Starting phenix.real_space_refine (version: dev) on Thu Feb 16 15:46:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us9_26729/02_2023/7us9_26729.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us9_26729/02_2023/7us9_26729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us9_26729/02_2023/7us9_26729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us9_26729/02_2023/7us9_26729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us9_26729/02_2023/7us9_26729.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us9_26729/02_2023/7us9_26729.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 1127 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1071 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 137} Chain breaks: 7 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.17, per 1000 atoms: 1.04 Number of scatterers: 1127 At special positions: 0 Unit cell: (50.58, 48.894, 59.853, 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 4 16.00 O 194 8.00 N 185 7.00 C 744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.09 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 301 " - " ASN A 42 " " NAG A 302 " - " ASN A 242 " " NAG B 1 " - " ASN A 249 " Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 159.2 milliseconds 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 274 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 3 sheets defined 9.7% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 4.150A pdb=" N ILE A 36 " --> pdb=" O HIS A 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 7.641A pdb=" N PHE A 202 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LYS A 110 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR A 204 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 109 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 112 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 130 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A 156 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 132 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 196 removed outlier: 3.514A pdb=" N ALA A 85 " --> pdb=" O VAL A 230 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 141 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: 0.26 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 251 1.33 - 1.46: 358 1.46 - 1.58: 546 1.58 - 1.71: 1 1.71 - 1.84: 6 Bond restraints: 1162 Sorted by residual: bond pdb=" N PRO A 111 " pdb=" CD PRO A 111 " ideal model delta sigma weight residual 1.474 1.381 0.093 1.40e-02 5.10e+03 4.37e+01 bond pdb=" CZ2 TRP A 225 " pdb=" CH2 TRP A 225 " ideal model delta sigma weight residual 1.368 1.455 -0.087 1.90e-02 2.77e+03 2.10e+01 bond pdb=" CD2 TRP A 225 " pdb=" CE3 TRP A 225 " ideal model delta sigma weight residual 1.398 1.468 -0.070 1.60e-02 3.91e+03 1.90e+01 bond pdb=" CB LEU A 76 " pdb=" CG LEU A 76 " ideal model delta sigma weight residual 1.530 1.615 -0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C5 NAG A 301 " pdb=" O5 NAG A 301 " ideal model delta sigma weight residual 1.435 1.480 -0.045 1.10e-02 8.26e+03 1.69e+01 ... (remaining 1157 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.51: 32 105.51 - 112.61: 561 112.61 - 119.71: 360 119.71 - 126.81: 608 126.81 - 133.91: 28 Bond angle restraints: 1589 Sorted by residual: angle pdb=" N ILE A 195 " pdb=" CA ILE A 195 " pdb=" C ILE A 195 " ideal model delta sigma weight residual 108.11 117.48 -9.37 1.40e+00 5.10e-01 4.47e+01 angle pdb=" C PHE A 159 " pdb=" N PRO A 160 " pdb=" CA PRO A 160 " ideal model delta sigma weight residual 120.31 126.85 -6.54 9.80e-01 1.04e+00 4.45e+01 angle pdb=" C PRO A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.84 127.79 -7.95 1.25e+00 6.40e-01 4.05e+01 angle pdb=" C LEU A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta sigma weight residual 120.38 126.66 -6.28 1.03e+00 9.43e-01 3.72e+01 angle pdb=" N VAL A 78 " pdb=" CA VAL A 78 " pdb=" CB VAL A 78 " ideal model delta sigma weight residual 110.72 104.39 6.33 1.09e+00 8.42e-01 3.37e+01 ... (remaining 1584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.01: 555 8.01 - 16.02: 56 16.02 - 24.03: 9 24.03 - 32.04: 6 32.04 - 40.05: 2 Dihedral angle restraints: 628 sinusoidal: 206 harmonic: 422 Sorted by residual: dihedral pdb=" C GLN A 63 " pdb=" N GLN A 63 " pdb=" CA GLN A 63 " pdb=" CB GLN A 63 " ideal model delta harmonic sigma weight residual -122.60 -130.32 7.72 0 2.50e+00 1.60e-01 9.54e+00 dihedral pdb=" CA ILE A 195 " pdb=" CB ILE A 195 " pdb=" CG1 ILE A 195 " pdb=" CD1 ILE A 195 " ideal model delta sinusoidal sigma weight residual 60.00 100.05 -40.05 3 1.50e+01 4.44e-03 7.12e+00 dihedral pdb=" C LYS A 110 " pdb=" N LYS A 110 " pdb=" CA LYS A 110 " pdb=" CB LYS A 110 " ideal model delta harmonic sigma weight residual -122.60 -116.09 -6.51 0 2.50e+00 1.60e-01 6.77e+00 ... (remaining 625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 122 0.079 - 0.157: 33 0.157 - 0.235: 13 0.235 - 0.314: 6 0.314 - 0.392: 4 Chirality restraints: 178 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.42e+01 chirality pdb=" C2 NAG B 1 " pdb=" C1 NAG B 1 " pdb=" C3 NAG B 1 " pdb=" N2 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.88 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CG LEU A 76 " pdb=" CB LEU A 76 " pdb=" CD1 LEU A 76 " pdb=" CD2 LEU A 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 175 not shown) Planarity restraints: 196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 42 " -0.046 2.00e-02 2.50e+03 4.80e-02 2.88e+01 pdb=" CG ASN A 42 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 42 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 42 " 0.075 2.00e-02 2.50e+03 pdb=" C1 NAG A 301 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 242 " -0.039 2.00e-02 2.50e+03 4.07e-02 2.07e+01 pdb=" CG ASN A 242 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 242 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 242 " 0.063 2.00e-02 2.50e+03 pdb=" C1 NAG A 302 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 64 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C PRO A 64 " 0.029 2.00e-02 2.50e+03 pdb=" O PRO A 64 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP A 65 " -0.010 2.00e-02 2.50e+03 ... (remaining 193 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 519 2.97 - 3.45: 846 3.45 - 3.94: 1656 3.94 - 4.42: 1735 4.42 - 4.90: 3029 Nonbonded interactions: 7785 Sorted by model distance: nonbonded pdb=" O LYS A 110 " pdb=" CD PRO A 111 " model vdw 2.489 2.752 nonbonded pdb=" O GLN A 178 " pdb=" CA TRP A 179 " model vdw 2.627 2.776 nonbonded pdb=" N GLY A 109 " pdb=" O GLY A 109 " model vdw 2.636 2.496 nonbonded pdb=" N MET A 80 " pdb=" O MET A 80 " model vdw 2.641 2.496 nonbonded pdb=" O HIS A 189 " pdb=" ND1 HIS A 189 " model vdw 2.643 2.520 ... (remaining 7780 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 4 5.16 5 C 744 2.51 5 N 185 2.21 5 O 194 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: 10.600 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: 26.350 Check model and map are aligned: 0.030 Process input model: 11.560 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.014 0.093 1162 Z= 0.873 Angle : 1.553 11.720 1589 Z= 1.059 Chirality : 0.107 0.392 178 Planarity : 0.005 0.017 193 Dihedral : 7.453 40.047 351 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.73), residues: 129 helix: 3.26 (1.42), residues: 12 sheet: 1.80 (0.75), residues: 47 loop : -0.57 (0.71), residues: 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1318 time to fit residues: 4.9816 Evaluate side-chains 21 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.145 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.0570 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 0.0970 chunk 9 optimal weight: 0.0870 overall best weight: 0.1272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 1162 Z= 0.208 Angle : 0.616 5.431 1589 Z= 0.344 Chirality : 0.054 0.269 178 Planarity : 0.004 0.026 193 Dihedral : 5.063 14.114 175 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.78), residues: 129 helix: 3.80 (1.27), residues: 12 sheet: 1.54 (0.58), residues: 76 loop : -1.09 (1.09), residues: 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.131 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.0684 time to fit residues: 1.9329 Evaluate side-chains 15 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.131 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0167 time to fit residues: 0.1998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.0050 chunk 13 optimal weight: 0.0980 chunk 3 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 chunk 0 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 5 optimal weight: 0.0980 overall best weight: 0.0772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 1162 Z= 0.169 Angle : 0.633 7.120 1589 Z= 0.357 Chirality : 0.053 0.283 178 Planarity : 0.006 0.057 193 Dihedral : 4.878 11.952 175 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.77), residues: 129 helix: 3.62 (1.18), residues: 12 sheet: 1.22 (0.60), residues: 78 loop : -1.03 (1.05), residues: 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.151 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0711 time to fit residues: 1.5252 Evaluate side-chains 14 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 0 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 2 optimal weight: 0.1980 chunk 7 optimal weight: 0.3980 chunk 13 optimal weight: 0.0570 chunk 1 optimal weight: 0.3980 overall best weight: 0.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 1162 Z= 0.219 Angle : 0.575 6.536 1589 Z= 0.319 Chirality : 0.050 0.191 178 Planarity : 0.006 0.045 193 Dihedral : 4.822 12.990 175 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.78), residues: 129 helix: 3.33 (1.25), residues: 12 sheet: 1.12 (0.60), residues: 78 loop : -1.31 (1.06), residues: 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.118 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0714 time to fit residues: 1.3403 Evaluate side-chains 12 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.133 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 0.0970 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 8 optimal weight: 0.1980 chunk 6 optimal weight: 0.3980 chunk 5 optimal weight: 0.2980 chunk 2 optimal weight: 0.0970 chunk 10 optimal weight: 0.4980 overall best weight: 0.1576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 1162 Z= 0.215 Angle : 0.610 8.922 1589 Z= 0.351 Chirality : 0.052 0.233 178 Planarity : 0.005 0.038 193 Dihedral : 4.822 12.412 175 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.75), residues: 129 helix: 2.61 (1.33), residues: 12 sheet: 1.07 (0.61), residues: 78 loop : -1.61 (0.89), residues: 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.118 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.1005 time to fit residues: 2.0823 Evaluate side-chains 12 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.143 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0169 time to fit residues: 0.2186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.0060 chunk 8 optimal weight: 0.2980 chunk 13 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 1162 Z= 0.250 Angle : 0.664 8.865 1589 Z= 0.377 Chirality : 0.109 1.291 178 Planarity : 0.005 0.036 193 Dihedral : 5.984 38.660 175 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: 0.31 (0.73), residues: 129 helix: 2.41 (1.32), residues: 12 sheet: 1.03 (0.63), residues: 73 loop : -1.97 (0.75), residues: 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.119 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.0667 time to fit residues: 1.2690 Evaluate side-chains 12 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.137 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 1 optimal weight: 0.0870 chunk 3 optimal weight: 0.0970 chunk 11 optimal weight: 0.0870 chunk 4 optimal weight: 0.1980 chunk 2 optimal weight: 0.0770 chunk 9 optimal weight: 0.0770 chunk 0 optimal weight: 0.3980 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 overall best weight: 0.0810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 1162 Z= 0.142 Angle : 0.512 6.223 1589 Z= 0.299 Chirality : 0.069 0.662 178 Planarity : 0.006 0.067 193 Dihedral : 5.631 34.889 175 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: 0.52 (0.74), residues: 129 helix: 3.70 (1.24), residues: 12 sheet: 0.98 (0.63), residues: 74 loop : -1.89 (0.76), residues: 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.129 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.1021 time to fit residues: 1.8911 Evaluate side-chains 15 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.128 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 0.2980 chunk 13 optimal weight: 0.2980 chunk 0 optimal weight: 0.7980 chunk 2 optimal weight: 0.0470 chunk 1 optimal weight: 0.0980 chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 chunk 9 optimal weight: 0.1980 chunk 4 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.1878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 1162 Z= 0.207 Angle : 0.556 8.041 1589 Z= 0.310 Chirality : 0.060 0.470 178 Planarity : 0.006 0.057 193 Dihedral : 5.523 33.193 175 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.75), residues: 129 helix: 3.96 (1.18), residues: 12 sheet: 1.02 (0.63), residues: 74 loop : -1.87 (0.78), residues: 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.143 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0981 time to fit residues: 1.7285 Evaluate side-chains 13 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.135 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 0 optimal weight: 0.2980 chunk 4 optimal weight: 0.3980 chunk 3 optimal weight: 0.0370 chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 overall best weight: 0.1214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 1162 Z= 0.155 Angle : 0.529 8.020 1589 Z= 0.289 Chirality : 0.059 0.442 178 Planarity : 0.006 0.050 193 Dihedral : 5.336 31.866 175 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: 0.75 (0.75), residues: 129 helix: 4.16 (1.23), residues: 12 sheet: 1.13 (0.64), residues: 74 loop : -1.85 (0.76), residues: 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.121 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1065 time to fit residues: 1.8341 Evaluate side-chains 14 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.0170 chunk 5 optimal weight: 0.0670 chunk 11 optimal weight: 0.0980 chunk 3 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 1162 Z= 0.276 Angle : 0.591 8.267 1589 Z= 0.330 Chirality : 0.130 1.599 178 Planarity : 0.006 0.051 193 Dihedral : 5.645 24.917 175 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.77), residues: 129 helix: 3.80 (1.22), residues: 12 sheet: 1.04 (0.64), residues: 74 loop : -1.96 (0.87), residues: 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1019 time to fit residues: 1.6576 Evaluate side-chains 12 residues out of total 133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.128 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.0570 chunk 5 optimal weight: 0.0010 chunk 12 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 overall best weight: 0.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** 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 = 0.3856 r_free = 0.3856 target = 0.165333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.142316 restraints weight = 1788.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144994 restraints weight = 1188.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.147095 restraints weight = 903.873| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 1162 Z= 0.198 Angle : 0.563 8.346 1589 Z= 0.306 Chirality : 0.072 0.678 178 Planarity : 0.006 0.051 193 Dihedral : 5.275 25.247 175 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.76), residues: 129 helix: 3.71 (1.18), residues: 12 sheet: 1.11 (0.64), residues: 74 loop : -2.23 (0.83), residues: 43 =============================================================================== Job complete usr+sys time: 1304.29 seconds wall clock time: 24 minutes 8.85 seconds (1448.85 seconds total)