Starting phenix.real_space_refine on Fri Mar 15 08:08:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7g_22698/03_2024/7k7g_22698.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7g_22698/03_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_22698/03_2024/7k7g_22698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7g_22698/03_2024/7k7g_22698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7g_22698/03_2024/7k7g_22698.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7g_22698/03_2024/7k7g_22698.pdb" } 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 Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G ARG 34": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "H GLU 117": "OE1" <-> "OE2" Residue "H ARG 120": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 26": "NH1" <-> "NH2" Residue "M ARG 36": "NH1" <-> "NH2" Residue "M GLU 41": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11098 Number of models: 1 Model: "" Number of chains: 11 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: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 338 Unusual residues: {' ZN': 2} Classifications: {'peptide': 43, 'undetermined': 2} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 40, None: 2} Not linked: pdbres="LEU M 48 " pdbres=" ZN M 701 " Not linked: pdbres=" ZN M 701 " pdbres=" ZN M 702 " 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: 5.87, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.74 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 5.01 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: 4.17 Time building geometry restraints manager: 6.06 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: 96.98 - 104.20: 920 104.20 - 111.42: 5742 111.42 - 118.64: 3798 118.64 - 125.87: 5684 125.87 - 133.09: 801 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 2.440 nonbonded pdb=" OH TYR A 100 " pdb=" OE2 GLU A 134 " model vdw 2.268 2.440 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 2.520 ... (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 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: 0.990 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: 5.070 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.820 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.480 ------------------------------------------------------------------------------- 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 : 0.967 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: 0.3029 time to fit residues: 61.0975 Evaluate side-chains 74 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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: 9.9990 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 GLN E 109 ASN G 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11779 Z= 0.241 Angle : 0.677 7.343 16945 Z= 0.399 Chirality : 0.040 0.251 1938 Planarity : 0.005 0.046 1293 Dihedral : 32.203 162.488 3592 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % 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: -0.50 (0.29), residues: 748 helix: 0.59 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -2.31 (0.33), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 114 PHE 0.023 0.002 PHE A 105 TYR 0.015 0.002 TYR B 99 ARG 0.004 0.001 ARG H 37 *********************** 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 102 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8512 (pm20) REVERT: A 106 GLU cc_start: 0.9064 (pp20) cc_final: 0.8855 (pp20) REVERT: A 124 ASP cc_start: 0.9015 (m-30) cc_final: 0.8609 (m-30) REVERT: B 97 THR cc_start: 0.8654 (m) cc_final: 0.8348 (p) REVERT: D 63 MET cc_start: 0.9050 (mtp) cc_final: 0.8634 (mtt) REVERT: E 74 GLU cc_start: 0.8241 (tp30) cc_final: 0.7851 (tt0) REVERT: F 28 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8627 (mm-40) REVERT: G 66 GLU cc_start: 0.8504 (tt0) cc_final: 0.8213 (tp30) REVERT: G 73 ARG cc_start: 0.8378 (ttp-170) cc_final: 0.7906 (tpt90) REVERT: G 90 ARG cc_start: 0.9251 (mmt-90) cc_final: 0.8914 (mmm-85) REVERT: G 106 GLN cc_start: 0.8274 (mt0) cc_final: 0.7799 (mp10) REVERT: H 38 LYS cc_start: 0.5828 (mtpp) cc_final: 0.5534 (mtmm) REVERT: H 99 GLN cc_start: 0.8875 (tt0) cc_final: 0.8550 (tm-30) REVERT: H 103 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7787 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2661 time to fit residues: 36.8521 Evaluate side-chains 65 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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: 0.9990 chunk 27 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 0.0370 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: 1.9464 ------------------------------------------------------------------------------- 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** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11779 Z= 0.218 Angle : 0.654 6.987 16945 Z= 0.382 Chirality : 0.038 0.192 1938 Planarity : 0.004 0.044 1293 Dihedral : 32.013 161.428 3592 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % 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: -0.07 (0.30), residues: 748 helix: 1.00 (0.23), residues: 503 sheet: None (None), residues: 0 loop : -2.31 (0.33), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS E 114 PHE 0.019 0.002 PHE A 105 TYR 0.020 0.002 TYR F 52 ARG 0.014 0.001 ARG C 38 *********************** 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 92 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8525 (pm20) REVERT: A 124 ASP cc_start: 0.9068 (m-30) cc_final: 0.8702 (m-30) REVERT: B 97 THR cc_start: 0.8696 (m) cc_final: 0.8303 (p) REVERT: D 63 MET cc_start: 0.9001 (mtp) cc_final: 0.8598 (mtt) REVERT: D 72 ASP cc_start: 0.9142 (t0) cc_final: 0.8805 (t0) REVERT: E 74 GLU cc_start: 0.8395 (tp30) cc_final: 0.7940 (tt0) REVERT: G 73 ARG cc_start: 0.8396 (ttp-170) cc_final: 0.8015 (tpt90) REVERT: G 74 ASP cc_start: 0.8558 (p0) cc_final: 0.8204 (p0) REVERT: G 106 GLN cc_start: 0.8259 (mt0) cc_final: 0.7841 (mm-40) REVERT: H 38 LYS cc_start: 0.5995 (mtpp) cc_final: 0.5720 (mtmm) REVERT: H 125 TYR cc_start: 0.8587 (t80) cc_final: 0.8378 (t80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2502 time to fit residues: 32.3893 Evaluate side-chains 61 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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: 6.9990 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 26 ASN C 33 HIS ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN F 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 11779 Z= 0.391 Angle : 0.768 8.947 16945 Z= 0.443 Chirality : 0.044 0.217 1938 Planarity : 0.006 0.047 1293 Dihedral : 32.461 161.619 3592 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.46 % Allowed : 6.66 % 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: -0.21 (0.29), residues: 748 helix: 0.78 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -2.14 (0.34), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 84 PHE 0.032 0.003 PHE A 105 TYR 0.017 0.002 TYR B 99 ARG 0.005 0.001 ARG C 38 *********************** 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 78 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9380 (t0) cc_final: 0.9145 (t0) REVERT: F 89 TYR cc_start: 0.8707 (m-80) cc_final: 0.8371 (m-80) REVERT: G 73 ARG cc_start: 0.8287 (ttp-170) cc_final: 0.7874 (tpt90) REVERT: G 74 ASP cc_start: 0.8513 (p0) cc_final: 0.8271 (p0) REVERT: G 106 GLN cc_start: 0.8201 (mt0) cc_final: 0.7826 (mp10) REVERT: H 39 GLU cc_start: 0.9086 (tp30) cc_final: 0.8668 (tm-30) REVERT: H 109 GLU cc_start: 0.8975 (mp0) cc_final: 0.8771 (mp0) outliers start: 3 outliers final: 0 residues processed: 78 average time/residue: 0.2731 time to fit residues: 29.2165 Evaluate side-chains 56 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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: 6.9990 chunk 54 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 11779 Z= 0.364 Angle : 0.741 8.418 16945 Z= 0.428 Chirality : 0.042 0.183 1938 Planarity : 0.005 0.043 1293 Dihedral : 32.467 162.690 3592 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % 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: -0.39 (0.29), residues: 748 helix: 0.64 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -2.29 (0.34), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS A 114 PHE 0.025 0.002 PHE E 105 TYR 0.015 0.002 TYR B 99 ARG 0.006 0.001 ARG M 34 *********************** 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 77 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9391 (t0) cc_final: 0.9175 (t0) REVERT: B 85 LEU cc_start: 0.9727 (mp) cc_final: 0.9314 (mt) REVERT: B 89 TYR cc_start: 0.9227 (m-80) cc_final: 0.8761 (m-80) REVERT: D 63 MET cc_start: 0.9400 (ttm) cc_final: 0.9136 (mtt) REVERT: E 74 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8362 (tt0) REVERT: E 126 LYS cc_start: 0.9656 (pptt) cc_final: 0.9383 (pptt) REVERT: F 89 TYR cc_start: 0.8503 (m-80) cc_final: 0.8242 (m-80) REVERT: G 73 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.7920 (tpt90) REVERT: G 94 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7670 (tp30) REVERT: G 104 ILE cc_start: 0.9106 (mp) cc_final: 0.8872 (mp) REVERT: G 106 GLN cc_start: 0.8120 (mt0) cc_final: 0.7677 (mp10) REVERT: H 39 GLU cc_start: 0.9063 (tp30) cc_final: 0.8644 (tm-30) REVERT: M 26 ARG cc_start: 0.8240 (mmm160) cc_final: 0.8039 (mmm160) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2702 time to fit residues: 28.8313 Evaluate side-chains 55 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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: 3.9990 chunk 86 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 ASN ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11779 Z= 0.231 Angle : 0.650 7.550 16945 Z= 0.380 Chirality : 0.038 0.154 1938 Planarity : 0.004 0.045 1293 Dihedral : 32.176 162.166 3592 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: 0.11 (0.30), residues: 748 helix: 1.10 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -2.40 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS A 114 PHE 0.026 0.002 PHE A 105 TYR 0.014 0.001 TYR C 41 ARG 0.007 0.001 ARG G 38 *********************** 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 85 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 89 TYR cc_start: 0.9087 (m-80) cc_final: 0.8858 (m-80) REVERT: C 40 ASN cc_start: 0.8632 (p0) cc_final: 0.8097 (p0) REVERT: D 72 ASP cc_start: 0.8961 (t0) cc_final: 0.8758 (t0) REVERT: E 74 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8370 (tt0) REVERT: E 126 LYS cc_start: 0.9640 (pptt) cc_final: 0.9349 (pptt) REVERT: G 40 ASN cc_start: 0.9032 (m110) cc_final: 0.8189 (t0) REVERT: G 73 ARG cc_start: 0.8347 (ttp-170) cc_final: 0.7933 (tpt90) REVERT: G 74 ASP cc_start: 0.8439 (p0) cc_final: 0.8172 (p0) REVERT: G 94 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7670 (tp30) REVERT: G 106 GLN cc_start: 0.8056 (mt0) cc_final: 0.7677 (mp10) REVERT: H 99 GLN cc_start: 0.9190 (tt0) cc_final: 0.8811 (tm-30) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2789 time to fit residues: 32.1782 Evaluate side-chains 61 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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: 10.0000 chunk 54 optimal weight: 0.0980 chunk 69 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 overall best weight: 2.8584 ------------------------------------------------------------------------------- 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** H 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11779 Z= 0.258 Angle : 0.666 7.988 16945 Z= 0.386 Chirality : 0.038 0.164 1938 Planarity : 0.004 0.045 1293 Dihedral : 32.134 161.923 3592 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: 0.20 (0.30), residues: 748 helix: 1.11 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -2.26 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.002 HIS A 114 PHE 0.030 0.002 PHE A 105 TYR 0.016 0.002 TYR H 125 ARG 0.008 0.000 ARG G 38 *********************** 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 80 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 TYR cc_start: 0.9138 (m-80) cc_final: 0.8913 (m-80) REVERT: C 40 ASN cc_start: 0.8777 (p0) cc_final: 0.8231 (p0) REVERT: D 63 MET cc_start: 0.9069 (ttt) cc_final: 0.8577 (mtp) REVERT: E 74 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8338 (tt0) REVERT: E 126 LYS cc_start: 0.9648 (pptt) cc_final: 0.9373 (pptt) REVERT: G 40 ASN cc_start: 0.9082 (m110) cc_final: 0.8200 (t0) REVERT: G 73 ARG cc_start: 0.8365 (ttp-170) cc_final: 0.7958 (tpt90) REVERT: G 74 ASP cc_start: 0.8418 (p0) cc_final: 0.8180 (p0) REVERT: G 90 ARG cc_start: 0.9107 (mmt90) cc_final: 0.8620 (mmt90) REVERT: G 94 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7795 (tp30) REVERT: G 104 ILE cc_start: 0.8965 (mp) cc_final: 0.8378 (mp) REVERT: G 106 GLN cc_start: 0.7971 (mt0) cc_final: 0.7594 (mp10) REVERT: H 99 GLN cc_start: 0.9179 (tt0) cc_final: 0.8807 (tm-30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2395 time to fit residues: 26.7831 Evaluate side-chains 58 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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: 10.0000 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 0.0470 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.1882 ------------------------------------------------------------------------------- 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 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11779 Z= 0.220 Angle : 0.642 10.061 16945 Z= 0.370 Chirality : 0.037 0.157 1938 Planarity : 0.004 0.045 1293 Dihedral : 31.933 161.181 3592 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 0.35 (0.30), residues: 748 helix: 1.23 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.21 (0.34), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS A 114 PHE 0.024 0.001 PHE A 105 TYR 0.011 0.001 TYR F 89 ARG 0.008 0.001 ARG G 38 *********************** 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 84 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9191 (t70) cc_final: 0.8962 (t0) REVERT: B 89 TYR cc_start: 0.9043 (m-80) cc_final: 0.8466 (m-80) REVERT: C 40 ASN cc_start: 0.8754 (p0) cc_final: 0.8143 (p0) REVERT: D 63 MET cc_start: 0.9029 (ttt) cc_final: 0.8514 (mtp) REVERT: D 72 ASP cc_start: 0.9089 (t0) cc_final: 0.8844 (t0) REVERT: D 87 TYR cc_start: 0.7875 (t80) cc_final: 0.7284 (t80) REVERT: E 74 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8353 (tt0) REVERT: E 126 LYS cc_start: 0.9624 (pptt) cc_final: 0.9344 (pptt) REVERT: G 40 ASN cc_start: 0.9067 (m110) cc_final: 0.8159 (t0) REVERT: G 63 GLU cc_start: 0.9454 (tp30) cc_final: 0.9247 (tm-30) REVERT: G 73 ARG cc_start: 0.8343 (ttp-170) cc_final: 0.7960 (tpt90) REVERT: G 74 ASP cc_start: 0.8411 (p0) cc_final: 0.8189 (p0) REVERT: G 90 ARG cc_start: 0.9175 (mmt90) cc_final: 0.8697 (mmt90) REVERT: G 94 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7764 (tp30) REVERT: G 104 ILE cc_start: 0.8923 (mp) cc_final: 0.8273 (mp) REVERT: G 106 GLN cc_start: 0.7889 (mt0) cc_final: 0.7573 (mp10) REVERT: H 99 GLN cc_start: 0.9172 (tt0) cc_final: 0.8805 (tm-30) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2537 time to fit residues: 29.8544 Evaluate side-chains 60 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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: 10.0000 chunk 38 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11779 Z= 0.290 Angle : 0.685 9.059 16945 Z= 0.394 Chirality : 0.039 0.164 1938 Planarity : 0.004 0.045 1293 Dihedral : 32.049 161.964 3592 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: 0.14 (0.30), residues: 748 helix: 1.07 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -2.33 (0.34), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS A 114 PHE 0.030 0.002 PHE E 105 TYR 0.013 0.002 TYR F 89 ARG 0.006 0.001 ARG G 38 *********************** 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 78 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9268 (t70) cc_final: 0.9035 (t0) REVERT: B 85 LEU cc_start: 0.9591 (mp) cc_final: 0.9249 (mp) REVERT: B 89 TYR cc_start: 0.9101 (m-80) cc_final: 0.8327 (m-80) REVERT: C 40 ASN cc_start: 0.8823 (p0) cc_final: 0.8182 (p0) REVERT: D 87 TYR cc_start: 0.7976 (t80) cc_final: 0.7264 (t80) REVERT: E 74 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8303 (tt0) REVERT: E 126 LYS cc_start: 0.9628 (pptt) cc_final: 0.9366 (pptt) REVERT: G 40 ASN cc_start: 0.9183 (m110) cc_final: 0.8311 (t0) REVERT: G 73 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.7963 (tpt90) REVERT: G 94 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7761 (tp30) REVERT: G 104 ILE cc_start: 0.8934 (mp) cc_final: 0.8695 (mp) REVERT: G 106 GLN cc_start: 0.7947 (mt0) cc_final: 0.7635 (mp10) REVERT: H 99 GLN cc_start: 0.9200 (tt0) cc_final: 0.8825 (tm-30) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2519 time to fit residues: 27.6457 Evaluate side-chains 53 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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: 9.9990 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** M 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11779 Z= 0.185 Angle : 0.632 11.006 16945 Z= 0.362 Chirality : 0.036 0.180 1938 Planarity : 0.004 0.045 1293 Dihedral : 31.747 162.118 3592 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % 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: 0.41 (0.31), residues: 748 helix: 1.28 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -2.17 (0.35), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS A 114 PHE 0.017 0.001 PHE A 105 TYR 0.016 0.001 TYR F 89 ARG 0.006 0.000 ARG C 83 ********************** 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 87 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.9263 (pp20) cc_final: 0.9058 (pp20) REVERT: A 107 ASP cc_start: 0.9111 (t70) cc_final: 0.8873 (t0) REVERT: B 89 TYR cc_start: 0.9039 (m-80) cc_final: 0.8379 (m-80) REVERT: C 40 ASN cc_start: 0.8725 (p0) cc_final: 0.7966 (p0) REVERT: D 87 TYR cc_start: 0.7644 (t80) cc_final: 0.7135 (t80) REVERT: E 74 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8352 (tt0) REVERT: E 126 LYS cc_start: 0.9596 (pptt) cc_final: 0.9308 (pptt) REVERT: F 85 LEU cc_start: 0.9133 (tp) cc_final: 0.8780 (tp) REVERT: G 40 ASN cc_start: 0.9010 (m110) cc_final: 0.8124 (t0) REVERT: G 73 ARG cc_start: 0.8340 (ttp-170) cc_final: 0.7989 (tpt90) REVERT: G 94 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7766 (tp30) REVERT: G 106 GLN cc_start: 0.7887 (mt0) cc_final: 0.7577 (mp10) REVERT: H 99 GLN cc_start: 0.9204 (tt0) cc_final: 0.8852 (tm-30) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2102 time to fit residues: 25.8995 Evaluate side-chains 58 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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: 10.0000 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 116 ASN M 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.047943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.034606 restraints weight = 110765.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.035271 restraints weight = 64411.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.035810 restraints weight = 44784.714| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11779 Z= 0.244 Angle : 0.652 10.291 16945 Z= 0.374 Chirality : 0.037 0.187 1938 Planarity : 0.004 0.046 1293 Dihedral : 31.819 162.487 3592 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.31 (0.30), residues: 748 helix: 1.23 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -2.33 (0.34), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS A 114 PHE 0.009 0.001 PHE E 105 TYR 0.019 0.002 TYR G 59 ARG 0.012 0.001 ARG C 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1691.74 seconds wall clock time: 32 minutes 3.57 seconds (1923.57 seconds total)