Starting phenix.real_space_refine on Fri Aug 22 20:45:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kbb_22788/08_2025/7kbb_22788_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kbb_22788/08_2025/7kbb_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 { model { file = "/net/cci-nas-00/data/ceres_data/7kbb_22788/08_2025/7kbb_22788_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kbb_22788/08_2025/7kbb_22788_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kbb_22788/08_2025/7kbb_22788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kbb_22788/08_2025/7kbb_22788.map" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.33, per 1000 atoms: 0.21 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 339.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.26 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: 0.70 Time building geometry restraints manager: 0.69 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: 0.00 - 5.70: 8888 5.70 - 11.39: 21 11.39 - 17.09: 3 17.09 - 22.79: 1 22.79 - 28.48: 1 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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.450 ------------------------------------------------------------------------------- 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 6586 Z= 0.349 Angle : 1.159 28.484 8930 Z= 0.719 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.107 0.014 ARG H 67 TYR 0.031 0.006 TYR L 91 PHE 0.027 0.003 PHE D 183 TRP 0.033 0.004 TRP H 100 HIS 0.008 0.002 HIS D 150 Details of bonding type rmsd covalent geometry : bond 0.00620 ( 6578) covalent geometry : angle 1.15591 ( 8914) SS BOND : bond 0.00675 ( 8) SS BOND : angle 2.39027 ( 16) hydrogen bonds : bond 0.14414 ( 270) hydrogen bonds : angle 8.02498 ( 753) *********************** 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 to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.253 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: 0.0795 time to fit residues: 13.7018 Evaluate side-chains 114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.181001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.168685 restraints weight = 11542.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.171511 restraints weight = 6968.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.173431 restraints weight = 4555.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.174757 restraints weight = 3218.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.175418 restraints weight = 2405.230| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5793 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 6586 Z= 0.213 Angle : 0.769 11.490 8930 Z= 0.408 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG A 66 TYR 0.023 0.002 TYR L 91 PHE 0.024 0.002 PHE L 99 TRP 0.016 0.002 TRP A 47 HIS 0.006 0.001 HIS D 150 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 6578) covalent geometry : angle 0.76648 ( 8914) SS BOND : bond 0.00674 ( 8) SS BOND : angle 1.58656 ( 16) hydrogen bonds : bond 0.04784 ( 270) hydrogen bonds : angle 6.57092 ( 753) *********************** 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 to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4 MET cc_start: 0.6994 (mmm) cc_final: 0.6685 (mmp) REVERT: B 44 PRO cc_start: 0.8440 (Cg_exo) cc_final: 0.7955 (Cg_endo) REVERT: D 77 VAL cc_start: 0.7882 (t) cc_final: 0.7444 (m) REVERT: D 131 LYS cc_start: 0.7246 (mmtt) cc_final: 0.7017 (mmtt) REVERT: E 59 LEU cc_start: 0.6689 (mp) cc_final: 0.6489 (mp) REVERT: H 6 GLU cc_start: 0.6327 (mp0) cc_final: 0.5476 (mp0) REVERT: H 16 ARG cc_start: 0.6035 (mmt-90) cc_final: 0.5443 (mtt90) REVERT: L 4 MET cc_start: 0.6219 (mmm) cc_final: 0.5999 (mmt) REVERT: L 18 ARG cc_start: 0.7413 (mtm110) cc_final: 0.7033 (ttm110) REVERT: L 56 SER cc_start: 0.8307 (m) cc_final: 0.8005 (p) REVERT: L 63 SER cc_start: 0.7893 (p) cc_final: 0.7451 (t) outliers start: 2 outliers final: 0 residues processed: 112 average time/residue: 0.0771 time to fit residues: 11.5630 Evaluate side-chains 102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.0980 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 0.0770 chunk 3 optimal weight: 0.6980 chunk 77 optimal weight: 0.0570 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- 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** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN D 97 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.181464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.174801 restraints weight = 12744.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.175707 restraints weight = 10108.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.176252 restraints weight = 8182.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.176460 restraints weight = 6983.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.176460 restraints weight = 6375.268| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6586 Z= 0.143 Angle : 0.625 6.960 8930 Z= 0.334 Chirality : 0.044 0.243 953 Planarity : 0.005 0.050 1151 Dihedral : 5.174 26.863 901 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.29), residues: 794 helix: 0.98 (0.48), residues: 116 sheet: 0.58 (0.31), residues: 262 loop : -0.93 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 64 TYR 0.019 0.001 TYR L 91 PHE 0.015 0.002 PHE D 183 TRP 0.018 0.002 TRP A 47 HIS 0.009 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6578) covalent geometry : angle 0.62340 ( 8914) SS BOND : bond 0.00389 ( 8) SS BOND : angle 1.18453 ( 16) hydrogen bonds : bond 0.03685 ( 270) hydrogen bonds : angle 5.84074 ( 753) *********************** 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 109 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: B 4 MET cc_start: 0.6935 (mmm) cc_final: 0.6652 (mmp) REVERT: B 44 PRO cc_start: 0.8381 (Cg_exo) cc_final: 0.8025 (Cg_endo) REVERT: D 174 MET cc_start: 0.6076 (ttp) cc_final: 0.5623 (ttp) REVERT: H 45 LEU cc_start: 0.7959 (tt) cc_final: 0.7613 (tp) REVERT: H 72 ARG cc_start: 0.4608 (ttm-80) cc_final: 0.4286 (ttm-80) REVERT: L 18 ARG cc_start: 0.7363 (mtm110) cc_final: 0.7078 (ttm110) REVERT: L 56 SER cc_start: 0.8312 (m) cc_final: 0.8027 (p) REVERT: L 63 SER cc_start: 0.7873 (p) cc_final: 0.7428 (t) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0799 time to fit residues: 11.3385 Evaluate side-chains 101 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 28 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN D 97 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.183284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.175142 restraints weight = 13027.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.175783 restraints weight = 11109.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.175953 restraints weight = 9418.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.176774 restraints weight = 8353.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.176783 restraints weight = 7223.162| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6586 Z= 0.208 Angle : 0.687 7.241 8930 Z= 0.369 Chirality : 0.047 0.250 953 Planarity : 0.006 0.065 1151 Dihedral : 5.507 28.916 901 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.29), residues: 794 helix: 0.41 (0.46), residues: 123 sheet: 0.53 (0.32), residues: 258 loop : -0.94 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 38 TYR 0.022 0.002 TYR L 91 PHE 0.021 0.002 PHE D 196 TRP 0.020 0.002 TRP A 47 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 6578) covalent geometry : angle 0.68414 ( 8914) SS BOND : bond 0.00502 ( 8) SS BOND : angle 1.66936 ( 16) hydrogen bonds : bond 0.04105 ( 270) hydrogen bonds : angle 6.06272 ( 753) *********************** 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 to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: H 112 TRP cc_start: 0.7161 (m100) cc_final: 0.5944 (m100) REVERT: L 18 ARG cc_start: 0.7233 (mtm110) cc_final: 0.6882 (ttm110) REVERT: L 20 THR cc_start: 0.7785 (m) cc_final: 0.7317 (p) REVERT: L 63 SER cc_start: 0.7779 (p) cc_final: 0.7415 (t) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.0675 time to fit residues: 10.1342 Evaluate side-chains 105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 0.0070 chunk 11 optimal weight: 0.0020 overall best weight: 0.4206 ------------------------------------------------------------------------------- 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 D 97 GLN E 64 HIS ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.184321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.176504 restraints weight = 13249.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.176852 restraints weight = 11688.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.177024 restraints weight = 10041.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.177341 restraints weight = 9155.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.177455 restraints weight = 7932.971| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6586 Z= 0.156 Angle : 0.621 6.383 8930 Z= 0.331 Chirality : 0.044 0.172 953 Planarity : 0.005 0.047 1151 Dihedral : 5.270 26.281 901 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.30), residues: 794 helix: 0.35 (0.45), residues: 123 sheet: 0.56 (0.32), residues: 259 loop : -0.88 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 66 TYR 0.020 0.001 TYR E 63 PHE 0.014 0.002 PHE D 196 TRP 0.013 0.002 TRP L 94 HIS 0.005 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6578) covalent geometry : angle 0.61928 ( 8914) SS BOND : bond 0.00563 ( 8) SS BOND : angle 1.19486 ( 16) hydrogen bonds : bond 0.03728 ( 270) hydrogen bonds : angle 5.87293 ( 753) *********************** 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 111 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.6973 (ttt180) cc_final: 0.6287 (ttt90) REVERT: B 4 MET cc_start: 0.7536 (mmp) cc_final: 0.7202 (mmp) REVERT: D 174 MET cc_start: 0.6083 (ttp) cc_final: 0.5663 (ttp) REVERT: H 112 TRP cc_start: 0.7188 (m100) cc_final: 0.5830 (m100) REVERT: L 18 ARG cc_start: 0.7187 (mtm110) cc_final: 0.6866 (ttp-170) REVERT: L 20 THR cc_start: 0.7750 (m) cc_final: 0.7295 (p) REVERT: L 63 SER cc_start: 0.7967 (p) cc_final: 0.7604 (t) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0764 time to fit residues: 11.3280 Evaluate side-chains 107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 0.0070 chunk 8 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 72 optimal weight: 0.3980 chunk 45 optimal weight: 0.0050 chunk 64 optimal weight: 0.6980 overall best weight: 0.2812 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN B 92 ASN D 97 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.185001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.176872 restraints weight = 13207.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.177968 restraints weight = 9832.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.178679 restraints weight = 7686.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.179051 restraints weight = 6408.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.179525 restraints weight = 5695.085| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6586 Z= 0.132 Angle : 0.596 5.210 8930 Z= 0.319 Chirality : 0.044 0.159 953 Planarity : 0.005 0.067 1151 Dihedral : 5.122 24.996 901 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.14 % Allowed : 1.58 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.30), residues: 794 helix: 0.50 (0.46), residues: 123 sheet: 0.69 (0.32), residues: 258 loop : -0.82 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 66 TYR 0.022 0.001 TYR E 63 PHE 0.012 0.002 PHE H 68 TRP 0.015 0.002 TRP B 35 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6578) covalent geometry : angle 0.59473 ( 8914) SS BOND : bond 0.00373 ( 8) SS BOND : angle 0.98755 ( 16) hydrogen bonds : bond 0.03516 ( 270) hydrogen bonds : angle 5.68001 ( 753) *********************** 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 112 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 35 ASP cc_start: 0.5597 (m-30) cc_final: 0.5307 (m-30) REVERT: A 45 PHE cc_start: 0.7643 (m-80) cc_final: 0.7284 (m-10) REVERT: B 4 MET cc_start: 0.7597 (mmp) cc_final: 0.7152 (mmp) REVERT: D 100 VAL cc_start: 0.7817 (p) cc_final: 0.7602 (m) REVERT: E 61 LEU cc_start: 0.8039 (tp) cc_final: 0.7743 (tp) REVERT: H 112 TRP cc_start: 0.7099 (m100) cc_final: 0.6893 (m100) REVERT: L 18 ARG cc_start: 0.7165 (mtm110) cc_final: 0.6821 (ttp-170) REVERT: L 20 THR cc_start: 0.7737 (m) cc_final: 0.7297 (p) REVERT: L 63 SER cc_start: 0.7910 (p) cc_final: 0.7561 (t) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.0774 time to fit residues: 11.5801 Evaluate side-chains 110 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.180354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.172125 restraints weight = 13006.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.173191 restraints weight = 9773.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.173932 restraints weight = 7724.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.174336 restraints weight = 6410.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.174810 restraints weight = 5682.740| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6586 Z= 0.249 Angle : 0.732 7.122 8930 Z= 0.393 Chirality : 0.049 0.288 953 Planarity : 0.006 0.061 1151 Dihedral : 5.823 26.126 901 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.29), residues: 794 helix: 0.03 (0.45), residues: 123 sheet: 0.40 (0.32), residues: 265 loop : -1.12 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 22 TYR 0.023 0.002 TYR L 91 PHE 0.037 0.003 PHE D 196 TRP 0.016 0.003 TRP H 47 HIS 0.007 0.002 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 6578) covalent geometry : angle 0.72822 ( 8914) SS BOND : bond 0.00680 ( 8) SS BOND : angle 1.93343 ( 16) hydrogen bonds : bond 0.04461 ( 270) hydrogen bonds : angle 6.34637 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 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 to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.233 Fit side-chains REVERT: A 94 ARG cc_start: 0.7055 (ttt180) cc_final: 0.6487 (ttt90) REVERT: D 117 ARG cc_start: 0.6331 (tpt90) cc_final: 0.6100 (tpt90) REVERT: E 61 LEU cc_start: 0.8072 (tp) cc_final: 0.7772 (tp) REVERT: H 112 TRP cc_start: 0.7257 (m100) cc_final: 0.6238 (m100) REVERT: L 18 ARG cc_start: 0.7034 (mtm110) cc_final: 0.6703 (ttp-170) REVERT: L 20 THR cc_start: 0.7881 (m) cc_final: 0.7413 (p) REVERT: L 63 SER cc_start: 0.7956 (p) cc_final: 0.7557 (t) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0870 time to fit residues: 12.9273 Evaluate side-chains 106 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 10 optimal weight: 0.0270 chunk 46 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 overall best weight: 0.1436 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN D 76 GLN D 97 GLN D 181 HIS ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.184769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.176691 restraints weight = 13130.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.177783 restraints weight = 9830.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.178500 restraints weight = 7781.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.178859 restraints weight = 6470.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.179349 restraints weight = 5792.308| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5777 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6586 Z= 0.116 Angle : 0.584 4.964 8930 Z= 0.311 Chirality : 0.043 0.158 953 Planarity : 0.005 0.055 1151 Dihedral : 5.147 25.601 901 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.14 % Allowed : 1.15 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.30), residues: 794 helix: 0.41 (0.46), residues: 123 sheet: 0.50 (0.32), residues: 262 loop : -0.79 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.023 0.001 TYR E 63 PHE 0.013 0.002 PHE L 99 TRP 0.019 0.002 TRP B 35 HIS 0.003 0.001 HIS E 64 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 6578) covalent geometry : angle 0.58278 ( 8914) SS BOND : bond 0.00268 ( 8) SS BOND : angle 1.03818 ( 16) hydrogen bonds : bond 0.03241 ( 270) hydrogen bonds : angle 5.61397 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 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 to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7633 (m-80) cc_final: 0.7191 (m-10) REVERT: A 94 ARG cc_start: 0.7033 (ttt180) cc_final: 0.6657 (ttt90) REVERT: B 4 MET cc_start: 0.7501 (mmp) cc_final: 0.7103 (mmp) REVERT: D 127 GLN cc_start: 0.7372 (tp40) cc_final: 0.7140 (tp-100) REVERT: D 174 MET cc_start: 0.5971 (ttp) cc_final: 0.5509 (ttp) REVERT: H 112 TRP cc_start: 0.7154 (m100) cc_final: 0.6878 (m100) REVERT: L 18 ARG cc_start: 0.6981 (mtm110) cc_final: 0.6732 (ttp-170) REVERT: L 20 THR cc_start: 0.7756 (m) cc_final: 0.7309 (p) REVERT: L 63 SER cc_start: 0.7878 (p) cc_final: 0.7509 (t) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.0880 time to fit residues: 12.7483 Evaluate side-chains 106 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.7275 > 50: distance: 2 - 24: 6.955 distance: 11 - 31: 4.181 distance: 21 - 24: 4.194 distance: 25 - 26: 15.473 distance: 25 - 28: 6.316 distance: 26 - 27: 12.090 distance: 26 - 31: 10.529 distance: 28 - 29: 11.623 distance: 28 - 30: 10.847 distance: 31 - 32: 3.103 distance: 32 - 33: 12.352 distance: 32 - 35: 7.023 distance: 33 - 34: 15.770 distance: 33 - 42: 25.210 distance: 36 - 37: 5.372 distance: 36 - 38: 6.496 distance: 38 - 40: 5.335 distance: 39 - 41: 5.189 distance: 40 - 41: 4.571 distance: 42 - 43: 12.188 distance: 43 - 44: 20.248 distance: 43 - 46: 8.189 distance: 44 - 45: 14.545 distance: 44 - 54: 57.820 distance: 46 - 47: 6.837 distance: 47 - 48: 6.237 distance: 47 - 49: 7.350 distance: 48 - 50: 7.342 distance: 49 - 51: 9.423 distance: 50 - 52: 11.366 distance: 51 - 52: 11.296 distance: 54 - 55: 6.966 distance: 55 - 56: 20.542 distance: 55 - 58: 42.367 distance: 56 - 57: 12.416 distance: 56 - 60: 6.666 distance: 58 - 59: 21.263 distance: 59 - 132: 32.924 distance: 60 - 61: 11.410 distance: 60 - 66: 26.065 distance: 61 - 62: 10.561 distance: 61 - 64: 8.907 distance: 62 - 63: 25.229 distance: 62 - 67: 8.034 distance: 64 - 65: 22.174 distance: 65 - 66: 8.173 distance: 67 - 68: 3.547 distance: 68 - 69: 13.268 distance: 68 - 71: 3.572 distance: 69 - 70: 13.905 distance: 69 - 78: 22.042 distance: 72 - 73: 5.601 distance: 72 - 74: 3.075 distance: 73 - 75: 15.789 distance: 74 - 76: 10.431 distance: 76 - 77: 9.043 distance: 78 - 79: 27.012 distance: 79 - 80: 26.715 distance: 79 - 82: 22.243 distance: 80 - 81: 20.054 distance: 80 - 86: 39.613 distance: 82 - 83: 33.309 distance: 83 - 84: 22.035 distance: 83 - 85: 18.133 distance: 86 - 87: 51.494 distance: 87 - 88: 31.232 distance: 87 - 90: 28.158 distance: 88 - 89: 19.997 distance: 88 - 98: 16.097 distance: 90 - 91: 20.826 distance: 91 - 92: 23.135 distance: 91 - 93: 21.431 distance: 93 - 95: 20.944 distance: 94 - 96: 24.974 distance: 95 - 96: 36.940 distance: 96 - 97: 14.934 distance: 98 - 99: 4.615 distance: 98 - 104: 24.990 distance: 99 - 100: 18.557 distance: 99 - 102: 23.347 distance: 100 - 101: 9.641 distance: 100 - 105: 4.795 distance: 102 - 103: 4.714 distance: 103 - 104: 13.742 distance: 105 - 106: 25.395 distance: 106 - 107: 19.187 distance: 106 - 109: 34.195 distance: 107 - 108: 7.814 distance: 107 - 111: 29.515 distance: 109 - 110: 23.175