Starting phenix.real_space_refine on Mon Sep 23 12:34:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/09_2024/7rzv_24779.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/09_2024/7rzv_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_24779/09_2024/7rzv_24779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/09_2024/7rzv_24779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/09_2024/7rzv_24779.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzv_24779/09_2024/7rzv_24779.cif" } 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. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2562 Number of models: 1 Model: "" Number of chains: 2 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: "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} Restraints were copied for chains: D, F, C, B Time building chain proxies: 1.68, per 1000 atoms: 0.66 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 - 3.00 Amino acid : True - 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: 0.63 Conformation dependent library (CDL) restraints added in 306.4 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: 0.70 Time building geometry restraints manager: 0.72 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: 0.00 - 0.73: 3340 0.73 - 1.45: 112 1.45 - 2.18: 7 2.18 - 2.90: 6 2.90 - 3.63: 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 3.040 nonbonded pdb=" OG SER B 943 " pdb=" OE2 GLU D1182 " model vdw 2.348 3.040 nonbonded pdb=" OG SER A 943 " pdb=" OE2 GLU F1182 " model vdw 2.372 3.040 nonbonded pdb=" OD1 ASP F1163 " pdb=" N VAL F1164 " model vdw 2.395 3.120 nonbonded pdb=" OD1 ASP E1163 " pdb=" N VAL E1164 " model vdw 2.395 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.600 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.900 ------------------------------------------------------------------------------- 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 : 0.290 Fit side-chains revert: symmetry clash REVERT: A 978 ASN cc_start: 0.7770 (m-40) cc_final: 0.7421 (m-40) REVERT: B 969 ASN cc_start: 0.7937 (m-40) cc_final: 0.7733 (m-40) REVERT: D 1187 ASN cc_start: 0.8454 (m-40) cc_final: 0.8228 (m-40) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.6303 time to fit residues: 19.3460 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 ------------------------------------------------------------------------------- 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: 0.6980 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN B 935 GLN B 949 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1060 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= 0.166 Angle : 0.277 2.703 3471 Z= 0.159 Chirality : 0.031 0.106 432 Planarity : 0.001 0.011 459 Dihedral : 2.806 9.297 339 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 5.72 % Favored : 93.60 % 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: 5.20 (0.43), residues: 327 helix: 4.61 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -0.72 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E1159 PHE 0.005 0.001 PHE A 970 ARG 0.002 0.000 ARG C 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 : 0.281 Fit side-chains REVERT: A 978 ASN cc_start: 0.7883 (m-40) cc_final: 0.7645 (m-40) REVERT: B 966 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8222 (mm) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.5066 time to fit residues: 13.1114 Evaluate side-chains 24 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN 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: 0.1980 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 29 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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: 0.7551 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2571 Z= 0.153 Angle : 0.260 2.930 3471 Z= 0.155 Chirality : 0.030 0.105 432 Planarity : 0.001 0.010 459 Dihedral : 2.662 8.759 339 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 6.40 % 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: 5.92 (0.43), residues: 327 helix: 5.09 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.30 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D1159 PHE 0.006 0.001 PHE A 970 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 25 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.297 Fit side-chains REVERT: A 978 ASN cc_start: 0.7882 (m-40) cc_final: 0.7674 (m-40) REVERT: B 966 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8231 (mm) outliers start: 4 outliers final: 2 residues processed: 23 average time/residue: 0.5165 time to fit residues: 12.8446 Evaluate side-chains 24 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.0060 chunk 31 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 overall best weight: 0.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 2571 Z= 0.085 Angle : 0.236 2.964 3471 Z= 0.143 Chirality : 0.030 0.105 432 Planarity : 0.001 0.005 459 Dihedral : 2.410 7.284 339 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.34 % Allowed : 7.74 % Favored : 91.92 % 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: 6.61 (0.41), residues: 327 helix: 5.57 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.04 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.002 0.000 PHE A 970 ARG 0.000 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 24 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 978 ASN cc_start: 0.7849 (m-40) cc_final: 0.7639 (m110) REVERT: B 966 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8183 (mm) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.5264 time to fit residues: 13.6245 Evaluate side-chains 24 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7564 moved from start: 0.1589 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= 0.209 Angle : 0.279 3.039 3471 Z= 0.164 Chirality : 0.031 0.106 432 Planarity : 0.001 0.015 459 Dihedral : 2.683 9.050 339 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 6.06 % 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: 6.23 (0.42), residues: 327 helix: 5.23 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.12 (0.67), 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 0.001 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 30 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8254 (mm) outliers start: 5 outliers final: 2 residues processed: 26 average time/residue: 0.5062 time to fit residues: 14.1501 Evaluate side-chains 28 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.0370 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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: 0.7560 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2571 Z= 0.179 Angle : 0.290 3.815 3471 Z= 0.173 Chirality : 0.031 0.106 432 Planarity : 0.001 0.015 459 Dihedral : 2.661 8.386 339 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.50 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: 5.70 (0.42), residues: 327 helix: 4.48 (0.27), residues: 264 sheet: None (None), residues: 0 loop : 0.16 (0.66), residues: 63 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 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8253 (mm) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.4780 time to fit residues: 12.9425 Evaluate side-chains 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 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: B 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1786 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= 0.243 Angle : 0.327 4.118 3471 Z= 0.192 Chirality : 0.032 0.105 432 Planarity : 0.001 0.010 459 Dihedral : 2.848 9.493 339 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.30 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: 5.88 (0.42), residues: 327 helix: 4.90 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.27 (0.69), 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 : 0.219 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8258 (mm) REVERT: B 977 LEU cc_start: 0.8588 (tp) cc_final: 0.8275 (tt) outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.5118 time to fit residues: 13.2118 Evaluate side-chains 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.0070 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1845 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= 0.154 Angle : 0.295 4.410 3471 Z= 0.176 Chirality : 0.031 0.105 432 Planarity : 0.001 0.005 459 Dihedral : 2.641 8.432 339 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.11 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: 5.73 (0.42), residues: 327 helix: 4.49 (0.27), residues: 264 sheet: None (None), residues: 0 loop : 0.23 (0.67), residues: 63 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 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 : 0.284 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8264 (mm) REVERT: B 977 LEU cc_start: 0.8557 (tp) cc_final: 0.8239 (tt) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.4556 time to fit residues: 12.3848 Evaluate side-chains 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.0770 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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: 0.7569 moved from start: 0.1874 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= 0.203 Angle : 0.312 4.528 3471 Z= 0.184 Chirality : 0.031 0.105 432 Planarity : 0.001 0.005 459 Dihedral : 2.745 8.930 339 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.50 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: 6.06 (0.41), residues: 327 helix: 5.03 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.32 (0.68), 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 0.001 0.000 ARG C 983 *********************** 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 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8268 (mm) REVERT: B 977 LEU cc_start: 0.8567 (tp) cc_final: 0.8252 (tt) outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.5217 time to fit residues: 13.5288 Evaluate side-chains 26 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7578 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2571 Z= 0.237 Angle : 0.330 4.608 3471 Z= 0.193 Chirality : 0.032 0.105 432 Planarity : 0.001 0.006 459 Dihedral : 2.863 9.402 339 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.30 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: 5.93 (0.41), residues: 327 helix: 4.90 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.42 (0.69), 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 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 27 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8265 (mm) REVERT: B 977 LEU cc_start: 0.8570 (tp) cc_final: 0.8264 (tt) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.4820 time to fit residues: 13.0459 Evaluate side-chains 27 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.149018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.130018 restraints weight = 3113.935| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 1.67 r_work: 0.3981 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2571 Z= 0.229 Angle : 0.326 4.631 3471 Z= 0.191 Chirality : 0.032 0.105 432 Planarity : 0.001 0.006 459 Dihedral : 2.846 9.231 339 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 9.09 % 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: 5.96 (0.41), residues: 327 helix: 4.91 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.48 (0.70), 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1162.87 seconds wall clock time: 21 minutes 2.94 seconds (1262.94 seconds total)