Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:36:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/11_2022/7abk_11698.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/11_2022/7abk_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_11698/11_2022/7abk_11698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/11_2022/7abk_11698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/11_2022/7abk_11698.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/11_2022/7abk_11698.pdb" } resolution = 3.6 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= 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 1.48, per 1000 atoms: 0.94 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: 0.71 Conformation dependent library (CDL) restraints added in 234.8 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: 0.04 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: 0.41 Time building geometry restraints manager: 0.77 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 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. 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: 3.210 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: 0.000 Extract box with map and model: 17.370 Check model and map are aligned: 0.020 Convert atoms to be neutral: 0.020 Process input model: 11.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 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 % 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 *********************** 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: 0.2340 time to fit residues: 19.9783 Evaluate side-chains 46 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.200 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2572 time to fit residues: 0.5400 ------------------------------------------------------------------------------- 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: 3.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.0970 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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: 0.8582 moved from start: 0.3846 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 : 0.575 4.981 2134 Z= 0.308 Chirality : 0.029 0.107 236 Planarity : 0.004 0.034 284 Dihedral : 3.601 13.230 216 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: 3.87 (0.58), residues: 194 helix: 2.85 (0.37), residues: 172 sheet: None (None), residues: 0 loop : -0.13 (1.37), residues: 22 *********************** 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 : 0.198 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 0.2378 time to fit residues: 15.8586 Evaluate side-chains 53 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.187 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0213 time to fit residues: 0.4050 ------------------------------------------------------------------------------- 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: 7.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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: 0.8568 moved from start: 0.4458 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= 0.174 Angle : 0.562 6.386 2134 Z= 0.291 Chirality : 0.031 0.110 236 Planarity : 0.003 0.018 284 Dihedral : 3.489 12.424 216 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 1.23 % 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: 4.44 (0.57), residues: 194 helix: 3.32 (0.37), residues: 173 sheet: None (None), residues: 0 loop : -1.00 (1.14), residues: 21 *********************** 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 56 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.213 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 0.1796 time to fit residues: 10.8811 Evaluate side-chains 57 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.207 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0322 time to fit residues: 0.3734 ------------------------------------------------------------------------------- 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: 5.9990 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.015 1590 Z= 0.196 Angle : 0.519 5.290 2134 Z= 0.273 Chirality : 0.031 0.112 236 Planarity : 0.003 0.018 284 Dihedral : 3.519 12.645 216 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 4.32 % 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: 4.92 (0.57), residues: 194 helix: 3.64 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.61 (1.22), residues: 22 *********************** 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 63 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.207 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 57 average time/residue: 0.1974 time to fit residues: 12.2869 Evaluate side-chains 56 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.211 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0208 time to fit residues: 0.4862 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.019 1590 Z= 0.253 Angle : 0.578 5.054 2134 Z= 0.307 Chirality : 0.033 0.114 236 Planarity : 0.003 0.021 284 Dihedral : 3.613 13.073 216 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 1.85 % 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: 4.61 (0.56), residues: 194 helix: 3.42 (0.35), residues: 172 sheet: None (None), residues: 0 loop : -0.59 (1.24), residues: 22 *********************** 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 59 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.205 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 0.2084 time to fit residues: 12.7051 Evaluate side-chains 55 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.215 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0191 time to fit residues: 0.3201 ------------------------------------------------------------------------------- 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: 1.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8584 moved from start: 0.4864 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= 0.173 Angle : 0.558 5.839 2134 Z= 0.289 Chirality : 0.030 0.115 236 Planarity : 0.003 0.020 284 Dihedral : 3.485 12.118 216 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: 4.87 (0.57), residues: 194 helix: 3.64 (0.36), residues: 173 sheet: None (None), residues: 0 loop : -1.27 (1.16), residues: 21 *********************** 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 63 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.203 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.1977 time to fit residues: 12.7105 Evaluate side-chains 55 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.204 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0207 time to fit residues: 0.4400 ------------------------------------------------------------------------------- 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: 6.9990 chunk 16 optimal weight: 0.0770 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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: 0.8563 moved from start: 0.5057 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= 0.187 Angle : 0.619 6.072 2134 Z= 0.319 Chirality : 0.032 0.144 236 Planarity : 0.003 0.022 284 Dihedral : 3.417 11.750 216 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 0.62 % 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: 5.00 (0.56), residues: 194 helix: 3.70 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.70 (1.22), residues: 22 *********************** 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 54 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.230 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.2167 time to fit residues: 12.4358 Evaluate side-chains 51 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.198 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2873 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- 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: 0.8501 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 1590 Z= 0.180 Angle : 0.612 6.386 2134 Z= 0.311 Chirality : 0.031 0.151 236 Planarity : 0.003 0.021 284 Dihedral : 3.241 10.881 216 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 1.85 % 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: 4.95 (0.56), residues: 194 helix: 3.71 (0.35), residues: 173 sheet: None (None), residues: 0 loop : -1.40 (1.16), residues: 21 *********************** 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 57 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.207 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.2396 time to fit residues: 13.9402 Evaluate side-chains 54 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.211 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0210 time to fit residues: 0.3826 ------------------------------------------------------------------------------- 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: 2.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 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: 0.8522 moved from start: 0.5409 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= 0.186 Angle : 0.629 6.091 2134 Z= 0.323 Chirality : 0.032 0.147 236 Planarity : 0.003 0.034 284 Dihedral : 3.277 10.783 216 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.62 % 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: 5.11 (0.56), residues: 194 helix: 3.80 (0.35), residues: 172 sheet: None (None), residues: 0 loop : -0.92 (1.21), residues: 22 *********************** 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 53 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.215 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.2326 time to fit residues: 13.0885 Evaluate side-chains 51 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2982 ------------------------------------------------------------------------------- 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: 0.7980 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.8515 moved from start: 0.5521 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= 0.179 Angle : 0.642 6.459 2134 Z= 0.327 Chirality : 0.032 0.150 236 Planarity : 0.003 0.033 284 Dihedral : 3.276 10.472 216 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.62 % 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: 5.19 (0.56), residues: 194 helix: 3.86 (0.35), residues: 172 sheet: None (None), residues: 0 loop : -0.90 (1.21), residues: 22 ********************** 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: 1 poor density : 53 time to evaluate : 0.175 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.2443 time to fit residues: 13.9387 Evaluate side-chains 55 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.208 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0272 time to fit residues: 0.3492 ------------------------------------------------------------------------------- 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: 0.8980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.105551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.084963 restraints weight = 3858.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.087412 restraints weight = 1830.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088992 restraints weight = 1155.210| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.5497 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= 0.183 Angle : 0.643 6.445 2134 Z= 0.329 Chirality : 0.032 0.151 236 Planarity : 0.004 0.032 284 Dihedral : 3.315 11.354 216 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.19 (0.56), residues: 194 helix: 3.84 (0.35), residues: 172 sheet: None (None), residues: 0 loop : -0.81 (1.22), residues: 22 =============================================================================== Job complete usr+sys time: 938.07 seconds wall clock time: 17 minutes 15.22 seconds (1035.22 seconds total)