Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 18:08:40 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/12_2021/7kbb_22788_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/12_2021/7kbb_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_22788/12_2021/7kbb_22788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/12_2021/7kbb_22788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/12_2021/7kbb_22788_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kbb_22788/12_2021/7kbb_22788_neut.pdb" } 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 ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/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: {'PTRANS': 4, 'TRANS': 100, 'PCIS': 2} 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: {'PTRANS': 10, 'TRANS': 158, 'PCIS': 1} 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: {'PTRANS': 5, 'TRANS': 100, 'PCIS': 2} Time building chain proxies: 3.90, per 1000 atoms: 0.61 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 Amimo 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 1.1 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: 0.47 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: 1.93 Time building geometry restraints manager: 2.50 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 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. 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 Write .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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.370 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.060 Process input model: 20.260 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 36.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 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 % 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 *********************** 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 : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 132 average time/residue: 0.1968 time to fit residues: 33.7287 Evaluate side-chains 113 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0626 time to fit residues: 1.8242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.0670 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 35 HIS ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5826 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 6578 Z= 0.265 Angle : 0.718 11.502 8914 Z= 0.382 Chirality : 0.046 0.267 953 Planarity : 0.007 0.141 1151 Dihedral : 5.309 27.823 901 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.43 % 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: -0.47 (0.29), residues: 794 helix: 0.85 (0.48), residues: 110 sheet: 0.16 (0.31), residues: 267 loop : -0.92 (0.29), residues: 417 *********************** 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 114 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 113 average time/residue: 0.1941 time to fit residues: 28.9122 Evaluate side-chains 102 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0192 ------------------------------------------------------------------------------- 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: 0.7980 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.0370 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.0970 chunk 24 optimal weight: 0.0270 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 overall best weight: 0.2714 ------------------------------------------------------------------------------- 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 37 GLN D 97 GLN E 21 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 6578 Z= 0.184 Angle : 0.600 7.936 8914 Z= 0.318 Chirality : 0.043 0.223 953 Planarity : 0.005 0.055 1151 Dihedral : 5.017 25.915 901 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.00 % 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: -0.07 (0.30), residues: 794 helix: 1.02 (0.48), residues: 116 sheet: 0.54 (0.32), residues: 265 loop : -0.73 (0.30), residues: 413 *********************** 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 108 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.672 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1953 time to fit residues: 27.7539 Evaluate side-chains 102 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.659 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0080 ------------------------------------------------------------------------------- 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: 0.5980 chunk 7 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 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: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 89 GLN D 97 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 6578 Z= 0.290 Angle : 0.680 7.679 8914 Z= 0.360 Chirality : 0.045 0.248 953 Planarity : 0.005 0.039 1151 Dihedral : 5.332 27.322 901 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.00 % 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: -0.15 (0.30), residues: 794 helix: 0.62 (0.47), residues: 117 sheet: 0.60 (0.32), residues: 263 loop : -0.76 (0.31), residues: 414 *********************** 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 112 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2002 time to fit residues: 29.3011 Evaluate side-chains 106 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.748 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1020 ------------------------------------------------------------------------------- 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: 0.9980 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.0020 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 25 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 overall best weight: 0.3788 ------------------------------------------------------------------------------- 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 3 GLN B 89 GLN B 92 ASN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 6578 Z= 0.205 Angle : 0.588 6.586 8914 Z= 0.314 Chirality : 0.043 0.166 953 Planarity : 0.005 0.080 1151 Dihedral : 5.143 24.394 901 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.00 % 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: -0.08 (0.30), residues: 794 helix: 1.06 (0.48), residues: 111 sheet: 0.59 (0.32), residues: 263 loop : -0.77 (0.31), residues: 420 *********************** 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 107 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.731 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1909 time to fit residues: 27.0561 Evaluate side-chains 102 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0310 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN ** B 90 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 97 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.3737 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= 0.343 Angle : 0.699 6.475 8914 Z= 0.377 Chirality : 0.047 0.186 953 Planarity : 0.007 0.107 1151 Dihedral : 5.787 28.758 901 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 0.00 % 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: -0.54 (0.30), residues: 794 helix: 0.05 (0.46), residues: 123 sheet: 0.30 (0.32), residues: 267 loop : -0.90 (0.32), residues: 404 *********************** 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 : 0.754 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2023 time to fit residues: 29.7696 Evaluate side-chains 103 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.626 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9756 ------------------------------------------------------------------------------- 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: 0.7980 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 0.1980 chunk 75 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 46 optimal weight: 0.0980 chunk 30 optimal weight: 0.0170 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.1418 ------------------------------------------------------------------------------- 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 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS L 32 ASN L 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 6578 Z= 0.168 Angle : 0.587 5.938 8914 Z= 0.312 Chirality : 0.043 0.186 953 Planarity : 0.005 0.059 1151 Dihedral : 5.169 26.057 901 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.14 % 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: -0.18 (0.30), residues: 794 helix: 0.63 (0.48), residues: 117 sheet: 0.48 (0.31), residues: 268 loop : -0.72 (0.32), residues: 409 *********************** 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 106 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.749 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.1787 time to fit residues: 25.2466 Evaluate side-chains 99 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.609 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0382 ------------------------------------------------------------------------------- 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: 0.0670 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** 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: 0.5946 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 6578 Z= 0.296 Angle : 0.659 8.040 8914 Z= 0.354 Chirality : 0.045 0.206 953 Planarity : 0.007 0.116 1151 Dihedral : 5.524 26.069 901 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.30), residues: 794 helix: 0.11 (0.46), residues: 123 sheet: 0.28 (0.31), residues: 270 loop : -0.97 (0.32), residues: 401 *********************** 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 113 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.744 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1945 time to fit residues: 28.8679 Evaluate side-chains 104 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0194 ------------------------------------------------------------------------------- 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: 0.0070 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.0000 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 chunk 46 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 35 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 overall best weight: 0.1320 ------------------------------------------------------------------------------- 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN D 97 GLN D 181 HIS ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 6578 Z= 0.156 Angle : 0.576 6.535 8914 Z= 0.303 Chirality : 0.042 0.168 953 Planarity : 0.005 0.046 1151 Dihedral : 5.022 27.326 901 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.00 % 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: -0.22 (0.30), residues: 794 helix: 0.76 (0.48), residues: 117 sheet: 0.44 (0.32), residues: 267 loop : -0.78 (0.32), residues: 410 *********************** 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 104 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1935 time to fit residues: 26.7021 Evaluate side-chains 95 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0440 ------------------------------------------------------------------------------- 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: 0.3980 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.0020 chunk 9 optimal weight: 0.5980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 3 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN D 181 HIS ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 6578 Z= 0.229 Angle : 0.617 6.457 8914 Z= 0.326 Chirality : 0.044 0.216 953 Planarity : 0.007 0.126 1151 Dihedral : 5.166 26.501 901 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.00 % 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 (0.30), residues: 794 helix: 0.39 (0.47), residues: 123 sheet: 0.36 (0.32), residues: 269 loop : -0.89 (0.32), residues: 402 ********************** 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 105 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.727 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2046 time to fit residues: 28.6259 Evaluate side-chains 99 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.760 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0783 ------------------------------------------------------------------------------- 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: 0.9980 chunk 61 optimal weight: 0.0020 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 3 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN D 181 HIS ** L 89 GLN ** 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 = 0.4307 r_free = 0.4307 target = 0.182878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.174992 restraints weight = 12937.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.175943 restraints weight = 9654.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.176630 restraints weight = 7668.421| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.471 6578 Z= 0.595 Angle : 1.112 74.595 8914 Z= 0.562 Chirality : 0.045 0.165 953 Planarity : 0.006 0.113 1151 Dihedral : 5.232 26.244 901 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 0.00 % 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: 0.35 (0.47), residues: 123 sheet: 0.33 (0.32), residues: 269 loop : -0.91 (0.32), residues: 402 =============================================================================== Job complete usr+sys time: 1701.02 seconds wall clock time: 31 minutes 30.35 seconds (1890.35 seconds total)