Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:53:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/11_2022/7rzv_24779.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/11_2022/7rzv_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_24779/11_2022/7rzv_24779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/11_2022/7rzv_24779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/11_2022/7rzv_24779.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/11_2022/7rzv_24779.pdb" } resolution = 2.11 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= 0.001 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 Convert atoms to be neutral 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-dev-4778/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: 2.10, per 1000 atoms: 0.82 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: 1.16 Conformation dependent library (CDL) restraints added in 340.3 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: 0.06 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: 0.72 Time building geometry restraints manager: 1.24 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 3.180 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 12.550 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 % 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 *********************** 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 : 0.318 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.6478 time to fit residues: 19.9284 Evaluate side-chains 28 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3909 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.8003 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 % 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 *********************** 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 : 0.304 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.4918 time to fit residues: 12.7920 Evaluate side-chains 23 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.285 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.5439 time to fit residues: 2.0007 ------------------------------------------------------------------------------- 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: 0.9980 chunk 30 optimal weight: 0.0270 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.0020 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.3646 ------------------------------------------------------------------------------- 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: 0.7991 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 2571 Z= 0.149 Angle : 0.270 2.924 3471 Z= 0.161 Chirality : 0.030 0.105 432 Planarity : 0.001 0.010 459 Dihedral : 2.655 7.941 339 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.34 % 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: 5.77 (0.43), residues: 327 helix: 5.04 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.61 (0.66), residues: 81 *********************** 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 : 0.226 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.4601 time to fit residues: 11.4378 Evaluate side-chains 23 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.306 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4471 ------------------------------------------------------------------------------- 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: 0.0870 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 26 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- 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** C 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.014 2571 Z= 0.119 Angle : 0.246 3.013 3471 Z= 0.149 Chirality : 0.030 0.105 432 Planarity : 0.001 0.007 459 Dihedral : 2.524 7.512 339 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.67 % 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: 6.19 (0.42), residues: 327 helix: 5.32 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.36 (0.66), residues: 81 *********************** 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 27 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.304 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.4373 time to fit residues: 12.4154 Evaluate side-chains 27 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.302 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.4685 time to fit residues: 1.9270 ------------------------------------------------------------------------------- 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: 0.6980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 7 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: 0.8002 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.018 2571 Z= 0.189 Angle : 0.291 4.242 3471 Z= 0.170 Chirality : 0.031 0.107 432 Planarity : 0.001 0.013 459 Dihedral : 2.688 8.526 339 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.67 % 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: 5.09 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.27 (0.67), residues: 81 *********************** 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 24 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.301 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 0.4871 time to fit residues: 12.1929 Evaluate side-chains 23 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4490 ------------------------------------------------------------------------------- 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: 0.7980 chunk 26 optimal weight: 0.2980 chunk 14 optimal weight: 0.0970 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.0170 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 overall best weight: 0.2616 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 2571 Z= 0.118 Angle : 0.268 3.850 3471 Z= 0.161 Chirality : 0.030 0.106 432 Planarity : 0.001 0.005 459 Dihedral : 2.484 7.470 339 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.67 % 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: 6.36 (0.42), residues: 327 helix: 5.39 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.10 (0.68), residues: 81 *********************** 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 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.296 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.4643 time to fit residues: 12.6376 Evaluate side-chains 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.305 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.3675 time to fit residues: 1.8377 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1739 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= 0.242 Angle : 0.317 4.073 3471 Z= 0.184 Chirality : 0.032 0.107 432 Planarity : 0.001 0.012 459 Dihedral : 2.807 9.128 339 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.34 % 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: 5.86 (0.42), residues: 327 helix: 4.97 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.07 (0.70), residues: 81 *********************** 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 25 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.313 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.4838 time to fit residues: 13.1464 Evaluate side-chains 25 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.304 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4277 ------------------------------------------------------------------------------- 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: 6.9990 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.0030 chunk 19 optimal weight: 0.7980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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: 0.8007 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 2571 Z= 0.203 Angle : 0.319 5.304 3471 Z= 0.182 Chirality : 0.031 0.106 432 Planarity : 0.001 0.005 459 Dihedral : 2.747 9.033 339 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.67 % 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: 5.95 (0.42), residues: 327 helix: 5.01 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.07 (0.71), residues: 81 *********************** 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 25 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.302 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.5052 time to fit residues: 13.1452 Evaluate side-chains 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.4404 time to fit residues: 1.8848 ------------------------------------------------------------------------------- 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: 0.9990 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 30 optimal weight: 0.0070 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 2571 Z= 0.141 Angle : 0.294 4.436 3471 Z= 0.172 Chirality : 0.030 0.106 432 Planarity : 0.001 0.005 459 Dihedral : 2.585 8.053 339 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.34 % 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: 6.25 (0.42), residues: 327 helix: 5.25 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.11 (0.71), residues: 81 *********************** 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 24 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.303 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.4876 time to fit residues: 12.6774 Evaluate side-chains 24 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4656 ------------------------------------------------------------------------------- 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: 0.4980 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.8006 moved from start: 0.1862 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= 0.197 Angle : 0.314 4.561 3471 Z= 0.181 Chirality : 0.031 0.107 432 Planarity : 0.001 0.005 459 Dihedral : 2.722 8.778 339 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.01 % 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: 6.06 (0.42), residues: 327 helix: 5.09 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.13 (0.72), residues: 81 ********************** 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 28 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.307 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.4456 time to fit residues: 12.6428 Evaluate side-chains 28 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.297 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.7784 time to fit residues: 2.0276 ------------------------------------------------------------------------------- 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: 0.4980 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.148694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.130311 restraints weight = 3104.365| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.63 r_work: 0.4108 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.4091 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work: 0.4074 rms_B_bonded: 1.56 restraints_weight: 0.1250 r_work: 0.4055 rms_B_bonded: 1.73 restraints_weight: 0.0625 r_work: 0.4034 rms_B_bonded: 1.97 restraints_weight: 0.0312 r_work: 0.4009 rms_B_bonded: 2.28 restraints_weight: 0.0156 r_work: 0.3980 rms_B_bonded: 2.66 restraints_weight: 0.0078 r_work: 0.3947 rms_B_bonded: 3.13 restraints_weight: 0.0039 r_work: 0.3907 rms_B_bonded: 3.71 restraints_weight: 0.0020 r_work: 0.3859 rms_B_bonded: 4.42 restraints_weight: 0.0010 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1921 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= 0.224 Angle : 0.326 4.559 3471 Z= 0.187 Chirality : 0.032 0.106 432 Planarity : 0.001 0.005 459 Dihedral : 2.827 9.225 339 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.34 % 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: 4.95 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.16 (0.73), residues: 81 =============================================================================== Job complete usr+sys time: 1017.85 seconds wall clock time: 19 minutes 18.08 seconds (1158.08 seconds total)