Starting phenix.real_space_refine on Thu Dec 7 15:49:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/12_2023/7abk_11698.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/12_2023/7abk_11698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/12_2023/7abk_11698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/12_2023/7abk_11698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/12_2023/7abk_11698.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/12_2023/7abk_11698.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 2 5.16 5 C 977 2.51 5 N 289 2.21 5 O 306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 1574 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1574 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 190} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.42, per 1000 atoms: 0.90 Number of scatterers: 1574 At special positions: 0 Unit cell: (69.6287, 180.364, 52.0118, 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 2 16.00 O 306 8.00 N 289 7.00 C 977 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 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: 0.73 Conformation dependent library (CDL) restraints added in 300.9 milliseconds 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 378 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 0 sheets defined 89.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 24 through 80 removed outlier: 3.593A pdb=" N LEU A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 155 removed outlier: 3.570A pdb=" N ALA A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ALA A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 186 removed outlier: 3.500A pdb=" N ASN A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 216 141 hydrogen bonds defined for protein. 423 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: 0.42 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 558 1.34 - 1.46: 133 1.46 - 1.57: 895 1.57 - 1.69: 0 1.69 - 1.80: 4 Bond restraints: 1590 Sorted by residual: bond pdb=" N LYS A 151 " pdb=" CA LYS A 151 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.77e+00 bond pdb=" N ILE A 152 " pdb=" CA ILE A 152 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.29e-02 6.01e+03 7.12e+00 bond pdb=" N PHE A 54 " pdb=" CA PHE A 54 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 4.98e+00 bond pdb=" N GLU A 153 " pdb=" CA GLU A 153 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.30e-02 5.92e+03 4.81e+00 bond pdb=" CA THR A 53 " pdb=" C THR A 53 " ideal model delta sigma weight residual 1.523 1.542 -0.019 1.35e-02 5.49e+03 2.00e+00 ... (remaining 1585 not shown) Histogram of bond angle deviations from ideal: 100.63 - 107.29: 31 107.29 - 113.96: 919 113.96 - 120.62: 689 120.62 - 127.29: 487 127.29 - 133.95: 8 Bond angle restraints: 2134 Sorted by residual: angle pdb=" N GLU A 153 " pdb=" CA GLU A 153 " pdb=" C GLU A 153 " ideal model delta sigma weight residual 112.23 105.18 7.05 1.26e+00 6.30e-01 3.13e+01 angle pdb=" N PHE A 54 " pdb=" CA PHE A 54 " pdb=" C PHE A 54 " ideal model delta sigma weight residual 111.07 106.74 4.33 1.07e+00 8.73e-01 1.64e+01 angle pdb=" N ALA A 52 " pdb=" CA ALA A 52 " pdb=" C ALA A 52 " ideal model delta sigma weight residual 111.02 115.79 -4.77 1.22e+00 6.72e-01 1.53e+01 angle pdb=" N ILE A 152 " pdb=" CA ILE A 152 " pdb=" C ILE A 152 " ideal model delta sigma weight residual 112.80 109.11 3.69 1.15e+00 7.56e-01 1.03e+01 angle pdb=" C THR A 53 " pdb=" CA THR A 53 " pdb=" CB THR A 53 " ideal model delta sigma weight residual 110.67 105.27 5.40 1.92e+00 2.71e-01 7.91e+00 ... (remaining 2129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 891 17.40 - 34.80: 93 34.80 - 52.20: 17 52.20 - 69.60: 8 69.60 - 87.00: 4 Dihedral angle restraints: 1013 sinusoidal: 436 harmonic: 577 Sorted by residual: dihedral pdb=" CA ASP A 160 " pdb=" C ASP A 160 " pdb=" N ASN A 161 " pdb=" CA ASN A 161 " ideal model delta harmonic sigma weight residual 180.00 164.23 15.77 0 5.00e+00 4.00e-02 9.94e+00 dihedral pdb=" CA LYS A 151 " pdb=" CB LYS A 151 " pdb=" CG LYS A 151 " pdb=" CD LYS A 151 " ideal model delta sinusoidal sigma weight residual -180.00 -124.17 -55.83 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CA LEU A 159 " pdb=" C LEU A 159 " pdb=" N ASP A 160 " pdb=" CA ASP A 160 " ideal model delta harmonic sigma weight residual 180.00 164.87 15.13 0 5.00e+00 4.00e-02 9.16e+00 ... (remaining 1010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 186 0.039 - 0.077: 39 0.077 - 0.116: 9 0.116 - 0.154: 1 0.154 - 0.192: 1 Chirality restraints: 236 Sorted by residual: chirality pdb=" CA ALA A 52 " pdb=" N ALA A 52 " pdb=" C ALA A 52 " pdb=" CB ALA A 52 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PHE A 54 " pdb=" N PHE A 54 " pdb=" C PHE A 54 " pdb=" CB PHE A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 233 not shown) Planarity restraints: 284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 150 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C GLN A 150 " 0.031 2.00e-02 2.50e+03 pdb=" O GLN A 150 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS A 151 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 188 " 0.016 5.00e-02 4.00e+02 2.41e-02 9.31e-01 pdb=" N PRO A 189 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 152 " -0.004 2.00e-02 2.50e+03 8.67e-03 7.52e-01 pdb=" C ILE A 152 " 0.015 2.00e-02 2.50e+03 pdb=" O ILE A 152 " -0.006 2.00e-02 2.50e+03 pdb=" N GLU A 153 " -0.005 2.00e-02 2.50e+03 ... (remaining 281 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 477 2.83 - 3.35: 1780 3.35 - 3.87: 2446 3.87 - 4.38: 2475 4.38 - 4.90: 4008 Nonbonded interactions: 11186 Sorted by model distance: nonbonded pdb=" OE2 GLU A 26 " pdb=" CD1 LEU A 143 " model vdw 2.315 3.460 nonbonded pdb=" O SER A 96 " pdb=" OG SER A 99 " model vdw 2.436 2.440 nonbonded pdb=" N GLU A 30 " pdb=" OE1 GLU A 30 " model vdw 2.443 2.520 nonbonded pdb=" OD1 ASN A 161 " pdb=" OG SER A 163 " model vdw 2.453 2.440 nonbonded pdb=" NH1 ARG A 44 " pdb=" OE2 GLU A 126 " model vdw 2.503 2.520 ... (remaining 11181 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.750 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: 18.270 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.750 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 0.034 1590 Z= 0.281 Angle : 0.660 7.053 2134 Z= 0.437 Chirality : 0.037 0.192 236 Planarity : 0.003 0.024 284 Dihedral : 16.299 87.004 635 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.23 % Allowed : 6.17 % Favored : 92.59 % 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: 0.91 (0.56), residues: 194 helix: 0.77 (0.36), residues: 169 sheet: None (None), residues: 0 loop : 0.20 (1.53), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.012 0.003 PHE A 168 TYR 0.004 0.001 TYR A 129 ARG 0.002 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.201 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 0.2578 time to fit residues: 21.9381 Evaluate side-chains 46 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.193 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2853 time to fit residues: 0.5620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 0.0670 chunk 14 optimal weight: 0.0170 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.0370 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1590 Z= 0.195 Angle : 0.577 5.087 2134 Z= 0.309 Chirality : 0.029 0.108 236 Planarity : 0.004 0.034 284 Dihedral : 3.610 13.302 216 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.70 % Allowed : 21.60 % Favored : 74.69 % 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: 3.86 (0.58), residues: 194 helix: 2.85 (0.37), residues: 172 sheet: None (None), residues: 0 loop : -0.12 (1.38), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.007 0.001 PHE A 168 TYR 0.010 0.001 TYR A 129 ARG 0.008 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.208 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 0.2460 time to fit residues: 16.4134 Evaluate side-chains 53 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.212 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0223 time to fit residues: 0.4230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1590 Z= 0.169 Angle : 0.564 6.809 2134 Z= 0.290 Chirality : 0.030 0.109 236 Planarity : 0.003 0.019 284 Dihedral : 3.456 12.195 216 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.23 % Allowed : 25.31 % Favored : 73.46 % 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: 4.64 (0.57), residues: 194 helix: 3.42 (0.37), residues: 172 sheet: None (None), residues: 0 loop : -0.44 (1.22), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.005 0.001 PHE A 168 TYR 0.006 0.001 TYR A 129 ARG 0.005 0.000 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.196 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.1789 time to fit residues: 11.2366 Evaluate side-chains 60 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.195 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0328 time to fit residues: 0.3619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1590 Z= 0.160 Angle : 0.520 5.352 2134 Z= 0.269 Chirality : 0.030 0.112 236 Planarity : 0.003 0.021 284 Dihedral : 3.444 11.788 216 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.70 % Allowed : 27.78 % Favored : 68.52 % 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: 4.99 (0.57), residues: 194 helix: 3.70 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.71 (1.19), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.005 0.001 PHE A 168 TYR 0.004 0.001 TYR A 129 ARG 0.005 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.210 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 59 average time/residue: 0.2204 time to fit residues: 14.0803 Evaluate side-chains 59 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.197 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0223 time to fit residues: 0.4106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1590 Z= 0.181 Angle : 0.525 5.268 2134 Z= 0.271 Chirality : 0.031 0.112 236 Planarity : 0.003 0.020 284 Dihedral : 3.434 11.963 216 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.85 % Allowed : 29.63 % Favored : 68.52 % 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: 5.17 (0.56), residues: 194 helix: 3.82 (0.35), residues: 172 sheet: None (None), residues: 0 loop : -0.71 (1.23), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.004 0.001 PHE A 168 TYR 0.004 0.001 TYR A 129 ARG 0.005 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.197 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 58 average time/residue: 0.2098 time to fit residues: 13.1450 Evaluate side-chains 50 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.165 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0174 time to fit residues: 0.2870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1590 Z= 0.152 Angle : 0.556 5.887 2134 Z= 0.280 Chirality : 0.030 0.112 236 Planarity : 0.003 0.031 284 Dihedral : 3.322 11.270 216 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.85 % Allowed : 32.72 % Favored : 65.43 % 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: 5.32 (0.56), residues: 194 helix: 3.95 (0.35), residues: 172 sheet: None (None), residues: 0 loop : -0.99 (1.19), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.005 0.001 PHE A 168 TYR 0.004 0.001 TYR A 129 ARG 0.006 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.207 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 0.2334 time to fit residues: 14.4507 Evaluate side-chains 56 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.199 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0200 time to fit residues: 0.3051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1590 Z= 0.191 Angle : 0.540 5.341 2134 Z= 0.283 Chirality : 0.031 0.115 236 Planarity : 0.003 0.019 284 Dihedral : 3.317 11.455 216 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.70 % Allowed : 27.78 % Favored : 68.52 % 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: 5.15 (0.56), residues: 194 helix: 3.83 (0.35), residues: 172 sheet: None (None), residues: 0 loop : -0.88 (1.22), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.004 0.001 PHE A 168 TYR 0.013 0.001 TYR A 129 ARG 0.006 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.196 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 0.2498 time to fit residues: 14.1915 Evaluate side-chains 55 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.144 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0165 time to fit residues: 0.3277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1590 Z= 0.201 Angle : 0.594 5.588 2134 Z= 0.304 Chirality : 0.031 0.114 236 Planarity : 0.003 0.030 284 Dihedral : 3.354 11.550 216 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.23 % Allowed : 27.16 % Favored : 71.60 % 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: 5.01 (0.56), residues: 194 helix: 3.72 (0.35), residues: 172 sheet: None (None), residues: 0 loop : -0.82 (1.23), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.004 0.001 PHE A 168 TYR 0.008 0.001 TYR A 129 ARG 0.007 0.001 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.195 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.2344 time to fit residues: 13.6420 Evaluate side-chains 52 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.193 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0196 time to fit residues: 0.2978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1590 Z= 0.189 Angle : 0.595 6.326 2134 Z= 0.302 Chirality : 0.031 0.120 236 Planarity : 0.003 0.030 284 Dihedral : 3.330 11.307 216 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.62 % Allowed : 29.63 % Favored : 69.75 % 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: 4.97 (0.56), residues: 194 helix: 3.70 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.89 (1.20), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.004 0.001 PHE A 168 TYR 0.007 0.001 TYR A 129 ARG 0.006 0.001 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.161 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.2526 time to fit residues: 13.8741 Evaluate side-chains 51 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.196 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0237 time to fit residues: 0.2980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1590 Z= 0.203 Angle : 0.618 6.544 2134 Z= 0.320 Chirality : 0.032 0.118 236 Planarity : 0.003 0.029 284 Dihedral : 3.411 11.546 216 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.23 % Allowed : 29.01 % Favored : 69.75 % 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: 4.90 (0.57), residues: 194 helix: 3.65 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.89 (1.21), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.004 0.001 PHE A 168 TYR 0.007 0.001 TYR A 129 ARG 0.007 0.001 ARG A 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.193 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 0.2345 time to fit residues: 13.4188 Evaluate side-chains 53 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.198 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0332 time to fit residues: 0.3627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.102477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.081547 restraints weight = 3854.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083890 restraints weight = 1834.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085361 restraints weight = 1155.933| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1590 Z= 0.245 Angle : 0.659 6.496 2134 Z= 0.340 Chirality : 0.033 0.121 236 Planarity : 0.003 0.028 284 Dihedral : 3.488 11.921 216 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.47 % Allowed : 29.63 % Favored : 67.90 % 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: 4.42 (0.57), residues: 194 helix: 3.35 (0.36), residues: 173 sheet: None (None), residues: 0 loop : -1.50 (1.08), residues: 21 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 71 HIS 0.001 0.000 HIS A 100 PHE 0.004 0.001 PHE A 168 TYR 0.012 0.001 TYR A 129 ARG 0.007 0.001 ARG A 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 954.38 seconds wall clock time: 23 minutes 27.47 seconds (1407.47 seconds total)