Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:00:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly0_23581/11_2022/7ly0_23581.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly0_23581/11_2022/7ly0_23581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly0_23581/11_2022/7ly0_23581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly0_23581/11_2022/7ly0_23581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly0_23581/11_2022/7ly0_23581.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly0_23581/11_2022/7ly0_23581.pdb" } resolution = 2.6 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2805 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1033 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 7 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 785 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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: 2.22, per 1000 atoms: 0.79 Number of scatterers: 2805 At special positions: 0 Unit cell: (73.5, 71.4, 74.55, 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 10 16.00 O 536 8.00 N 463 7.00 C 1796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 149 " " NAG B 1 " - " ASN A 17 " Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 389.0 milliseconds 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 7.6% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.185A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.544A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.445A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.467A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.467A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.710A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.002A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 225 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: 0.70 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 520 1.32 - 1.45: 807 1.45 - 1.57: 1528 1.57 - 1.70: 4 1.70 - 1.82: 13 Bond restraints: 2872 Sorted by residual: bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.435 1.468 -0.033 1.10e-02 8.26e+03 9.21e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.435 1.467 -0.032 1.10e-02 8.26e+03 8.62e+00 bond pdb=" N TRP H 104 " pdb=" CA TRP H 104 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.16e-02 7.43e+03 8.17e+00 bond pdb=" CB ILE A 235 " pdb=" CG1 ILE A 235 " ideal model delta sigma weight residual 1.530 1.584 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" CG ASP A 138 " pdb=" OD1 ASP A 138 " ideal model delta sigma weight residual 1.249 1.198 0.051 1.90e-02 2.77e+03 7.23e+00 ... (remaining 2867 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.33: 91 107.33 - 114.01: 1571 114.01 - 120.69: 1210 120.69 - 127.36: 1006 127.36 - 134.04: 27 Bond angle restraints: 3905 Sorted by residual: angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 125.78 -6.12 7.30e-01 1.88e+00 7.02e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.32 -7.29 9.90e-01 1.02e+00 5.42e+01 angle pdb=" C ILE L 57 " pdb=" N PRO L 58 " pdb=" CA PRO L 58 " ideal model delta sigma weight residual 120.03 126.82 -6.79 9.90e-01 1.02e+00 4.71e+01 angle pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta sigma weight residual 119.92 127.22 -7.30 1.07e+00 8.73e-01 4.65e+01 angle pdb=" C PRO L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta sigma weight residual 119.19 126.17 -6.98 1.06e+00 8.90e-01 4.33e+01 ... (remaining 3900 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.83: 1595 17.83 - 35.65: 35 35.65 - 53.48: 14 53.48 - 71.30: 3 71.30 - 89.12: 1 Dihedral angle restraints: 1648 sinusoidal: 631 harmonic: 1017 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.87 41.13 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 87 " pdb=" CB CYS L 87 " ideal model delta sinusoidal sigma weight residual 93.00 55.35 37.65 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CA ARG L 53 " pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 1645 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.062: 300 0.062 - 0.124: 108 0.124 - 0.186: 22 0.186 - 0.248: 15 0.248 - 0.310: 5 Chirality restraints: 450 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 -2.53 0.13 2.00e-02 2.50e+03 4.24e+01 chirality pdb=" C1 MAN B 3 " pdb=" O4 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.47 -0.07 2.00e-02 2.50e+03 1.19e+01 chirality pdb=" C1 FUC B 4 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 4 " pdb=" O5 FUC B 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.82e+00 ... (remaining 447 not shown) Planarity restraints: 484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 33 " 0.035 2.00e-02 2.50e+03 1.89e-02 7.18e+00 pdb=" CG TYR L 33 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR L 33 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR L 33 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR L 33 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR L 33 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR L 33 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 33 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 122 " 0.024 2.00e-02 2.50e+03 2.31e-02 6.67e+00 pdb=" CG ASN A 122 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 122 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 122 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 103 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C GLU H 103 " 0.032 2.00e-02 2.50e+03 pdb=" O GLU H 103 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP H 104 " -0.011 2.00e-02 2.50e+03 ... (remaining 481 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1504 2.99 - 3.47: 2388 3.47 - 3.95: 4816 3.95 - 4.42: 5482 4.42 - 4.90: 8858 Nonbonded interactions: 23048 Sorted by model distance: nonbonded pdb=" NZ LYS A 77 " pdb=" O THR A 250 " model vdw 2.515 2.520 nonbonded pdb=" NZ LYS A 147 " pdb=" O LEU L 27 " model vdw 2.575 2.520 nonbonded pdb=" OD1 ASP L 91 " pdb=" N GLY L 94 " model vdw 2.576 2.520 nonbonded pdb=" OD1 ASP H 107 " pdb=" N TYR H 108 " model vdw 2.577 2.520 nonbonded pdb=" OG SER A 155 " pdb=" N GLU A 156 " model vdw 2.591 2.520 ... (remaining 23043 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 10 5.16 5 C 1796 2.51 5 N 463 2.21 5 O 536 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 individual isotropic 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.360 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 13.230 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 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 : 0.012 0.054 2872 Z= 0.750 Angle : 1.171 7.298 3905 Z= 0.825 Chirality : 0.077 0.310 450 Planarity : 0.005 0.019 481 Dihedral : 9.710 89.124 989 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 1.04 (0.39), residues: 154 loop : 1.42 (0.50), residues: 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.317 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.6282 time to fit residues: 63.6170 Evaluate side-chains 76 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.300 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 0.1980 chunk 25 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 17 optimal weight: 0.0870 chunk 13 optimal weight: 0.0570 chunk 26 optimal weight: 0.0980 chunk 10 optimal weight: 0.0980 chunk 16 optimal weight: 0.0020 chunk 19 optimal weight: 0.0970 chunk 30 optimal weight: 0.1980 overall best weight: 0.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 2872 Z= 0.164 Angle : 0.513 6.264 3905 Z= 0.274 Chirality : 0.042 0.163 450 Planarity : 0.003 0.033 481 Dihedral : 4.605 17.882 427 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 1.11 (0.41), residues: 148 loop : 1.55 (0.50), residues: 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.294 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 83 average time/residue: 0.6454 time to fit residues: 55.9652 Evaluate side-chains 75 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.311 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0294 time to fit residues: 0.5362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 25 optimal weight: 0.2980 chunk 21 optimal weight: 0.1980 chunk 8 optimal weight: 0.2980 chunk 30 optimal weight: 0.0870 chunk 33 optimal weight: 0.0980 chunk 27 optimal weight: 0.0040 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.0970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 2872 Z= 0.151 Angle : 0.480 4.983 3905 Z= 0.259 Chirality : 0.041 0.159 450 Planarity : 0.003 0.036 481 Dihedral : 4.479 20.446 427 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.97 (0.41), residues: 151 loop : 1.43 (0.50), residues: 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.343 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 80 average time/residue: 0.6289 time to fit residues: 52.6198 Evaluate side-chains 78 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.5430 time to fit residues: 2.0675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.063 2872 Z= 0.485 Angle : 0.672 7.247 3905 Z= 0.354 Chirality : 0.048 0.204 450 Planarity : 0.006 0.049 481 Dihedral : 5.585 20.686 427 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 4.64 % 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: 0.77 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.55 (0.42), residues: 143 loop : 0.64 (0.47), residues: 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.316 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.7032 time to fit residues: 66.5967 Evaluate side-chains 82 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 0.7323 time to fit residues: 4.2008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.0370 chunk 13 optimal weight: 0.0670 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 29 optimal weight: 0.0980 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 0.3980 chunk 6 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 overall best weight: 0.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 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 : 0.002 0.039 2872 Z= 0.156 Angle : 0.502 5.121 3905 Z= 0.271 Chirality : 0.042 0.173 450 Planarity : 0.004 0.039 481 Dihedral : 4.759 22.631 427 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 4.29 % 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: 0.85 (0.48), residues: 334 helix: None (None), residues: 0 sheet: 0.59 (0.42), residues: 148 loop : 0.70 (0.50), residues: 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.337 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.6860 time to fit residues: 55.0305 Evaluate side-chains 75 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.4180 time to fit residues: 2.1869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 8 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.0970 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.0030 overall best weight: 0.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 2872 Z= 0.238 Angle : 0.536 5.955 3905 Z= 0.281 Chirality : 0.044 0.157 450 Planarity : 0.004 0.041 481 Dihedral : 4.924 21.958 427 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.75 (0.44), residues: 135 loop : 0.51 (0.47), residues: 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.284 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 78 average time/residue: 0.6797 time to fit residues: 55.2245 Evaluate side-chains 78 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.312 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.4026 time to fit residues: 2.1170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 15 optimal weight: 0.0980 chunk 13 optimal weight: 0.0010 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 0.0870 chunk 16 optimal weight: 0.6980 overall best weight: 0.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 2872 Z= 0.241 Angle : 0.541 6.170 3905 Z= 0.285 Chirality : 0.044 0.157 450 Planarity : 0.004 0.041 481 Dihedral : 4.944 21.986 427 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 3.57 % 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: 0.75 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.76 (0.44), residues: 135 loop : 0.43 (0.47), residues: 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.321 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 76 average time/residue: 0.6924 time to fit residues: 54.9465 Evaluate side-chains 78 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.4394 time to fit residues: 2.2711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 0.0870 chunk 25 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.0050 chunk 13 optimal weight: 0.0970 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 27 optimal weight: 0.3980 overall best weight: 0.1770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 2872 Z= 0.197 Angle : 0.510 5.734 3905 Z= 0.269 Chirality : 0.043 0.155 450 Planarity : 0.004 0.039 481 Dihedral : 4.766 21.993 427 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 3.57 % 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: 0.72 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.79 (0.44), residues: 134 loop : 0.36 (0.47), residues: 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.295 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.6575 time to fit residues: 54.8429 Evaluate side-chains 81 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.9511 time to fit residues: 2.3623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 15 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 2872 Z= 0.361 Angle : 0.623 6.993 3905 Z= 0.325 Chirality : 0.047 0.186 450 Planarity : 0.005 0.042 481 Dihedral : 5.288 21.561 427 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 3.57 % 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: 0.41 (0.46), residues: 334 helix: None (None), residues: 0 sheet: 0.49 (0.41), residues: 141 loop : 0.22 (0.48), residues: 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.301 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 79 average time/residue: 0.6654 time to fit residues: 54.8151 Evaluate side-chains 80 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.6258 time to fit residues: 2.3672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 20 optimal weight: 0.0000 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 24 optimal weight: 0.0070 chunk 3 optimal weight: 0.0980 chunk 7 optimal weight: 0.1980 chunk 27 optimal weight: 0.2980 chunk 11 optimal weight: 0.2980 chunk 4 optimal weight: 0.0670 overall best weight: 0.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 2872 Z= 0.149 Angle : 0.508 5.084 3905 Z= 0.271 Chirality : 0.043 0.163 450 Planarity : 0.004 0.038 481 Dihedral : 4.659 22.707 427 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 2.14 % 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: 0.66 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.77 (0.43), residues: 134 loop : 0.31 (0.47), residues: 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 668 Ramachandran restraints generated. 334 Oldfield, 0 Emsley, 334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.341 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 81 average time/residue: 0.6016 time to fit residues: 51.0236 Evaluate side-chains 78 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.305 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0324 time to fit residues: 0.4917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 18 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.0370 chunk 13 optimal weight: 0.0770 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.183896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.178482 restraints weight = 2816.100| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 0.69 r_work: 0.3902 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.3892 rms_B_bonded: 0.71 restraints_weight: 0.2500 r_work: 0.3879 rms_B_bonded: 0.92 restraints_weight: 0.1250 r_work: 0.3858 rms_B_bonded: 1.29 restraints_weight: 0.0625 r_work: 0.3825 rms_B_bonded: 1.92 restraints_weight: 0.0312 r_work: 0.3772 rms_B_bonded: 2.99 restraints_weight: 0.0156 r_work: 0.3682 rms_B_bonded: 4.89 restraints_weight: 0.0078 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 2872 Z= 0.222 Angle : 0.547 5.752 3905 Z= 0.287 Chirality : 0.044 0.172 450 Planarity : 0.004 0.040 481 Dihedral : 4.794 21.074 427 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 2.14 % 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: 0.60 (0.47), residues: 334 helix: None (None), residues: 0 sheet: 0.70 (0.41), residues: 142 loop : 0.27 (0.48), residues: 192 =============================================================================== Job complete usr+sys time: 1767.25 seconds wall clock time: 32 minutes 20.46 seconds (1940.46 seconds total)