Starting phenix.real_space_refine on Mon Mar 11 12:13:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/03_2024/7kbb_22788_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/03_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_22788/03_2024/7kbb_22788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/03_2024/7kbb_22788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/03_2024/7kbb_22788_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/03_2024/7kbb_22788_neut.pdb" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.87, per 1000 atoms: 0.60 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: 2.26 Conformation dependent library (CDL) restraints added in 1.2 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: 0.71 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: 1.79 Time building geometry restraints manager: 2.46 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 2.520 nonbonded pdb=" O SER E 41 " pdb=" NH1 ARG E 94 " model vdw 2.078 2.520 nonbonded pdb=" OG1 THR D 120 " pdb=" OG SER L 52 " model vdw 2.090 2.440 nonbonded pdb=" OH TYR A 100E" pdb=" O CYS E 40 " model vdw 2.117 2.440 nonbonded pdb=" OH TYR D 46 " pdb=" O ARG H 104 " model vdw 2.144 2.440 ... (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 ========== 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: 5.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 12.020 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.770 Find NCS groups from input model: 0.200 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.840 ------------------------------------------------------------------------------- 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 : 0.609 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: 0.1986 time to fit residues: 33.9119 Evaluate side-chains 114 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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: 0.5980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.0870 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.0030 chunk 70 optimal weight: 1.9990 overall best weight: 0.3768 ------------------------------------------------------------------------------- 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 37 GLN C 115 ASN D 75 GLN D 97 GLN E 21 GLN E 35 HIS ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 moved from start: 0.1817 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= 0.250 Angle : 0.715 11.037 8914 Z= 0.380 Chirality : 0.046 0.245 953 Planarity : 0.007 0.141 1151 Dihedral : 5.205 27.682 901 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.29 % Allowed : 2.87 % Favored : 96.84 % 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: -0.41 (0.29), residues: 794 helix: 0.88 (0.48), residues: 110 sheet: 0.27 (0.31), residues: 264 loop : -0.92 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 47 HIS 0.004 0.001 HIS A 98 PHE 0.023 0.002 PHE L 99 TYR 0.020 0.002 TYR L 91 ARG 0.006 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 115 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.696 Fit side-chains REVERT: A 33 ASP cc_start: 0.6347 (p0) cc_final: 0.6122 (p0) REVERT: A 47 TRP cc_start: 0.7118 (t60) cc_final: 0.6809 (t60) REVERT: B 4 MET cc_start: 0.6740 (mmm) cc_final: 0.6527 (mmp) REVERT: D 131 LYS cc_start: 0.7159 (mmtt) cc_final: 0.6842 (mmtt) REVERT: E 59 LEU cc_start: 0.6476 (mp) cc_final: 0.6256 (mp) REVERT: H 6 GLU cc_start: 0.6219 (mp0) cc_final: 0.5464 (mp0) REVERT: H 16 ARG cc_start: 0.5840 (mmt-90) cc_final: 0.5447 (mtt90) REVERT: H 116 THR cc_start: 0.7964 (m) cc_final: 0.7703 (m) REVERT: L 4 MET cc_start: 0.6284 (mmm) cc_final: 0.6068 (mmt) REVERT: L 18 ARG cc_start: 0.7418 (mtm110) cc_final: 0.7059 (ttm110) REVERT: L 37 GLN cc_start: 0.7514 (tt0) cc_final: 0.7118 (tt0) REVERT: L 56 SER cc_start: 0.8302 (m) cc_final: 0.7968 (p) REVERT: L 63 SER cc_start: 0.7860 (p) cc_final: 0.7482 (t) outliers start: 2 outliers final: 0 residues processed: 114 average time/residue: 0.1935 time to fit residues: 28.9741 Evaluate side-chains 102 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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: 1.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6578 Z= 0.311 Angle : 0.699 8.527 8914 Z= 0.376 Chirality : 0.047 0.287 953 Planarity : 0.005 0.040 1151 Dihedral : 5.591 27.727 901 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % 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: -0.34 (0.29), residues: 794 helix: 0.82 (0.47), residues: 110 sheet: 0.40 (0.31), residues: 273 loop : -0.94 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 47 HIS 0.009 0.002 HIS H 35 PHE 0.020 0.002 PHE D 196 TYR 0.027 0.002 TYR L 91 ARG 0.006 0.001 ARG E 32 *********************** 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 113 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 TRP cc_start: 0.7216 (t60) cc_final: 0.6890 (t60) REVERT: B 4 MET cc_start: 0.7058 (mmm) cc_final: 0.6795 (mmp) REVERT: B 94 PHE cc_start: 0.8062 (m-80) cc_final: 0.7818 (m-80) REVERT: D 118 ASN cc_start: 0.6113 (m-40) cc_final: 0.5501 (t0) REVERT: D 131 LYS cc_start: 0.7195 (mmtt) cc_final: 0.6933 (mmtt) REVERT: D 174 MET cc_start: 0.6098 (ttp) cc_final: 0.5739 (ttp) REVERT: E 59 LEU cc_start: 0.6541 (mp) cc_final: 0.6322 (mp) REVERT: H 47 TRP cc_start: 0.7073 (t60) cc_final: 0.6773 (t60) REVERT: L 18 ARG cc_start: 0.7416 (mtm110) cc_final: 0.7140 (ttp-170) REVERT: L 56 SER cc_start: 0.8357 (m) cc_final: 0.8013 (p) REVERT: L 63 SER cc_start: 0.7904 (p) cc_final: 0.7526 (t) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1915 time to fit residues: 28.2848 Evaluate side-chains 109 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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: 0.6980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN E 129 ASN H 39 GLN L 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6578 Z= 0.285 Angle : 0.661 6.973 8914 Z= 0.352 Chirality : 0.046 0.231 953 Planarity : 0.005 0.040 1151 Dihedral : 5.571 29.149 901 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.14 % Allowed : 2.87 % Favored : 96.98 % 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: -0.36 (0.30), residues: 794 helix: 0.71 (0.48), residues: 110 sheet: 0.39 (0.31), residues: 263 loop : -0.90 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP H 105 HIS 0.007 0.001 HIS H 35 PHE 0.014 0.002 PHE H 95 TYR 0.020 0.002 TYR L 91 ARG 0.006 0.000 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: 1 poor density : 112 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 94 PHE cc_start: 0.7984 (m-80) cc_final: 0.7776 (m-80) REVERT: D 118 ASN cc_start: 0.6154 (m-40) cc_final: 0.5516 (t0) REVERT: D 127 GLN cc_start: 0.6611 (tt0) cc_final: 0.6400 (tt0) REVERT: D 174 MET cc_start: 0.6092 (ttp) cc_final: 0.5767 (ttp) REVERT: E 59 LEU cc_start: 0.6623 (mp) cc_final: 0.6398 (mp) REVERT: H 112 TRP cc_start: 0.7122 (m100) cc_final: 0.5792 (m100) REVERT: L 18 ARG cc_start: 0.7312 (mtm110) cc_final: 0.6994 (ttp-170) REVERT: L 56 SER cc_start: 0.8369 (m) cc_final: 0.8014 (p) REVERT: L 63 SER cc_start: 0.7915 (p) cc_final: 0.7550 (t) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.2214 time to fit residues: 32.3405 Evaluate side-chains 107 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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: 0.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 67 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6578 Z= 0.280 Angle : 0.657 7.166 8914 Z= 0.351 Chirality : 0.045 0.187 953 Planarity : 0.005 0.064 1151 Dihedral : 5.596 25.249 901 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % 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 (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: -0.44 (0.30), residues: 794 helix: 0.44 (0.47), residues: 116 sheet: 0.32 (0.31), residues: 263 loop : -0.89 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 47 HIS 0.012 0.002 HIS H 35 PHE 0.012 0.002 PHE H 95 TYR 0.019 0.002 TYR L 91 ARG 0.005 0.001 ARG A 66 *********************** 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 fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 47 TRP cc_start: 0.7295 (t60) cc_final: 0.7023 (t60) REVERT: D 118 ASN cc_start: 0.5988 (m-40) cc_final: 0.5410 (t0) REVERT: D 125 MET cc_start: 0.7806 (mtt) cc_final: 0.7541 (mtm) REVERT: D 131 LYS cc_start: 0.7192 (mptt) cc_final: 0.6794 (mptt) REVERT: D 174 MET cc_start: 0.6146 (ttp) cc_final: 0.5870 (ttp) REVERT: H 83 MET cc_start: 0.4542 (ttt) cc_final: 0.4169 (mmm) REVERT: H 112 TRP cc_start: 0.7118 (m100) cc_final: 0.5919 (m100) REVERT: L 18 ARG cc_start: 0.7265 (mtm110) cc_final: 0.6937 (ttp-170) REVERT: L 20 THR cc_start: 0.7851 (m) cc_final: 0.7441 (p) REVERT: L 63 SER cc_start: 0.7982 (p) cc_final: 0.7638 (t) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2556 time to fit residues: 36.3271 Evaluate side-chains 106 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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: 0.5980 chunk 18 optimal weight: 0.0670 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6578 Z= 0.216 Angle : 0.614 6.439 8914 Z= 0.326 Chirality : 0.044 0.148 953 Planarity : 0.006 0.077 1151 Dihedral : 5.342 28.118 901 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: -0.43 (0.30), residues: 794 helix: 0.52 (0.47), residues: 117 sheet: 0.30 (0.31), residues: 268 loop : -0.90 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 47 HIS 0.005 0.001 HIS A 72 PHE 0.013 0.002 PHE B 98 TYR 0.020 0.001 TYR E 63 ARG 0.006 0.001 ARG E 22 *********************** 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 : 0.686 Fit side-chains revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7681 (m-80) cc_final: 0.7292 (m-10) REVERT: A 47 TRP cc_start: 0.7271 (t60) cc_final: 0.7017 (t60) REVERT: D 118 ASN cc_start: 0.5996 (m-40) cc_final: 0.5441 (t0) REVERT: D 125 MET cc_start: 0.7811 (mtt) cc_final: 0.7610 (mtp) REVERT: D 174 MET cc_start: 0.6111 (ttp) cc_final: 0.5748 (ttp) REVERT: H 83 MET cc_start: 0.4503 (ttt) cc_final: 0.4146 (mmm) REVERT: H 112 TRP cc_start: 0.7193 (m100) cc_final: 0.5875 (m100) REVERT: L 18 ARG cc_start: 0.7206 (mtm110) cc_final: 0.6902 (ttp-170) REVERT: L 20 THR cc_start: 0.7785 (m) cc_final: 0.7400 (p) REVERT: L 63 SER cc_start: 0.8036 (p) cc_final: 0.7684 (t) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1973 time to fit residues: 29.1278 Evaluate side-chains 110 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 0.0270 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6578 Z= 0.266 Angle : 0.635 5.944 8914 Z= 0.341 Chirality : 0.045 0.186 953 Planarity : 0.006 0.054 1151 Dihedral : 5.453 25.996 901 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % 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 (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: -0.48 (0.30), residues: 794 helix: 0.41 (0.46), residues: 117 sheet: 0.26 (0.31), residues: 270 loop : -0.91 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 47 HIS 0.014 0.002 HIS H 35 PHE 0.014 0.002 PHE H 95 TYR 0.018 0.001 TYR E 63 ARG 0.007 0.001 ARG H 72 *********************** 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 111 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 TRP cc_start: 0.7304 (t60) cc_final: 0.6989 (t60) REVERT: D 118 ASN cc_start: 0.6014 (m-40) cc_final: 0.5446 (t0) REVERT: D 151 MET cc_start: 0.4901 (mmm) cc_final: 0.4679 (mmt) REVERT: D 174 MET cc_start: 0.6138 (ttp) cc_final: 0.5820 (ttp) REVERT: H 83 MET cc_start: 0.4520 (ttt) cc_final: 0.4137 (mmm) REVERT: H 112 TRP cc_start: 0.7206 (m100) cc_final: 0.5969 (m100) REVERT: L 20 THR cc_start: 0.7794 (m) cc_final: 0.7342 (p) REVERT: L 63 SER cc_start: 0.8057 (p) cc_final: 0.7690 (t) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2002 time to fit residues: 28.9861 Evaluate side-chains 105 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN D 127 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6578 Z= 0.323 Angle : 0.688 6.764 8914 Z= 0.370 Chirality : 0.047 0.217 953 Planarity : 0.006 0.054 1151 Dihedral : 5.785 26.882 901 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -0.69 (0.30), residues: 794 helix: 0.35 (0.46), residues: 115 sheet: 0.13 (0.32), residues: 267 loop : -1.08 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 35 HIS 0.011 0.002 HIS H 35 PHE 0.016 0.002 PHE B 94 TYR 0.020 0.002 TYR L 91 ARG 0.007 0.001 ARG D 124 *********************** 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 115 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 94 ARG cc_start: 0.7274 (ttt180) cc_final: 0.6811 (ttm170) REVERT: D 117 ARG cc_start: 0.6589 (tpt90) cc_final: 0.6146 (tpt90) REVERT: D 118 ASN cc_start: 0.5908 (m-40) cc_final: 0.5354 (t0) REVERT: H 6 GLU cc_start: 0.6602 (mp0) cc_final: 0.6386 (mp0) REVERT: H 35 HIS cc_start: 0.6499 (m90) cc_final: 0.6259 (m-70) REVERT: H 83 MET cc_start: 0.4594 (ttt) cc_final: 0.4230 (mmm) REVERT: H 112 TRP cc_start: 0.7267 (m100) cc_final: 0.6956 (m100) REVERT: L 63 SER cc_start: 0.8015 (p) cc_final: 0.7687 (t) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2103 time to fit residues: 31.1683 Evaluate side-chains 107 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 chunk 66 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5887 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6578 Z= 0.252 Angle : 0.642 8.372 8914 Z= 0.340 Chirality : 0.046 0.205 953 Planarity : 0.005 0.055 1151 Dihedral : 5.574 29.815 901 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -0.74 (0.30), residues: 794 helix: 0.18 (0.44), residues: 122 sheet: 0.11 (0.31), residues: 267 loop : -1.10 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 35 HIS 0.007 0.001 HIS H 35 PHE 0.012 0.002 PHE H 95 TYR 0.021 0.001 TYR E 63 ARG 0.006 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 9 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 fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.5706 (m-30) cc_final: 0.5183 (m-30) REVERT: A 94 ARG cc_start: 0.7215 (ttt180) cc_final: 0.6672 (ttm170) REVERT: D 117 ARG cc_start: 0.6591 (tpt90) cc_final: 0.6281 (tpt90) REVERT: D 118 ASN cc_start: 0.5938 (m-40) cc_final: 0.5463 (t0) REVERT: D 174 MET cc_start: 0.6133 (ttp) cc_final: 0.5810 (ttp) REVERT: H 83 MET cc_start: 0.4517 (ttt) cc_final: 0.4216 (mmm) REVERT: H 112 TRP cc_start: 0.7270 (m100) cc_final: 0.6098 (m100) REVERT: L 20 THR cc_start: 0.7749 (m) cc_final: 0.7318 (p) REVERT: L 63 SER cc_start: 0.8081 (p) cc_final: 0.7716 (t) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2014 time to fit residues: 28.5489 Evaluate side-chains 102 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6578 Z= 0.249 Angle : 0.635 6.940 8914 Z= 0.338 Chirality : 0.046 0.170 953 Planarity : 0.005 0.054 1151 Dihedral : 5.526 28.243 901 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.72 (0.30), residues: 794 helix: 0.49 (0.46), residues: 116 sheet: 0.02 (0.32), residues: 267 loop : -1.08 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 35 HIS 0.011 0.001 HIS H 35 PHE 0.016 0.002 PHE H 95 TYR 0.024 0.002 TYR E 63 ARG 0.007 0.001 ARG H 72 ********************** REFINEMENT MACRO_CYCLE 10 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 : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.5695 (m-30) cc_final: 0.5196 (m-30) REVERT: A 94 ARG cc_start: 0.7233 (ttt180) cc_final: 0.6695 (ttm170) REVERT: D 117 ARG cc_start: 0.6635 (tpt90) cc_final: 0.6227 (tpt90) REVERT: D 118 ASN cc_start: 0.6004 (m-40) cc_final: 0.5500 (t0) REVERT: D 174 MET cc_start: 0.6149 (ttp) cc_final: 0.5823 (ttp) REVERT: E 61 LEU cc_start: 0.7450 (tp) cc_final: 0.7097 (tt) REVERT: H 83 MET cc_start: 0.4516 (ttt) cc_final: 0.4071 (mmm) REVERT: H 112 TRP cc_start: 0.7281 (m100) cc_final: 0.6926 (m100) REVERT: L 63 SER cc_start: 0.8023 (p) cc_final: 0.7808 (t) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1991 time to fit residues: 29.0626 Evaluate side-chains 104 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.174898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.163259 restraints weight = 11093.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.165676 restraints weight = 6825.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.167423 restraints weight = 4561.529| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6578 Z= 0.324 Angle : 0.694 9.219 8914 Z= 0.372 Chirality : 0.047 0.185 953 Planarity : 0.006 0.056 1151 Dihedral : 5.856 29.463 901 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -0.92 (0.29), residues: 794 helix: 0.36 (0.46), residues: 115 sheet: -0.05 (0.32), residues: 265 loop : -1.26 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 35 HIS 0.008 0.001 HIS H 35 PHE 0.017 0.002 PHE D 183 TYR 0.025 0.002 TYR L 91 ARG 0.008 0.001 ARG D 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1765.49 seconds wall clock time: 33 minutes 14.20 seconds (1994.20 seconds total)