 Angle : 0.792 9.373 16945 Z= 0.456 Chirality : 0.045 0.239 1938 Planarity : 0.006 0.043 1293 Dihedral : 32.360 163.856 3592 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.26 (0.29), residues: 748 helix: 0.80 (0.22), residues: 511 sheet: None (None), residues: 0 loop : -2.36 (0.32), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS A 114 PHE 0.032 0.003 PHE A 105 TYR 0.022 0.003 TYR D 87 ARG 0.004 0.001 ARG G 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 TYR cc_start: 0.9476 (m-10) cc_final: 0.9213 (m-10) REVERT: D 63 MET cc_start: 0.9243 (ttt) cc_final: 0.8863 (mpp) REVERT: D 72 ASP cc_start: 0.9081 (t70) cc_final: 0.8791 (t0) REVERT: F 89 TYR cc_start: 0.8825 (m-80) cc_final: 0.8565 (m-80) REVERT: G 38 ARG cc_start: 0.9164 (ptp-110) cc_final: 0.8851 (mtm110) REVERT: G 40 ASN cc_start: 0.9140 (m110) cc_final: 0.8405 (t0) REVERT: G 73 ARG cc_start: 0.8286 (ttp-170) cc_final: 0.7927 (tpt90) REVERT: G 74 ASP cc_start: 0.8400 (p0) cc_final: 0.8155 (p0) REVERT: G 90 ARG cc_start: 0.9330 (mmt90) cc_final: 0.9010 (mmm-85) REVERT: G 94 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7685 (tp30) REVERT: G 106 GLN cc_start: 0.8217 (mt0) cc_final: 0.7857 (mp10) REVERT: M 35 LYS cc_start: 0.7916 (pttp) cc_final: 0.7701 (pttt) outliers start: 1 outliers final: 1 residues processed: 75 average time/residue: 0.2859 time to fit residues: 29.0755 Evaluate side-chains 53 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 7 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11779 Z= 0.247 Angle : 0.676 7.835 16945 Z= 0.392 Chirality : 0.039 0.201 1938 Planarity : 0.004 0.042 1293 Dihedral : 32.146 161.699 3592 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.03 (0.30), residues: 748 helix: 1.02 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -2.36 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS A 114 PHE 0.021 0.002 PHE E 105 TYR 0.012 0.002 TYR B 99 ARG 0.006 0.000 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 LEU cc_start: 0.9604 (mp) cc_final: 0.9235 (mp) REVERT: B 89 TYR cc_start: 0.9416 (m-10) cc_final: 0.8946 (m-10) REVERT: C 40 ASN cc_start: 0.8851 (p0) cc_final: 0.8272 (p0) REVERT: D 72 ASP cc_start: 0.9061 (t70) cc_final: 0.8753 (t0) REVERT: E 74 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8291 (tt0) REVERT: F 89 TYR cc_start: 0.8596 (m-80) cc_final: 0.8392 (m-80) REVERT: G 38 ARG cc_start: 0.9192 (ptp-110) cc_final: 0.8863 (mtm110) REVERT: G 40 ASN cc_start: 0.9102 (m110) cc_final: 0.8233 (t0) REVERT: G 73 ARG cc_start: 0.8381 (ttp-170) cc_final: 0.7973 (tpt90) REVERT: G 74 ASP cc_start: 0.8399 (p0) cc_final: 0.8119 (p0) REVERT: G 106 GLN cc_start: 0.8023 (mt0) cc_final: 0.7603 (mp10) REVERT: H 109 GLU cc_start: 0.8962 (mp0) cc_final: 0.8709 (mp0) REVERT: M 35 LYS cc_start: 0.7898 (pttp) cc_final: 0.7683 (pttt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3013 time to fit residues: 33.2598 Evaluate side-chains 59 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11779 Z= 0.248 Angle : 0.667 9.090 16945 Z= 0.389 Chirality : 0.038 0.193 1938 Planarity : 0.004 0.044 1293 Dihedral : 32.008 161.636 3592 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.05 (0.30), residues: 748 helix: 1.00 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -2.58 (0.33), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 114 PHE 0.033 0.002 PHE A 105 TYR 0.016 0.002 TYR D 44 ARG 0.004 0.000 ARG E 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 LEU cc_start: 0.9608 (mp) cc_final: 0.9289 (mp) REVERT: B 89 TYR cc_start: 0.9423 (m-10) cc_final: 0.8995 (m-10) REVERT: C 40 ASN cc_start: 0.8726 (p0) cc_final: 0.8324 (p0) REVERT: D 72 ASP cc_start: 0.9049 (t70) cc_final: 0.8756 (t0) REVERT: E 74 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8253 (tt0) REVERT: F 89 TYR cc_start: 0.8379 (m-80) cc_final: 0.8058 (m-80) REVERT: G 38 ARG cc_start: 0.9198 (ptp-110) cc_final: 0.8947 (mtm110) REVERT: G 40 ASN cc_start: 0.9121 (m110) cc_final: 0.8263 (t0) REVERT: G 73 ARG cc_start: 0.8335 (ttp-170) cc_final: 0.7933 (tpt90) REVERT: G 74 ASP cc_start: 0.8419 (p0) cc_final: 0.8165 (p0) REVERT: G 90 ARG cc_start: 0.9356 (mmt90) cc_final: 0.9107 (mmm-85) REVERT: G 104 ILE cc_start: 0.8971 (mp) cc_final: 0.8714 (mp) REVERT: G 106 GLN cc_start: 0.8100 (mt0) cc_final: 0.7642 (mp10) REVERT: H 109 GLU cc_start: 0.8903 (mp0) cc_final: 0.8630 (mp0) REVERT: H 125 TYR cc_start: 0.8761 (t80) cc_final: 0.8516 (t80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2893 time to fit residues: 30.4735 Evaluate side-chains 57 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11779 Z= 0.252 Angle : 0.670 8.674 16945 Z= 0.388 Chirality : 0.038 0.189 1938 Planarity : 0.004 0.046 1293 Dihedral : 31.966 162.226 3592 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.30), residues: 748 helix: 1.17 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -2.51 (0.34), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS A 114 PHE 0.032 0.002 PHE A 105 TYR 0.011 0.001 TYR B 99 ARG 0.008 0.000 ARG G 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 LEU cc_start: 0.9599 (mp) cc_final: 0.9283 (mp) REVERT: B 89 TYR cc_start: 0.9421 (m-10) cc_final: 0.8993 (m-10) REVERT: C 40 ASN cc_start: 0.8708 (p0) cc_final: 0.8209 (p0) REVERT: D 72 ASP cc_start: 0.9038 (t70) cc_final: 0.8749 (t0) REVERT: E 74 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8260 (tt0) REVERT: F 89 TYR cc_start: 0.8469 (m-80) cc_final: 0.8111 (m-80) REVERT: G 38 ARG cc_start: 0.9200 (ptp-110) cc_final: 0.8874 (mtm110) REVERT: G 40 ASN cc_start: 0.9092 (m110) cc_final: 0.8332 (t0) REVERT: G 73 ARG cc_start: 0.8336 (ttp-170) cc_final: 0.7948 (tpt90) REVERT: G 74 ASP cc_start: 0.8401 (p0) cc_final: 0.8163 (p0) REVERT: G 90 ARG cc_start: 0.9357 (mmt90) cc_final: 0.9020 (mmm-85) REVERT: G 106 GLN cc_start: 0.8108 (mt0) cc_final: 0.7645 (mp10) REVERT: H 109 GLU cc_start: 0.8923 (mp0) cc_final: 0.8670 (mp0) REVERT: H 125 TYR cc_start: 0.8820 (t80) cc_final: 0.8620 (t80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.3057 time to fit residues: 33.2229 Evaluate side-chains 60 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 0.0270 chunk 80 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 overall best weight: 1.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11779 Z= 0.214 Angle : 0.659 9.807 16945 Z= 0.377 Chirality : 0.037 0.173 1938 Planarity : 0.004 0.046 1293 Dihedral : 31.835 162.408 3592 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.17 (0.30), residues: 748 helix: 1.20 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -2.57 (0.34), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS A 114 PHE 0.025 0.002 PHE A 105 TYR 0.011 0.001 TYR F 73 ARG 0.004 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 LEU cc_start: 0.9594 (mp) cc_final: 0.9296 (mp) REVERT: B 89 TYR cc_start: 0.9417 (m-10) cc_final: 0.9018 (m-10) REVERT: D 72 ASP cc_start: 0.9036 (t70) cc_final: 0.8752 (t0) REVERT: E 74 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8240 (tt0) REVERT: F 89 TYR cc_start: 0.8430 (m-80) cc_final: 0.8001 (m-80) REVERT: G 38 ARG cc_start: 0.9174 (ptp-110) cc_final: 0.8847 (mtm110) REVERT: G 40 ASN cc_start: 0.9085 (m110) cc_final: 0.8314 (t0) REVERT: G 58 GLU cc_start: 0.9085 (tt0) cc_final: 0.8750 (mt-10) REVERT: G 73 ARG cc_start: 0.8324 (ttp-170) cc_final: 0.7943 (tpt90) REVERT: G 74 ASP cc_start: 0.8450 (p0) cc_final: 0.8230 (p0) REVERT: G 90 ARG cc_start: 0.9374 (mmt90) cc_final: 0.9114 (mmm-85) REVERT: G 104 ILE cc_start: 0.8798 (mp) cc_final: 0.8540 (mp) REVERT: G 106 GLN cc_start: 0.8136 (mt0) cc_final: 0.7616 (mp10) REVERT: H 99 GLN cc_start: 0.8940 (tt0) cc_final: 0.8611 (tm-30) REVERT: H 103 ARG cc_start: 0.8225 (ttm170) cc_final: 0.7834 (ttm-80) REVERT: H 109 GLU cc_start: 0.8906 (mp0) cc_final: 0.8628 (mp0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3037 time to fit residues: 34.3118 Evaluate side-chains 57 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0970 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 overall best weight: 4.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 11779 Z= 0.360 Angle : 0.744 8.893 16945 Z= 0.426 Chirality : 0.041 0.188 1938 Planarity : 0.006 0.103 1293 Dihedral : 32.049 164.219 3592 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.30), residues: 748 helix: 0.97 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -2.50 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS A 114 PHE 0.034 0.002 PHE A 105 TYR 0.025 0.002 TYR H 125 ARG 0.010 0.001 ARG G 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 LEU cc_start: 0.9638 (mp) cc_final: 0.9264 (mp) REVERT: B 89 TYR cc_start: 0.9462 (m-10) cc_final: 0.8904 (m-10) REVERT: C 40 ASN cc_start: 0.8718 (p0) cc_final: 0.8212 (p0) REVERT: D 63 MET cc_start: 0.9045 (mtp) cc_final: 0.8669 (mtt) REVERT: D 72 ASP cc_start: 0.9081 (t70) cc_final: 0.8799 (t0) REVERT: E 69 GLN cc_start: 0.9368 (pm20) cc_final: 0.9163 (pm20) REVERT: E 74 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8341 (tt0) REVERT: G 38 ARG cc_start: 0.9321 (ptp-110) cc_final: 0.8991 (mtm110) REVERT: G 40 ASN cc_start: 0.9118 (m110) cc_final: 0.8336 (t0) REVERT: G 73 ARG cc_start: 0.8364 (ttp-170) cc_final: 0.7967 (tpt90) REVERT: G 90 ARG cc_start: 0.9357 (mmt90) cc_final: 0.9024 (mmm-85) REVERT: G 106 GLN cc_start: 0.8092 (mt0) cc_final: 0.7661 (mp10) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2864 time to fit residues: 28.8052 Evaluate side-chains 54 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.047673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.034349 restraints weight = 109349.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.035003 restraints weight = 62136.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.035513 restraints weight = 42872.135| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11779 Z= 0.234 Angle : 0.671 9.778 16945 Z= 0.386 Chirality : 0.038 0.215 1938 Planarity : 0.004 0.046 1293 Dihedral : 31.925 162.446 3592 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.13 (0.30), residues: 748 helix: 1.17 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -2.51 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS A 114 PHE 0.027 0.001 PHE A 105 TYR 0.010 0.001 TYR B 99 ARG 0.014 0.001 ARG C 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1704.83 seconds wall clock time: 36 minutes 9.71 seconds (2169.71 seconds total)