Starting phenix.real_space_refine on Sat Aug 3 10:01:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/08_2024/7kbb_22788_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/08_2024/7kbb_22788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/08_2024/7kbb_22788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/08_2024/7kbb_22788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/08_2024/7kbb_22788_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/08_2024/7kbb_22788_neut.cif" } resolution = 4.02 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1776 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 4046 2.51 5 N 1139 2.21 5 O 1208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 100": "NH1" <-> "NH2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D GLU 177": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "H GLU 3": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6422 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 979 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "B" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 Chain: "D" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1384 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 158} Chain: "E" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 893 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Time building chain proxies: 4.95, per 1000 atoms: 0.77 Number of scatterers: 6422 At special positions: 0 Unit cell: (78.525, 106.794, 126.687, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1208 8.00 N 1139 7.00 C 4046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 111 " distance=2.04 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 83 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS E 40 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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: 2.46 Conformation dependent library (CDL) restraints added in 1.0 seconds 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 14 sheets defined 19.2% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 100 through 100D removed outlier: 3.509A pdb=" N GLY A 100C" --> pdb=" O ASP A 100 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 100D" --> pdb=" O ARG A 100A" (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 100D' Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.083A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 145 through 155 removed outlier: 4.038A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 104 through 118 removed outlier: 4.325A pdb=" N ASN D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 131 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 35 through 41 Processing helix chain 'E' and resid 45 through 69 Processing helix chain 'E' and resid 73 through 79 removed outlier: 3.635A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG E 79 " --> pdb=" O ASP E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 95 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.671A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.759A pdb=" N ASP A 33 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.458A pdb=" N ILE A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.572A pdb=" N THR B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER B 63 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.682A pdb=" N GLU B 105 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AA7, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AA8, first strand: chain 'D' and resid 71 through 78 Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.526A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.586A pdb=" N VAL H 12 " --> pdb=" O THR H 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.624A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU H 106 " --> pdb=" O LEU H 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.624A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.615A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.121A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1030 1.31 - 1.44: 1965 1.44 - 1.58: 3540 1.58 - 1.71: 2 1.71 - 1.85: 41 Bond restraints: 6578 Sorted by residual: bond pdb=" CA ARG H 87 " pdb=" C ARG H 87 " ideal model delta sigma weight residual 1.523 1.639 -0.116 1.34e-02 5.57e+03 7.48e+01 bond pdb=" CA LEU H 86 " pdb=" C LEU H 86 " ideal model delta sigma weight residual 1.524 1.619 -0.095 1.26e-02 6.30e+03 5.65e+01 bond pdb=" N ARG H 87 " pdb=" CA ARG H 87 " ideal model delta sigma weight residual 1.457 1.552 -0.094 1.29e-02 6.01e+03 5.34e+01 bond pdb=" C LEU B 78 " pdb=" N GLN B 79 " ideal model delta sigma weight residual 1.327 1.228 0.098 1.71e-02 3.42e+03 3.31e+01 bond pdb=" C ARG H 87 " pdb=" O ARG H 87 " ideal model delta sigma weight residual 1.235 1.173 0.063 1.26e-02 6.30e+03 2.46e+01 ... (remaining 6573 not shown) Histogram of bond angle deviations from ideal: 99.84 - 107.80: 357 107.80 - 115.76: 3846 115.76 - 123.71: 4362 123.71 - 131.67: 330 131.67 - 139.62: 19 Bond angle restraints: 8914 Sorted by residual: angle pdb=" N LEU H 86 " pdb=" CA LEU H 86 " pdb=" C LEU H 86 " ideal model delta sigma weight residual 111.14 139.62 -28.48 1.08e+00 8.57e-01 6.96e+02 angle pdb=" N ARG H 87 " pdb=" CA ARG H 87 " pdb=" C ARG H 87 " ideal model delta sigma weight residual 110.80 129.85 -19.05 2.13e+00 2.20e-01 8.00e+01 angle pdb=" C ALA H 88 " pdb=" N GLU H 89 " pdb=" CA GLU H 89 " ideal model delta sigma weight residual 122.33 110.68 11.65 1.68e+00 3.54e-01 4.81e+01 angle pdb=" N ALA H 88 " pdb=" CA ALA H 88 " pdb=" C ALA H 88 " ideal model delta sigma weight residual 107.98 120.97 -12.99 1.88e+00 2.83e-01 4.77e+01 angle pdb=" O SER H 85 " pdb=" C SER H 85 " pdb=" N LEU H 86 " ideal model delta sigma weight residual 123.32 114.89 8.43 1.27e+00 6.20e-01 4.41e+01 ... (remaining 8909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 3460 16.91 - 33.81: 321 33.81 - 50.72: 72 50.72 - 67.63: 19 67.63 - 84.54: 16 Dihedral angle restraints: 3888 sinusoidal: 1553 harmonic: 2335 Sorted by residual: dihedral pdb=" CB CYS D 57 " pdb=" SG CYS D 57 " pdb=" SG CYS D 83 " pdb=" CB CYS D 83 " ideal model delta sinusoidal sigma weight residual -86.00 -135.12 49.12 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CB CYS C 96 " pdb=" SG CYS C 96 " pdb=" SG CYS C 111 " pdb=" CB CYS C 111 " ideal model delta sinusoidal sigma weight residual -86.00 -115.98 29.98 1 1.00e+01 1.00e-02 1.28e+01 dihedral pdb=" CB CYS D 172 " pdb=" SG CYS D 172 " pdb=" SG CYS D 207 " pdb=" CB CYS D 207 " ideal model delta sinusoidal sigma weight residual -86.00 -58.04 -27.96 1 1.00e+01 1.00e-02 1.12e+01 ... (remaining 3885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 940 0.150 - 0.301: 9 0.301 - 0.451: 1 0.451 - 0.602: 2 0.602 - 0.752: 1 Chirality restraints: 953 Sorted by residual: chirality pdb=" CA LEU H 86 " pdb=" N LEU H 86 " pdb=" C LEU H 86 " pdb=" CB LEU H 86 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CG LEU E 59 " pdb=" CB LEU E 59 " pdb=" CD1 LEU E 59 " pdb=" CD2 LEU E 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CG LEU L 78 " pdb=" CB LEU L 78 " pdb=" CD1 LEU L 78 " pdb=" CD2 LEU L 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 950 not shown) Planarity restraints: 1151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 67 " 0.152 9.50e-02 1.11e+02 8.78e-02 4.10e+01 pdb=" NE ARG H 67 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG H 67 " 0.105 2.00e-02 2.50e+03 pdb=" NH1 ARG H 67 " -0.037 2.00e-02 2.50e+03 pdb=" NH2 ARG H 67 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 71 " -0.133 9.50e-02 1.11e+02 7.66e-02 3.14e+01 pdb=" NE ARG A 71 " 0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 71 " -0.092 2.00e-02 2.50e+03 pdb=" NH1 ARG A 71 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 71 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 38 " 0.106 9.50e-02 1.11e+02 6.19e-02 2.12e+01 pdb=" NE ARG H 38 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG H 38 " 0.076 2.00e-02 2.50e+03 pdb=" NH1 ARG H 38 " -0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG H 38 " -0.022 2.00e-02 2.50e+03 ... (remaining 1148 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 121 2.64 - 3.20: 5851 3.20 - 3.77: 9713 3.77 - 4.33: 13531 4.33 - 4.90: 22229 Nonbonded interactions: 51445 Sorted by model distance: nonbonded pdb=" NH1 ARG H 38 " pdb=" OE1 GLU H 89 " model vdw 2.073 3.120 nonbonded pdb=" O SER E 41 " pdb=" NH1 ARG E 94 " model vdw 2.078 3.120 nonbonded pdb=" OG1 THR D 120 " pdb=" OG SER L 52 " model vdw 2.090 3.040 nonbonded pdb=" OH TYR A 100E" pdb=" O CYS E 40 " model vdw 2.117 3.040 nonbonded pdb=" OH TYR D 46 " pdb=" O ARG H 104 " model vdw 2.144 3.040 ... (remaining 51440 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 7.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.120 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5721 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 : 0.006 0.116 6578 Z= 0.420 Angle : 1.156 28.484 8914 Z= 0.718 Chirality : 0.065 0.752 953 Planarity : 0.009 0.088 1151 Dihedral : 14.883 84.536 2372 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.42 % Favored : 94.08 % Rotamer: Outliers : 1.58 % Allowed : 9.20 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.59 (0.26), residues: 794 helix: -1.40 (0.40), residues: 109 sheet: -0.16 (0.31), residues: 259 loop : -1.53 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP H 100 HIS 0.008 0.002 HIS D 150 PHE 0.027 0.003 PHE D 183 TYR 0.031 0.006 TYR L 91 ARG 0.107 0.014 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TRP cc_start: 0.7113 (t60) cc_final: 0.6913 (t60) REVERT: B 4 MET cc_start: 0.6754 (mmm) cc_final: 0.6538 (mmp) REVERT: B 44 PRO cc_start: 0.8464 (Cg_exo) cc_final: 0.8049 (Cg_endo) REVERT: B 94 PHE cc_start: 0.7638 (m-80) cc_final: 0.7151 (m-10) REVERT: D 106 TRP cc_start: 0.7328 (p-90) cc_final: 0.6637 (p-90) REVERT: D 118 ASN cc_start: 0.6021 (m-40) cc_final: 0.5507 (t0) REVERT: D 174 MET cc_start: 0.5646 (ttp) cc_final: 0.5307 (ttp) REVERT: H 6 GLU cc_start: 0.6182 (mp0) cc_final: 0.5740 (mp0) REVERT: H 112 TRP cc_start: 0.6880 (m100) cc_final: 0.6641 (m100) REVERT: L 4 MET cc_start: 0.6375 (mmm) cc_final: 0.6121 (mmt) REVERT: L 18 ARG cc_start: 0.7241 (mtm110) cc_final: 0.6924 (ttm110) REVERT: L 39 LYS cc_start: 0.7907 (mttt) cc_final: 0.7679 (ttmt) REVERT: L 56 SER cc_start: 0.8230 (m) cc_final: 0.7919 (p) outliers start: 11 outliers final: 7 residues processed: 132 average time/residue: 0.2023 time to fit residues: 34.4968 Evaluate side-chains 114 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 37 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN E 35 HIS ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5771 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6578 Z= 0.310 Angle : 0.766 11.490 8914 Z= 0.407 Chirality : 0.048 0.281 953 Planarity : 0.007 0.136 1151 Dihedral : 5.451 28.533 901 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.29 % Allowed : 3.02 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.57 (0.28), residues: 794 helix: 0.44 (0.48), residues: 116 sheet: 0.22 (0.31), residues: 267 loop : -1.01 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 47 HIS 0.006 0.001 HIS D 150 PHE 0.024 0.002 PHE L 99 TYR 0.023 0.002 TYR L 91 ARG 0.009 0.001 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4 MET cc_start: 0.6827 (mmm) cc_final: 0.6557 (mmp) REVERT: B 44 PRO cc_start: 0.8470 (Cg_exo) cc_final: 0.7912 (Cg_endo) REVERT: D 77 VAL cc_start: 0.7831 (t) cc_final: 0.7378 (m) REVERT: D 131 LYS cc_start: 0.7186 (mmtt) cc_final: 0.6905 (mmtt) REVERT: E 59 LEU cc_start: 0.6506 (mp) cc_final: 0.6289 (mp) REVERT: H 6 GLU cc_start: 0.6328 (mp0) cc_final: 0.5436 (mp0) REVERT: H 16 ARG cc_start: 0.6110 (mmt-90) cc_final: 0.5427 (mtt90) REVERT: L 4 MET cc_start: 0.6286 (mmm) cc_final: 0.6062 (mmt) REVERT: L 18 ARG cc_start: 0.7446 (mtm110) cc_final: 0.7054 (ttm110) REVERT: L 56 SER cc_start: 0.8326 (m) cc_final: 0.7988 (p) REVERT: L 63 SER cc_start: 0.7910 (p) cc_final: 0.7482 (t) outliers start: 2 outliers final: 0 residues processed: 112 average time/residue: 0.1894 time to fit residues: 28.2416 Evaluate side-chains 102 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6578 Z= 0.348 Angle : 0.730 8.028 8914 Z= 0.395 Chirality : 0.049 0.298 953 Planarity : 0.006 0.064 1151 Dihedral : 5.811 29.370 901 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.56 (0.29), residues: 794 helix: 0.31 (0.46), residues: 116 sheet: 0.47 (0.32), residues: 258 loop : -1.12 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 47 HIS 0.012 0.002 HIS H 35 PHE 0.022 0.002 PHE D 196 TYR 0.027 0.002 TYR L 91 ARG 0.005 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: D 127 GLN cc_start: 0.6609 (tt0) cc_final: 0.6354 (tt0) REVERT: D 131 LYS cc_start: 0.7197 (mmtt) cc_final: 0.6944 (mmtt) REVERT: H 34 MET cc_start: 0.5622 (mmt) cc_final: 0.4937 (mmt) REVERT: L 18 ARG cc_start: 0.7403 (mtm110) cc_final: 0.7098 (ttp-170) REVERT: L 56 SER cc_start: 0.8408 (m) cc_final: 0.8074 (p) REVERT: L 63 SER cc_start: 0.7968 (p) cc_final: 0.7552 (t) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2045 time to fit residues: 29.5050 Evaluate side-chains 108 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 0.0770 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN C 115 ASN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN E 129 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6578 Z= 0.248 Angle : 0.642 5.994 8914 Z= 0.345 Chirality : 0.045 0.204 953 Planarity : 0.006 0.052 1151 Dihedral : 5.540 27.399 901 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 794 helix: 0.23 (0.46), residues: 123 sheet: 0.40 (0.31), residues: 261 loop : -0.99 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 47 HIS 0.010 0.002 HIS H 35 PHE 0.011 0.002 PHE E 122 TYR 0.020 0.002 TYR E 63 ARG 0.007 0.001 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: B 4 MET cc_start: 0.7193 (mmp) cc_final: 0.6845 (mmp) REVERT: D 174 MET cc_start: 0.6102 (ttp) cc_final: 0.5771 (ttp) REVERT: H 112 TRP cc_start: 0.7091 (m100) cc_final: 0.5791 (m100) REVERT: L 18 ARG cc_start: 0.7359 (mtm110) cc_final: 0.7039 (ttp-170) REVERT: L 56 SER cc_start: 0.8384 (m) cc_final: 0.8047 (p) REVERT: L 63 SER cc_start: 0.7958 (p) cc_final: 0.7548 (t) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2047 time to fit residues: 29.8495 Evaluate side-chains 108 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.0050 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN D 97 GLN E 64 HIS ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6578 Z= 0.227 Angle : 0.615 6.042 8914 Z= 0.330 Chirality : 0.044 0.164 953 Planarity : 0.005 0.066 1151 Dihedral : 5.411 26.987 901 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.14 % Allowed : 2.30 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.46 (0.30), residues: 794 helix: 0.26 (0.46), residues: 123 sheet: 0.45 (0.31), residues: 261 loop : -0.97 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.016 0.002 PHE H 68 TYR 0.020 0.001 TYR E 63 ARG 0.005 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 94 ARG cc_start: 0.7335 (ttt180) cc_final: 0.7055 (ttt180) REVERT: B 4 MET cc_start: 0.7243 (mmp) cc_final: 0.6852 (mmp) REVERT: D 131 LYS cc_start: 0.7182 (mptt) cc_final: 0.6781 (mptt) REVERT: D 174 MET cc_start: 0.6116 (ttp) cc_final: 0.5813 (ttp) REVERT: H 112 TRP cc_start: 0.7076 (m100) cc_final: 0.5676 (m100) REVERT: L 18 ARG cc_start: 0.7299 (mtm110) cc_final: 0.6973 (ttp-170) REVERT: L 20 THR cc_start: 0.7784 (m) cc_final: 0.7403 (p) REVERT: L 63 SER cc_start: 0.7945 (p) cc_final: 0.7506 (t) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.2093 time to fit residues: 29.6955 Evaluate side-chains 107 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6578 Z= 0.295 Angle : 0.660 5.790 8914 Z= 0.357 Chirality : 0.046 0.174 953 Planarity : 0.006 0.058 1151 Dihedral : 5.609 24.502 901 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.60 (0.29), residues: 794 helix: 0.05 (0.45), residues: 123 sheet: 0.40 (0.32), residues: 257 loop : -1.05 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.007 0.002 HIS H 35 PHE 0.018 0.002 PHE H 109 TYR 0.019 0.002 TYR L 91 ARG 0.008 0.001 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 117 ARG cc_start: 0.6621 (tpt90) cc_final: 0.6401 (tpt90) REVERT: H 112 TRP cc_start: 0.7077 (m100) cc_final: 0.5874 (m100) REVERT: L 18 ARG cc_start: 0.7205 (mtm110) cc_final: 0.6850 (ttp-170) REVERT: L 20 THR cc_start: 0.7830 (m) cc_final: 0.7461 (p) REVERT: L 63 SER cc_start: 0.8046 (p) cc_final: 0.7612 (t) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2027 time to fit residues: 29.6074 Evaluate side-chains 108 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.1659 > 50: distance: 2 - 24: 9.976 distance: 11 - 31: 5.715 distance: 21 - 24: 8.782 distance: 24 - 25: 11.117 distance: 25 - 26: 26.774 distance: 25 - 28: 14.105 distance: 26 - 31: 22.518 distance: 28 - 29: 8.823 distance: 28 - 30: 6.946 distance: 31 - 32: 16.261 distance: 32 - 33: 19.302 distance: 32 - 35: 12.778 distance: 33 - 34: 18.026 distance: 33 - 42: 33.483 distance: 35 - 36: 7.772 distance: 36 - 37: 3.586 distance: 36 - 38: 6.587 distance: 37 - 39: 10.021 distance: 38 - 40: 7.108 distance: 39 - 41: 9.033 distance: 40 - 41: 7.505 distance: 42 - 43: 29.614 distance: 43 - 44: 19.978 distance: 43 - 46: 13.539 distance: 44 - 45: 12.529 distance: 44 - 54: 55.857 distance: 46 - 47: 15.682 distance: 47 - 48: 8.002 distance: 47 - 49: 8.786 distance: 48 - 50: 21.017 distance: 49 - 51: 15.223 distance: 50 - 52: 15.320 distance: 51 - 52: 12.230 distance: 52 - 53: 13.213 distance: 54 - 55: 17.477 distance: 55 - 56: 29.808 distance: 55 - 58: 9.626 distance: 56 - 57: 12.659 distance: 56 - 60: 16.534 distance: 58 - 59: 44.313 distance: 59 - 133: 35.025 distance: 60 - 61: 15.211 distance: 60 - 66: 34.859 distance: 61 - 62: 25.597 distance: 61 - 64: 25.377 distance: 62 - 63: 17.814 distance: 62 - 67: 36.828 distance: 64 - 65: 41.689 distance: 67 - 68: 9.032 distance: 68 - 69: 9.887 distance: 68 - 71: 9.733 distance: 69 - 70: 23.466 distance: 69 - 78: 24.474 distance: 71 - 72: 8.729 distance: 72 - 73: 6.645 distance: 72 - 74: 3.366 distance: 73 - 75: 27.302 distance: 74 - 76: 18.334 distance: 75 - 77: 3.747 distance: 76 - 77: 13.416 distance: 78 - 79: 50.044 distance: 79 - 80: 38.705 distance: 79 - 82: 44.153 distance: 80 - 81: 57.049 distance: 82 - 83: 15.071 distance: 83 - 84: 40.368 distance: 83 - 85: 36.365 distance: 86 - 87: 44.740 distance: 87 - 88: 27.130 distance: 87 - 90: 38.326 distance: 88 - 89: 20.291 distance: 88 - 98: 32.880 distance: 90 - 91: 44.383 distance: 91 - 92: 31.735 distance: 91 - 93: 3.715 distance: 92 - 94: 14.652 distance: 93 - 95: 15.670 distance: 94 - 96: 7.542 distance: 95 - 96: 45.623 distance: 96 - 97: 33.981 distance: 98 - 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