Starting phenix.real_space_refine on Thu Dec 7 16:33:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/12_2023/7rzv_24779.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/12_2023/7rzv_24779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/12_2023/7rzv_24779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/12_2023/7rzv_24779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/12_2023/7rzv_24779.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/12_2023/7rzv_24779.pdb" } resolution = 2.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1578 2.51 5 N 447 2.21 5 O 537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2562 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "D" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "E" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "F" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Time building chain proxies: 1.80, per 1000 atoms: 0.70 Number of scatterers: 2562 At special positions: 0 Unit cell: (53.8725, 42.445, 116.724, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 537 8.00 N 447 7.00 C 1578 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: 1.13 Conformation dependent library (CDL) restraints added in 497.8 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 removed outlier: 3.649A pdb=" N LEU D1197 " --> pdb=" O ASN D1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1194 through 1197' Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 removed outlier: 3.649A pdb=" N LEU E1197 " --> pdb=" O ASN E1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1194 through 1197' Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 removed outlier: 3.649A pdb=" N LEU F1197 " --> pdb=" O ASN F1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1194 through 1197' 232 hydrogen bonds defined for protein. 696 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: 0.68 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 486 1.29 - 1.35: 420 1.35 - 1.42: 82 1.42 - 1.48: 380 1.48 - 1.54: 1203 Bond restraints: 2571 Sorted by residual: bond pdb=" CG LEU B 977 " pdb=" CD1 LEU B 977 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.14e-01 bond pdb=" CG LEU C 977 " pdb=" CD1 LEU C 977 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.90e-01 bond pdb=" CG LEU A 977 " pdb=" CD1 LEU A 977 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.79e-01 bond pdb=" CG LEU B 966 " pdb=" CD2 LEU B 966 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.26e-01 bond pdb=" CB ASN C 955 " pdb=" CG ASN C 955 " ideal model delta sigma weight residual 1.516 1.498 0.018 2.50e-02 1.60e+03 5.16e-01 ... (remaining 2566 not shown) Histogram of bond angle deviations from ideal: 102.47 - 108.22: 36 108.22 - 113.97: 1581 113.97 - 119.71: 648 119.71 - 125.46: 1200 125.46 - 131.21: 6 Bond angle restraints: 3471 Sorted by residual: angle pdb=" CB LEU B 977 " pdb=" CG LEU B 977 " pdb=" CD1 LEU B 977 " ideal model delta sigma weight residual 110.70 114.33 -3.63 3.00e+00 1.11e-01 1.46e+00 angle pdb=" CB LEU A 977 " pdb=" CG LEU A 977 " pdb=" CD1 LEU A 977 " ideal model delta sigma weight residual 110.70 114.29 -3.59 3.00e+00 1.11e-01 1.43e+00 angle pdb=" CB LEU C 977 " pdb=" CG LEU C 977 " pdb=" CD1 LEU C 977 " ideal model delta sigma weight residual 110.70 114.26 -3.56 3.00e+00 1.11e-01 1.41e+00 angle pdb=" C LEU A 977 " pdb=" N ASN A 978 " pdb=" CA ASN A 978 " ideal model delta sigma weight residual 120.29 118.73 1.56 1.42e+00 4.96e-01 1.21e+00 angle pdb=" C LEU B 977 " pdb=" N ASN B 978 " pdb=" CA ASN B 978 " ideal model delta sigma weight residual 120.29 118.73 1.56 1.42e+00 4.96e-01 1.20e+00 ... (remaining 3466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 1461 17.81 - 35.63: 114 35.63 - 53.44: 9 53.44 - 71.25: 12 71.25 - 89.07: 6 Dihedral angle restraints: 1602 sinusoidal: 621 harmonic: 981 Sorted by residual: dihedral pdb=" CA ARG D1185 " pdb=" CB ARG D1185 " pdb=" CG ARG D1185 " pdb=" CD ARG D1185 " ideal model delta sinusoidal sigma weight residual 60.00 99.79 -39.79 3 1.50e+01 4.44e-03 7.07e+00 dihedral pdb=" CA ARG E1185 " pdb=" CB ARG E1185 " pdb=" CG ARG E1185 " pdb=" CD ARG E1185 " ideal model delta sinusoidal sigma weight residual 60.00 99.77 -39.77 3 1.50e+01 4.44e-03 7.06e+00 dihedral pdb=" CA ARG F1185 " pdb=" CB ARG F1185 " pdb=" CG ARG F1185 " pdb=" CD ARG F1185 " ideal model delta sinusoidal sigma weight residual 60.00 99.76 -39.76 3 1.50e+01 4.44e-03 7.06e+00 ... (remaining 1599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 208 0.022 - 0.043: 159 0.043 - 0.065: 41 0.065 - 0.086: 7 0.086 - 0.108: 17 Chirality restraints: 432 Sorted by residual: chirality pdb=" CA LEU A 977 " pdb=" N LEU A 977 " pdb=" C LEU A 977 " pdb=" CB LEU A 977 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.89e-01 chirality pdb=" CA LEU B 977 " pdb=" N LEU B 977 " pdb=" C LEU B 977 " pdb=" CB LEU B 977 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.83e-01 chirality pdb=" CA LEU C 977 " pdb=" N LEU C 977 " pdb=" C LEU C 977 " pdb=" CB LEU C 977 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.64e-01 ... (remaining 429 not shown) Planarity restraints: 459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F1177 " -0.002 2.00e-02 2.50e+03 5.03e-03 2.53e-01 pdb=" C VAL F1177 " 0.009 2.00e-02 2.50e+03 pdb=" O VAL F1177 " -0.003 2.00e-02 2.50e+03 pdb=" N ASN F1178 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E1177 " 0.002 2.00e-02 2.50e+03 4.94e-03 2.45e-01 pdb=" C VAL E1177 " -0.009 2.00e-02 2.50e+03 pdb=" O VAL E1177 " 0.003 2.00e-02 2.50e+03 pdb=" N ASN E1178 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 952 " 0.002 2.00e-02 2.50e+03 4.90e-03 2.40e-01 pdb=" C VAL C 952 " -0.008 2.00e-02 2.50e+03 pdb=" O VAL C 952 " 0.003 2.00e-02 2.50e+03 pdb=" N ASN C 953 " 0.003 2.00e-02 2.50e+03 ... (remaining 456 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 873 2.86 - 3.37: 2778 3.37 - 3.88: 4432 3.88 - 4.39: 4741 4.39 - 4.90: 8106 Nonbonded interactions: 20930 Sorted by model distance: nonbonded pdb=" OG SER C 943 " pdb=" OE2 GLU E1182 " model vdw 2.348 2.440 nonbonded pdb=" OG SER B 943 " pdb=" OE2 GLU D1182 " model vdw 2.348 2.440 nonbonded pdb=" OG SER A 943 " pdb=" OE2 GLU F1182 " model vdw 2.372 2.440 nonbonded pdb=" OD1 ASP F1163 " pdb=" N VAL F1164 " model vdw 2.395 2.520 nonbonded pdb=" OD1 ASP E1163 " pdb=" N VAL E1164 " model vdw 2.395 2.520 ... (remaining 20925 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' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.010 Normalize map: mean=0, sd=1: 0.800 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: 3.390 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.180 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.005 0.026 2571 Z= 0.319 Angle : 0.354 3.628 3471 Z= 0.203 Chirality : 0.034 0.108 432 Planarity : 0.002 0.012 459 Dihedral : 14.679 89.066 954 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 3.06 (0.43), residues: 327 helix: 3.03 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -1.36 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D1159 PHE 0.002 0.001 PHE E1176 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.311 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.6619 time to fit residues: 20.3194 Evaluate side-chains 28 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.292 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 949 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2571 Z= 0.198 Angle : 0.282 2.795 3471 Z= 0.162 Chirality : 0.031 0.105 432 Planarity : 0.002 0.018 459 Dihedral : 2.849 8.775 339 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 6.73 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.01 (0.43), residues: 327 helix: 4.49 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.86 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.006 0.001 PHE E1176 ARG 0.003 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.297 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.5025 time to fit residues: 13.0628 Evaluate side-chains 23 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.289 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.4938 time to fit residues: 1.9568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.0020 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2571 Z= 0.159 Angle : 0.273 2.843 3471 Z= 0.162 Chirality : 0.030 0.105 432 Planarity : 0.001 0.011 459 Dihedral : 2.668 8.039 339 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.34 % Allowed : 7.41 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.73 (0.43), residues: 327 helix: 5.01 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.62 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.005 0.001 PHE E1176 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.312 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.5420 time to fit residues: 13.5059 Evaluate side-chains 23 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.299 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.0770 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2571 Z= 0.177 Angle : 0.268 3.102 3471 Z= 0.160 Chirality : 0.031 0.106 432 Planarity : 0.001 0.011 459 Dihedral : 2.681 8.370 339 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 7.74 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.84 (0.42), residues: 327 helix: 5.07 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.46 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.005 0.001 PHE E1176 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.314 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.5142 time to fit residues: 13.8854 Evaluate side-chains 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.3791 time to fit residues: 1.8027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.0030 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2571 Z= 0.190 Angle : 0.290 4.150 3471 Z= 0.170 Chirality : 0.031 0.106 432 Planarity : 0.001 0.010 459 Dihedral : 2.711 8.331 339 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 7.41 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.85 (0.42), residues: 327 helix: 5.03 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.31 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.006 0.001 PHE E1176 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.295 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.5004 time to fit residues: 13.5268 Evaluate side-chains 25 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2571 Z= 0.190 Angle : 0.293 3.866 3471 Z= 0.173 Chirality : 0.031 0.107 432 Planarity : 0.001 0.009 459 Dihedral : 2.706 8.627 339 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 8.08 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.93 (0.42), residues: 327 helix: 5.06 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.15 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.006 0.001 PHE E1176 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.405 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.4883 time to fit residues: 13.8160 Evaluate side-chains 27 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.292 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.4729 time to fit residues: 1.9038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2571 Z= 0.250 Angle : 0.334 4.667 3471 Z= 0.191 Chirality : 0.032 0.106 432 Planarity : 0.001 0.007 459 Dihedral : 2.867 9.708 339 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 7.74 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.70 (0.42), residues: 327 helix: 4.84 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.05 (0.71), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.008 0.001 PHE E1176 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.315 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.4950 time to fit residues: 13.3979 Evaluate side-chains 25 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.262 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.3891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.0470 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2571 Z= 0.200 Angle : 0.312 4.489 3471 Z= 0.182 Chirality : 0.031 0.106 432 Planarity : 0.001 0.005 459 Dihedral : 2.766 8.885 339 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 8.42 % Favored : 90.57 % 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: 5.90 (0.42), residues: 327 helix: 4.98 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.05 (0.72), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.007 0.001 PHE E1176 ARG 0.000 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.263 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.5077 time to fit residues: 13.7248 Evaluate side-chains 25 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.305 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 30 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2571 Z= 0.217 Angle : 0.319 4.504 3471 Z= 0.186 Chirality : 0.032 0.106 432 Planarity : 0.001 0.005 459 Dihedral : 2.824 9.316 339 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 8.42 % Favored : 90.57 % 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: 5.81 (0.42), residues: 327 helix: 4.90 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.08 (0.73), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.007 0.001 PHE E1176 ARG 0.000 0.000 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.309 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.5142 time to fit residues: 14.4257 Evaluate side-chains 27 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.5109 time to fit residues: 1.9249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2571 Z= 0.202 Angle : 0.311 4.515 3471 Z= 0.183 Chirality : 0.031 0.107 432 Planarity : 0.001 0.005 459 Dihedral : 2.779 8.868 339 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 9.09 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.91 (0.42), residues: 327 helix: 4.96 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.14 (0.73), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.007 0.001 PHE E1176 ARG 0.000 0.000 ARG D1185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.315 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.5141 time to fit residues: 14.4307 Evaluate side-chains 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.276 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.148748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.130226 restraints weight = 3087.073| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.63 r_work: 0.3981 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2571 Z= 0.264 Angle : 0.338 4.596 3471 Z= 0.196 Chirality : 0.033 0.106 432 Planarity : 0.001 0.005 459 Dihedral : 2.941 9.790 339 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 9.43 % Favored : 89.90 % 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: 5.66 (0.43), residues: 327 helix: 4.76 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.11 (0.75), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.008 0.001 PHE E1176 ARG 0.001 0.000 ARG D1185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1190.58 seconds wall clock time: 22 minutes 0.83 seconds (1320.83 seconds total)