Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:26:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3u_31441/11_2022/7f3u_31441.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3u_31441/11_2022/7f3u_31441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3u_31441/11_2022/7f3u_31441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3u_31441/11_2022/7f3u_31441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3u_31441/11_2022/7f3u_31441.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3u_31441/11_2022/7f3u_31441.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2137 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 8, 'TRANS': 319} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 653 Unresolved non-hydrogen angles: 828 Unresolved non-hydrogen dihedrals: 568 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 18, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 397 Chain: "B" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2137 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 8, 'TRANS': 319} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 653 Unresolved non-hydrogen angles: 828 Unresolved non-hydrogen dihedrals: 568 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 18, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 397 Time building chain proxies: 3.08, per 1000 atoms: 0.72 Number of scatterers: 4274 At special positions: 0 Unit cell: (71.34, 113.98, 88.56, 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 18 16.00 O 800 8.00 N 740 7.00 C 2716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 769.1 milliseconds 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 7 through 72 Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 73 through 99 removed outlier: 4.186A pdb=" N ALA A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 122 through 154 Processing helix chain 'A' and resid 157 through 186 removed outlier: 3.623A pdb=" N ASP A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 Processing helix chain 'A' and resid 213 through 252 removed outlier: 4.526A pdb=" N ASN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 297 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 306 through 334 Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 8 through 72 Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 73 through 99 removed outlier: 4.185A pdb=" N ALA B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 122 through 154 Processing helix chain 'B' and resid 157 through 186 removed outlier: 3.623A pdb=" N ASP B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 213 through 252 removed outlier: 4.527A pdb=" N ASN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 297 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 306 through 334 Proline residue: B 313 - end of helix 461 hydrogen bonds defined for protein. 1383 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: 1.23 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1428 1.34 - 1.45: 646 1.45 - 1.57: 2258 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 4356 Sorted by residual: bond pdb=" CG ARG A 178 " pdb=" CD ARG A 178 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.80e+00 bond pdb=" CG ARG B 178 " pdb=" CD ARG B 178 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.79e+00 bond pdb=" CA VAL A 233 " pdb=" CB VAL A 233 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.25e-02 6.40e+03 1.51e+00 bond pdb=" CB TRP A 170 " pdb=" CG TRP A 170 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.49e+00 bond pdb=" CA ILE B 145 " pdb=" CB ILE B 145 " ideal model delta sigma weight residual 1.540 1.525 0.014 1.17e-02 7.31e+03 1.49e+00 ... (remaining 4351 not shown) Histogram of bond angle deviations from ideal: 97.23 - 104.59: 40 104.59 - 111.94: 2201 111.94 - 119.30: 1312 119.30 - 126.65: 2399 126.65 - 134.01: 42 Bond angle restraints: 5994 Sorted by residual: angle pdb=" N PRO B 8 " pdb=" CA PRO B 8 " pdb=" CB PRO B 8 " ideal model delta sigma weight residual 103.39 110.08 -6.69 1.08e+00 8.57e-01 3.84e+01 angle pdb=" N PRO A 8 " pdb=" CA PRO A 8 " pdb=" CB PRO A 8 " ideal model delta sigma weight residual 103.39 110.07 -6.68 1.08e+00 8.57e-01 3.83e+01 angle pdb=" NE ARG B 178 " pdb=" CZ ARG B 178 " pdb=" NH1 ARG B 178 " ideal model delta sigma weight residual 121.50 117.42 4.08 1.00e+00 1.00e+00 1.66e+01 angle pdb=" NE ARG A 178 " pdb=" CZ ARG A 178 " pdb=" NH1 ARG A 178 " ideal model delta sigma weight residual 121.50 117.52 3.98 1.00e+00 1.00e+00 1.58e+01 angle pdb=" CB MET A 87 " pdb=" CG MET A 87 " pdb=" SD MET A 87 " ideal model delta sigma weight residual 112.70 123.98 -11.28 3.00e+00 1.11e-01 1.41e+01 ... (remaining 5989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.29: 2272 12.29 - 24.58: 152 24.58 - 36.86: 74 36.86 - 49.15: 6 49.15 - 61.44: 6 Dihedral angle restraints: 2510 sinusoidal: 586 harmonic: 1924 Sorted by residual: dihedral pdb=" CA LEU B 154 " pdb=" C LEU B 154 " pdb=" N LEU B 155 " pdb=" CA LEU B 155 " ideal model delta harmonic sigma weight residual -180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA LEU A 154 " pdb=" C LEU A 154 " pdb=" N LEU A 155 " pdb=" CA LEU A 155 " ideal model delta harmonic sigma weight residual -180.00 -153.53 -26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA GLY A 106 " pdb=" C GLY A 106 " pdb=" N LEU A 107 " pdb=" CA LEU A 107 " ideal model delta harmonic sigma weight residual 180.00 154.77 25.23 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 2507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 524 0.046 - 0.093: 174 0.093 - 0.139: 17 0.139 - 0.185: 7 0.185 - 0.231: 2 Chirality restraints: 724 Sorted by residual: chirality pdb=" CA PRO A 8 " pdb=" N PRO A 8 " pdb=" C PRO A 8 " pdb=" CB PRO A 8 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO B 8 " pdb=" N PRO B 8 " pdb=" C PRO B 8 " pdb=" CB PRO B 8 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU B 140 " pdb=" CB LEU B 140 " pdb=" CD1 LEU B 140 " pdb=" CD2 LEU B 140 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 721 not shown) Planarity restraints: 790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 139 " 0.016 2.00e-02 2.50e+03 1.39e-02 3.84e+00 pdb=" CG TYR B 139 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 139 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 139 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 139 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 139 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 139 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 139 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.016 2.00e-02 2.50e+03 1.38e-02 3.79e+00 pdb=" CG TYR A 139 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 238 " 0.016 2.00e-02 2.50e+03 9.75e-03 1.90e+00 pdb=" CG TYR A 238 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 238 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 238 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 238 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 238 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 238 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 238 " 0.000 2.00e-02 2.50e+03 ... (remaining 787 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1454 2.82 - 3.34: 5127 3.34 - 3.86: 7295 3.86 - 4.38: 7293 4.38 - 4.90: 11642 Nonbonded interactions: 32811 Sorted by model distance: nonbonded pdb=" ND2 ASN A 105 " pdb=" O ASN A 115 " model vdw 2.295 2.520 nonbonded pdb=" ND2 ASN B 105 " pdb=" O ASN B 115 " model vdw 2.295 2.520 nonbonded pdb=" ND2 ASN B 165 " pdb=" OG SER B 204 " model vdw 2.320 2.520 nonbonded pdb=" ND2 ASN A 165 " pdb=" OG SER A 204 " model vdw 2.321 2.520 nonbonded pdb=" O MET A 228 " pdb=" OG SER A 231 " model vdw 2.324 2.440 ... (remaining 32806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 18 5.16 5 C 2716 2.51 5 N 740 2.21 5 O 800 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=0.00 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: 0.620 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: 3.930 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 17.310 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 : 0.006 0.050 4356 Z= 0.390 Angle : 0.885 11.280 5994 Z= 0.512 Chirality : 0.045 0.231 724 Planarity : 0.004 0.029 790 Dihedral : 11.591 61.439 1266 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.33), residues: 652 helix: 2.47 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -3.11 (0.53), residues: 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.890 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1669 time to fit residues: 36.0215 Evaluate side-chains 118 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 4356 Z= 0.182 Angle : 0.718 10.744 5994 Z= 0.367 Chirality : 0.039 0.146 724 Planarity : 0.004 0.024 790 Dihedral : 4.720 23.182 690 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer Outliers : 5.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.34), residues: 652 helix: 3.38 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -2.91 (0.54), residues: 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 164 average time/residue: 0.1431 time to fit residues: 29.8712 Evaluate side-chains 140 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0456 time to fit residues: 1.7310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 0.0970 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 50.0000 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4356 Z= 0.199 Angle : 0.735 8.654 5994 Z= 0.381 Chirality : 0.040 0.166 724 Planarity : 0.003 0.022 790 Dihedral : 4.581 24.012 690 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.34), residues: 652 helix: 3.52 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -2.82 (0.54), residues: 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 0.539 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 149 average time/residue: 0.1483 time to fit residues: 27.9930 Evaluate side-chains 141 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0443 time to fit residues: 1.0874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 40.0000 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 0.0000 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 237 GLN A 306 GLN B 237 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 4356 Z= 0.168 Angle : 0.709 8.591 5994 Z= 0.353 Chirality : 0.039 0.147 724 Planarity : 0.003 0.019 790 Dihedral : 4.383 21.450 690 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.33), residues: 652 helix: 3.50 (0.21), residues: 518 sheet: None (None), residues: 0 loop : -2.66 (0.52), residues: 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 0.536 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 151 average time/residue: 0.1475 time to fit residues: 28.1559 Evaluate side-chains 144 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0389 time to fit residues: 0.9028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 50.0000 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4356 Z= 0.195 Angle : 0.718 8.500 5994 Z= 0.371 Chirality : 0.040 0.196 724 Planarity : 0.003 0.020 790 Dihedral : 4.428 24.422 690 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 4.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.34), residues: 652 helix: 3.53 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -2.38 (0.57), residues: 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 148 average time/residue: 0.1512 time to fit residues: 28.3692 Evaluate side-chains 141 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0460 time to fit residues: 1.1779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 0.0060 chunk 6 optimal weight: 0.0060 chunk 35 optimal weight: 0.9980 overall best weight: 1.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4356 Z= 0.175 Angle : 0.718 8.380 5994 Z= 0.362 Chirality : 0.039 0.190 724 Planarity : 0.003 0.018 790 Dihedral : 4.369 23.079 690 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.34), residues: 652 helix: 3.56 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -2.45 (0.57), residues: 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 0.541 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 155 average time/residue: 0.1492 time to fit residues: 29.1446 Evaluate side-chains 141 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0467 time to fit residues: 1.0806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 0.0010 chunk 37 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 30.0000 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4356 Z= 0.192 Angle : 0.750 8.501 5994 Z= 0.387 Chirality : 0.040 0.169 724 Planarity : 0.004 0.082 790 Dihedral : 4.421 23.906 690 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.34), residues: 652 helix: 3.51 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -2.31 (0.58), residues: 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 0.587 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 146 average time/residue: 0.1551 time to fit residues: 28.4183 Evaluate side-chains 145 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0469 time to fit residues: 1.0129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 30 optimal weight: 0.0060 chunk 5 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4356 Z= 0.193 Angle : 0.753 8.771 5994 Z= 0.385 Chirality : 0.041 0.168 724 Planarity : 0.004 0.066 790 Dihedral : 4.436 23.841 690 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.34), residues: 652 helix: 3.43 (0.21), residues: 516 sheet: None (None), residues: 0 loop : -2.02 (0.56), residues: 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 147 time to evaluate : 0.539 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 148 average time/residue: 0.1468 time to fit residues: 27.5612 Evaluate side-chains 148 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0462 time to fit residues: 0.9948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 25 optimal weight: 50.0000 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 0.0060 chunk 37 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4356 Z= 0.191 Angle : 0.769 10.457 5994 Z= 0.390 Chirality : 0.041 0.216 724 Planarity : 0.003 0.051 790 Dihedral : 4.415 23.634 690 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.34), residues: 652 helix: 3.40 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -2.00 (0.57), residues: 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 0.542 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 146 average time/residue: 0.1426 time to fit residues: 26.4015 Evaluate side-chains 143 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 0.454 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0694 time to fit residues: 0.7757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 4356 Z= 0.289 Angle : 0.828 10.760 5994 Z= 0.437 Chirality : 0.043 0.189 724 Planarity : 0.005 0.068 790 Dihedral : 4.799 24.489 690 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.34), residues: 652 helix: 2.98 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -2.10 (0.55), residues: 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 0.546 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 146 average time/residue: 0.1378 time to fit residues: 26.0232 Evaluate side-chains 141 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0483 time to fit residues: 1.0317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 0.0010 chunk 9 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN ** B 306 GLN ** 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 = 0.3752 r_free = 0.3752 target = 0.098833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.079928 restraints weight = 15670.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.081932 restraints weight = 9680.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.083373 restraints weight = 6937.593| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 4356 Z= 0.266 Angle : 0.816 10.470 5994 Z= 0.431 Chirality : 0.043 0.174 724 Planarity : 0.004 0.067 790 Dihedral : 4.833 24.869 690 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.34), residues: 652 helix: 3.09 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.47 (0.60), residues: 114 =============================================================================== Job complete usr+sys time: 1158.76 seconds wall clock time: 21 minutes 38.70 seconds (1298.70 seconds total)