Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 10:29:09 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5a_4413/01_2021/6i5a_4413.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5a_4413/01_2021/6i5a_4413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5a_4413/01_2021/6i5a_4413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5a_4413/01_2021/6i5a_4413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5a_4413/01_2021/6i5a_4413.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5a_4413/01_2021/6i5a_4413.pdb" } resolution = 2.3 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= 0.000 sd= 0.006 Set model interpretation parameters 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 Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 1206 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Time building chain proxies: 1.09, per 1000 atoms: 0.90 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Number of scatterers: 1206 At special positions: 0 Unit cell: (53.175, 78.699, 49.9845, 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 1 16.00 O 236 8.00 N 210 7.00 C 759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.45 Conformation dependent library (CDL) restraints added in 273.4 milliseconds 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 296 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 1 sheets defined 64.7% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 removed outlier: 4.309A pdb=" N VAL A 12 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 32 Processing helix chain 'A' and resid 38 through 52 removed outlier: 3.530A pdb=" N VAL A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.987A pdb=" N LEU A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 104 through 136 Processing helix chain 'A' and resid 141 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 72 hydrogen bonds defined for protein. 198 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: 0.32 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 242 1.32 - 1.45: 300 1.45 - 1.57: 687 1.57 - 1.69: 0 1.69 - 1.81: 1 Bond restraints: 1230 Sorted by residual: bond pdb=" N LYS A 54 " pdb=" CA LYS A 54 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.56e+01 bond pdb=" N VAL A 61 " pdb=" CA VAL A 61 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N LEU A 151 " pdb=" CA LEU A 151 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.27e-02 6.20e+03 1.00e+01 bond pdb=" N TYR A 3 " pdb=" CA TYR A 3 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.17e-02 7.31e+03 9.16e+00 bond pdb=" N TRP A 18 " pdb=" CA TRP A 18 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.25e-02 6.40e+03 8.87e+00 ... (remaining 1225 not shown) Histogram of bond angle deviations from ideal: 102.59 - 108.93: 126 108.93 - 115.27: 638 115.27 - 121.61: 561 121.61 - 127.95: 346 127.95 - 134.29: 10 Bond angle restraints: 1681 Sorted by residual: angle pdb=" C THR A 38 " pdb=" N GLN A 39 " pdb=" CA GLN A 39 " ideal model delta sigma weight residual 120.28 127.51 -7.23 1.34e+00 5.57e-01 2.91e+01 angle pdb=" CA PHE A 49 " pdb=" C PHE A 49 " pdb=" O PHE A 49 " ideal model delta sigma weight residual 120.90 115.63 5.27 1.07e+00 8.73e-01 2.43e+01 angle pdb=" CB GLU A 132 " pdb=" CG GLU A 132 " pdb=" CD GLU A 132 " ideal model delta sigma weight residual 112.60 120.28 -7.68 1.70e+00 3.46e-01 2.04e+01 angle pdb=" CB GLU A 146 " pdb=" CG GLU A 146 " pdb=" CD GLU A 146 " ideal model delta sigma weight residual 112.60 120.06 -7.46 1.70e+00 3.46e-01 1.92e+01 angle pdb=" C ALA A 118 " pdb=" N THR A 119 " pdb=" CA THR A 119 " ideal model delta sigma weight residual 120.28 126.11 -5.83 1.34e+00 5.57e-01 1.89e+01 ... (remaining 1676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.71: 649 14.71 - 29.41: 69 29.41 - 44.12: 10 44.12 - 58.83: 5 58.83 - 73.54: 4 Dihedral angle restraints: 737 sinusoidal: 285 harmonic: 452 Sorted by residual: dihedral pdb=" C PHE A 36 " pdb=" N PHE A 36 " pdb=" CA PHE A 36 " pdb=" CB PHE A 36 " ideal model delta harmonic sigma weight residual -122.60 -136.38 13.78 0 2.50e+00 1.60e-01 3.04e+01 dihedral pdb=" N PHE A 36 " pdb=" C PHE A 36 " pdb=" CA PHE A 36 " pdb=" CB PHE A 36 " ideal model delta harmonic sigma weight residual 122.80 133.25 -10.45 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" CA PRO A 64 " pdb=" C PRO A 64 " pdb=" N ASP A 65 " pdb=" CA ASP A 65 " ideal model delta harmonic sigma weight residual -180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 121 0.090 - 0.181: 65 0.181 - 0.271: 10 0.271 - 0.362: 0 0.362 - 0.452: 2 Chirality restraints: 198 Sorted by residual: chirality pdb=" CA PHE A 36 " pdb=" N PHE A 36 " pdb=" C PHE A 36 " pdb=" CB PHE A 36 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CB VAL A 131 " pdb=" CA VAL A 131 " pdb=" CG1 VAL A 131 " pdb=" CG2 VAL A 131 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA GLU A 98 " pdb=" N GLU A 98 " pdb=" C GLU A 98 " pdb=" CB GLU A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 195 not shown) Planarity restraints: 219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 49 " -0.021 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" C PHE A 49 " 0.076 2.00e-02 2.50e+03 pdb=" O PHE A 49 " -0.028 2.00e-02 2.50e+03 pdb=" N SER A 50 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 53 " 0.030 2.00e-02 2.50e+03 1.64e-02 6.69e+00 pdb=" CG TRP A 53 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 53 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP A 53 " -0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP A 53 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 53 " 0.020 2.00e-02 2.50e+03 pdb=" CE3 TRP A 53 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 53 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 53 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 53 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 3 " 0.026 2.00e-02 2.50e+03 1.46e-02 4.27e+00 pdb=" CG TYR A 3 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 3 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 3 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 3 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 3 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 3 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 3 " 0.005 2.00e-02 2.50e+03 ... (remaining 216 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 481 2.92 - 3.42: 1315 3.42 - 3.91: 2082 3.91 - 4.41: 2252 4.41 - 4.90: 3625 Nonbonded interactions: 9755 Sorted by model distance: nonbonded pdb=" N ASP A 65 " pdb=" OD1 ASP A 65 " model vdw 2.431 2.520 nonbonded pdb=" N ASN A 99 " pdb=" OD1 ASN A 99 " model vdw 2.433 2.520 nonbonded pdb=" O SER A 16 " pdb=" OG SER A 16 " model vdw 2.499 2.440 nonbonded pdb=" N ASN A 141 " pdb=" O ASN A 141 " model vdw 2.544 2.496 nonbonded pdb=" O PHE A 36 " pdb=" NH1 ARG A 42 " model vdw 2.566 2.520 ... (remaining 9750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 1206 True True 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 1 5.16 5 C 759 2.51 5 N 210 2.21 5 O 236 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 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: 12.620 Set model interpretation parameters: 0.210 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: 43.650 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.030 Process input model: 12.650 Set up NCS constraints: 0.010 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: 0.000 Load rotamer database and sin/cos tables:10.470 Internal consistency checks: 0.000 Total: 79.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.012 0.040 1230 Angle : 1.837 8.286 1681 Chirality : 0.104 0.452 198 Planarity : 0.009 0.077 219 Dihedral : 14.159 73.535 441 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 1.32 % Allowed : 1.32 % Favored : 97.35 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.68 % 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: -0.89 (0.60), residues: 151 helix: -0.13 (0.49), residues: 80 sheet: None (None), residues: 0 loop : -1.06 (0.69), residues: 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.134 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.8345 time to fit residues: 29.4353 Evaluate side-chains 27 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.022 1230 Angle : 0.552 5.663 1681 Chirality : 0.037 0.116 198 Planarity : 0.005 0.034 219 Dihedral : 4.398 15.987 167 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 2.96 % 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: 1.89 (0.66), residues: 151 helix: 2.92 (0.50), residues: 80 sheet: None (None), residues: 0 loop : -0.78 (0.73), residues: 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.159 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.8571 time to fit residues: 25.0975 Evaluate side-chains 27 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.152 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.9365 time to fit residues: 2.0753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.025 1230 Angle : 0.531 5.827 1681 Chirality : 0.037 0.115 198 Planarity : 0.005 0.032 219 Dihedral : 4.278 16.195 167 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 2.96 % 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: 2.06 (0.68), residues: 151 helix: 2.58 (0.53), residues: 86 sheet: None (None), residues: 0 loop : -0.32 (0.80), residues: 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.153 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.9678 time to fit residues: 27.3389 Evaluate side-chains 29 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.154 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 2 average time/residue: 1.0265 time to fit residues: 2.2439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.030 1230 Angle : 0.513 5.969 1681 Chirality : 0.036 0.112 198 Planarity : 0.005 0.030 219 Dihedral : 4.212 16.294 167 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 3.70 % 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: 2.03 (0.70), residues: 151 helix: 2.97 (0.53), residues: 80 sheet: None (None), residues: 0 loop : -0.63 (0.79), residues: 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.151 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 27 average time/residue: 0.9344 time to fit residues: 25.4663 Evaluate side-chains 28 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.141 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0658 time to fit residues: 0.2618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.029 1230 Angle : 0.532 6.078 1681 Chirality : 0.037 0.112 198 Planarity : 0.005 0.035 219 Dihedral : 4.277 16.877 167 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 3.70 % 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: 1.97 (0.70), residues: 151 helix: 2.83 (0.53), residues: 80 sheet: None (None), residues: 0 loop : -0.52 (0.80), residues: 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.154 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 27 average time/residue: 0.8761 time to fit residues: 23.8960 Evaluate side-chains 29 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.160 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.7044 time to fit residues: 2.3177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.032 1230 Angle : 0.520 6.071 1681 Chirality : 0.037 0.111 198 Planarity : 0.005 0.031 219 Dihedral : 4.216 16.785 167 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 2.96 % 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: 2.06 (0.71), residues: 151 helix: 2.86 (0.54), residues: 80 sheet: None (None), residues: 0 loop : -0.42 (0.81), residues: 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.146 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 26 average time/residue: 0.8532 time to fit residues: 22.4200 Evaluate side-chains 27 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.151 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.7470 time to fit residues: 1.9460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.033 1230 Angle : 0.509 6.047 1681 Chirality : 0.036 0.110 198 Planarity : 0.004 0.028 219 Dihedral : 4.122 16.569 167 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 4.44 % 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: 2.27 (0.72), residues: 151 helix: 2.53 (0.55), residues: 86 sheet: None (None), residues: 0 loop : 0.15 (0.88), residues: 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.152 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 26 average time/residue: 0.8950 time to fit residues: 23.5688 Evaluate side-chains 26 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.165 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0786 time to fit residues: 0.3636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.028 1230 Angle : 0.557 6.220 1681 Chirality : 0.038 0.116 198 Planarity : 0.005 0.042 219 Dihedral : 4.377 17.374 167 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 2.96 % 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: 2.02 (0.71), residues: 151 helix: 2.70 (0.54), residues: 80 sheet: None (None), residues: 0 loop : -0.27 (0.82), residues: 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.160 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 24 average time/residue: 0.9622 time to fit residues: 23.3409 Evaluate side-chains 24 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.152 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0645 time to fit residues: 0.2623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.032 1230 Angle : 0.524 6.082 1681 Chirality : 0.037 0.111 198 Planarity : 0.005 0.029 219 Dihedral : 4.202 16.802 167 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 2.96 % 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: 2.17 (0.72), residues: 151 helix: 2.43 (0.54), residues: 86 sheet: None (None), residues: 0 loop : 0.12 (0.87), residues: 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.154 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 24 average time/residue: 0.8405 time to fit residues: 20.4130 Evaluate side-chains 24 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.148 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.1938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.032 1230 Angle : 0.521 6.146 1681 Chirality : 0.037 0.111 198 Planarity : 0.004 0.030 219 Dihedral : 4.175 16.794 167 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 2.22 % 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: 2.13 (0.71), residues: 151 helix: 2.84 (0.54), residues: 80 sheet: None (None), residues: 0 loop : -0.28 (0.81), residues: 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 302 Ramachandran restraints generated. 151 Oldfield and 0 Emsley and 151 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.142 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.9004 time to fit residues: 21.8544 Evaluate side-chains 25 residues out of total 135 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.158 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0680 time to fit residues: 0.2658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.189918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.174719 restraints weight = 1580.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.175411 restraints weight = 1217.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.176002 restraints weight = 1062.700| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.005 0.029 1230 ANGLE : 0.615 6.443 1681 CHIRALITY : 0.041 0.124 198 PLANARITY : 0.006 0.056 219 DIHEDRAL : 4.600 18.096 167 MIN NONBONDED DISTANCE : 2.314 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 2.93 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.32 % FAVORED : 98.68 % ROTAMER OUTLIERS : 1.48 % 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: 1.77 (0.70), RESIDUES: 151 HELIX: 2.50 (0.55), RESIDUES: 80 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -0.39 (0.80), RESIDUES: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.029 1230 Angle : 0.615 6.443 1681 Chirality : 0.041 0.124 198 Planarity : 0.006 0.056 219 Dihedral : 4.600 18.096 167 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 1.48 % 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: 1.77 (0.70), residues: 151 helix: 2.50 (0.55), residues: 80 sheet: None (None), residues: 0 loop : -0.39 (0.80), residues: 71 =============================================================================== Job complete usr+sys time: 1508.53 seconds wall clock time: 27 minutes 25.39 seconds (1645.39 seconds total)