Starting phenix.real_space_refine (version: dev) on Sun Dec 11 14:36:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p16_13157/12_2022/7p16_13157_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p16_13157/12_2022/7p16_13157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p16_13157/12_2022/7p16_13157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p16_13157/12_2022/7p16_13157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p16_13157/12_2022/7p16_13157_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p16_13157/12_2022/7p16_13157_updated.pdb" } resolution = 4.3 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= 0.003 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A GLU 260": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 3621 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2617 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 7, 'TRANS': 310} Chain breaks: 2 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 2.56, per 1000 atoms: 0.71 Number of scatterers: 3621 At special positions: 0 Unit cell: (76.818, 102.858, 70.308, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 1 15.00 O 624 8.00 N 561 7.00 C 2412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 102 " distance=2.03 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: 1.42 Conformation dependent library (CDL) restraints added in 620.1 milliseconds 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 2 sheets defined 61.3% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 removed outlier: 3.815A pdb=" N MET A 10 " --> pdb=" O CYS A 6 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY A 14 " --> pdb=" O MET A 10 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 66 removed outlier: 3.565A pdb=" N PHE A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 88 through 104 removed outlier: 3.605A pdb=" N PHE A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 140 removed outlier: 3.521A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 removed outlier: 4.092A pdb=" N LEU A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 199 through 226 removed outlier: 3.719A pdb=" N LEU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 249 removed outlier: 3.606A pdb=" N PHE A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.761A pdb=" N VAL A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 285 through 307 removed outlier: 3.513A pdb=" N VAL A 293 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 342 removed outlier: 3.992A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Proline residue: A 320 - end of helix removed outlier: 3.754A pdb=" N VAL A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing sheet with id= A, first strand: chain 'B' and resid 9 through 13 Processing sheet with id= B, first strand: chain 'B' and resid 126 through 128 removed outlier: 3.764A pdb=" N VAL B 128 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 98 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 101 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 103 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 55 " --> pdb=" O TRP B 42 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG B 44 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY B 53 " --> pdb=" O ARG B 44 " (cutoff:3.500A) 212 hydrogen bonds defined for protein. 624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 526 1.31 - 1.44: 1140 1.44 - 1.56: 2016 1.56 - 1.69: 2 1.69 - 1.81: 34 Bond restraints: 3718 Sorted by residual: bond pdb=" C' PLC A 401 " pdb=" O2 PLC A 401 " ideal model delta sigma weight residual 1.332 1.425 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CB PLC A 401 " pdb=" O3 PLC A 401 " ideal model delta sigma weight residual 1.327 1.420 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C' PLC A 401 " pdb=" C1' PLC A 401 " ideal model delta sigma weight residual 1.503 1.553 -0.050 2.00e-02 2.50e+03 6.23e+00 bond pdb=" C4 PLC A 401 " pdb=" C5 PLC A 401 " ideal model delta sigma weight residual 1.511 1.558 -0.047 2.00e-02 2.50e+03 5.62e+00 bond pdb=" CB PLC A 401 " pdb=" C1B PLC A 401 " ideal model delta sigma weight residual 1.504 1.551 -0.047 2.00e-02 2.50e+03 5.48e+00 ... (remaining 3713 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.96: 70 106.96 - 113.72: 2033 113.72 - 120.47: 1486 120.47 - 127.23: 1424 127.23 - 133.99: 39 Bond angle restraints: 5052 Sorted by residual: angle pdb=" O3P PLC A 401 " pdb=" P PLC A 401 " pdb=" O4P PLC A 401 " ideal model delta sigma weight residual 93.62 109.68 -16.06 3.00e+00 1.11e-01 2.87e+01 angle pdb=" C5 PLC A 401 " pdb=" N PLC A 401 " pdb=" C7 PLC A 401 " ideal model delta sigma weight residual 106.97 119.04 -12.07 3.00e+00 1.11e-01 1.62e+01 angle pdb=" N LEU B 114 " pdb=" CA LEU B 114 " pdb=" C LEU B 114 " ideal model delta sigma weight residual 114.56 109.89 4.67 1.27e+00 6.20e-01 1.35e+01 angle pdb=" C ILE A 278 " pdb=" N LYS A 279 " pdb=" CA LYS A 279 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" O1P PLC A 401 " pdb=" P PLC A 401 " pdb=" O2P PLC A 401 " ideal model delta sigma weight residual 119.61 109.03 10.58 3.00e+00 1.11e-01 1.24e+01 ... (remaining 5047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 1891 17.99 - 35.97: 162 35.97 - 53.96: 48 53.96 - 71.95: 5 71.95 - 89.93: 4 Dihedral angle restraints: 2110 sinusoidal: 813 harmonic: 1297 Sorted by residual: dihedral pdb=" CA ILE A 16 " pdb=" C ILE A 16 " pdb=" N ILE A 17 " pdb=" CA ILE A 17 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CG ARG B 118 " pdb=" CD ARG B 118 " pdb=" NE ARG B 118 " pdb=" CZ ARG B 118 " ideal model delta sinusoidal sigma weight residual 90.00 130.89 -40.89 2 1.50e+01 4.44e-03 9.14e+00 dihedral pdb=" CB GLU A 260 " pdb=" CG GLU A 260 " pdb=" CD GLU A 260 " pdb=" OE1 GLU A 260 " ideal model delta sinusoidal sigma weight residual 0.00 -81.53 81.53 1 3.00e+01 1.11e-03 9.09e+00 ... (remaining 2107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 385 0.033 - 0.067: 148 0.067 - 0.100: 30 0.100 - 0.133: 8 0.133 - 0.166: 1 Chirality restraints: 572 Sorted by residual: chirality pdb=" C2 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C3 PLC A 401 " pdb=" O2 PLC A 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.48 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CG LEU B 87 " pdb=" CB LEU B 87 " pdb=" CD1 LEU B 87 " pdb=" CD2 LEU B 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.71 0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 569 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 190 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 191 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 73 " 0.130 9.50e-02 1.11e+02 5.86e-02 2.24e+00 pdb=" NE ARG B 73 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 73 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 73 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 73 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 123 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" CD GLU A 123 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLU A 123 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU A 123 " 0.008 2.00e-02 2.50e+03 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 101 2.72 - 3.27: 3874 3.27 - 3.81: 5813 3.81 - 4.36: 6628 4.36 - 4.90: 11146 Nonbonded interactions: 27562 Sorted by model distance: nonbonded pdb=" O THR A 139 " pdb=" N GLY A 143 " model vdw 2.178 2.520 nonbonded pdb=" NZ LYS A 209 " pdb=" OG1 THR A 274 " model vdw 2.261 2.520 nonbonded pdb=" OG SER A 132 " pdb=" OD2 ASP A 181 " model vdw 2.291 2.440 nonbonded pdb=" OE1 GLU B 12 " pdb=" N GLY B 125 " model vdw 2.347 2.520 nonbonded pdb=" O CYS B 28 " pdb=" OG1 THR B 84 " model vdw 2.357 2.440 ... (remaining 27557 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 23 5.16 5 C 2412 2.51 5 N 561 2.21 5 O 624 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 Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.510 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 14.090 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.004 0.093 3718 Z= 0.266 Angle : 0.733 16.060 5052 Z= 0.340 Chirality : 0.037 0.166 572 Planarity : 0.004 0.059 604 Dihedral : 15.072 89.932 1283 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.40), residues: 436 helix: 0.55 (0.32), residues: 249 sheet: 0.04 (0.84), residues: 44 loop : -1.00 (0.54), residues: 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.437 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1681 time to fit residues: 26.5271 Evaluate side-chains 115 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 183 GLN A 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3718 Z= 0.228 Angle : 0.594 7.063 5052 Z= 0.306 Chirality : 0.040 0.137 572 Planarity : 0.004 0.054 604 Dihedral : 6.535 57.255 510 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.40), residues: 436 helix: 1.16 (0.30), residues: 257 sheet: 0.77 (0.92), residues: 36 loop : -1.03 (0.55), residues: 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.418 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1496 time to fit residues: 24.6639 Evaluate side-chains 116 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3718 Z= 0.207 Angle : 0.581 7.457 5052 Z= 0.295 Chirality : 0.040 0.139 572 Planarity : 0.004 0.055 604 Dihedral : 5.948 54.136 510 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.41), residues: 436 helix: 1.34 (0.30), residues: 257 sheet: 0.78 (0.83), residues: 50 loop : -1.13 (0.59), residues: 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.463 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1534 time to fit residues: 26.2039 Evaluate side-chains 118 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3718 Z= 0.179 Angle : 0.564 7.413 5052 Z= 0.283 Chirality : 0.039 0.132 572 Planarity : 0.004 0.053 604 Dihedral : 5.839 56.449 510 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.41), residues: 436 helix: 1.48 (0.30), residues: 259 sheet: 0.69 (0.76), residues: 57 loop : -1.18 (0.61), residues: 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.417 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1412 time to fit residues: 23.5722 Evaluate side-chains 115 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.454 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.0370 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3718 Z= 0.165 Angle : 0.572 7.587 5052 Z= 0.281 Chirality : 0.039 0.133 572 Planarity : 0.004 0.053 604 Dihedral : 5.715 55.954 510 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.99 (0.41), residues: 436 helix: 1.56 (0.31), residues: 259 sheet: 0.48 (0.73), residues: 59 loop : -1.28 (0.63), residues: 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.446 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1421 time to fit residues: 23.9275 Evaluate side-chains 112 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3718 Z= 0.178 Angle : 0.574 7.399 5052 Z= 0.284 Chirality : 0.039 0.130 572 Planarity : 0.004 0.056 604 Dihedral : 5.611 54.942 510 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.41), residues: 436 helix: 1.61 (0.31), residues: 259 sheet: 0.73 (0.82), residues: 52 loop : -1.20 (0.60), residues: 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.432 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1618 time to fit residues: 26.4057 Evaluate side-chains 113 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 0.0000 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 overall best weight: 0.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 3718 Z= 0.146 Angle : 0.578 7.426 5052 Z= 0.281 Chirality : 0.038 0.134 572 Planarity : 0.004 0.057 604 Dihedral : 5.358 51.675 510 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.15 (0.42), residues: 436 helix: 1.71 (0.31), residues: 258 sheet: 0.78 (0.82), residues: 52 loop : -1.26 (0.60), residues: 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.404 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1713 time to fit residues: 28.2814 Evaluate side-chains 111 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 32 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 121 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 0.038 3718 Z= 0.198 Angle : 0.600 7.306 5052 Z= 0.300 Chirality : 0.040 0.204 572 Planarity : 0.004 0.059 604 Dihedral : 5.478 51.586 510 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.41), residues: 436 helix: 1.56 (0.31), residues: 261 sheet: 0.73 (0.81), residues: 45 loop : -1.33 (0.58), residues: 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.361 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1441 time to fit residues: 23.6974 Evaluate side-chains 113 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3718 Z= 0.189 Angle : 0.607 7.832 5052 Z= 0.300 Chirality : 0.040 0.131 572 Planarity : 0.004 0.061 604 Dihedral : 5.445 50.832 510 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.42), residues: 436 helix: 1.64 (0.31), residues: 258 sheet: 0.48 (0.73), residues: 59 loop : -1.39 (0.62), residues: 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.439 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1560 time to fit residues: 25.6127 Evaluate side-chains 109 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 3718 Z= 0.271 Angle : 0.691 8.307 5052 Z= 0.343 Chirality : 0.043 0.143 572 Planarity : 0.005 0.062 604 Dihedral : 5.785 54.118 510 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.41), residues: 436 helix: 1.44 (0.31), residues: 258 sheet: 0.50 (0.72), residues: 57 loop : -1.38 (0.61), residues: 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.411 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1469 time to fit residues: 23.5365 Evaluate side-chains 113 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.0370 chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 HIS A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.169262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140214 restraints weight = 5263.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.138197 restraints weight = 8019.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.139068 restraints weight = 7938.302| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3718 Z= 0.191 Angle : 0.672 8.450 5052 Z= 0.331 Chirality : 0.042 0.158 572 Planarity : 0.005 0.063 604 Dihedral : 5.660 52.695 510 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.41), residues: 436 helix: 1.36 (0.31), residues: 257 sheet: 0.32 (0.72), residues: 59 loop : -1.43 (0.62), residues: 120 =============================================================================== Job complete usr+sys time: 1192.61 seconds wall clock time: 22 minutes 9.66 seconds (1329.66 seconds total)