Starting phenix.real_space_refine on Mon Sep 23 12:22:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzq_24774/09_2024/7rzq_24774.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzq_24774/09_2024/7rzq_24774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzq_24774/09_2024/7rzq_24774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzq_24774/09_2024/7rzq_24774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzq_24774/09_2024/7rzq_24774.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzq_24774/09_2024/7rzq_24774.cif" } resolution = 2.09 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 1491 2.51 5 N 424 2.21 5 O 506 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: 2421 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: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 266 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "E" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "F" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 1.98, per 1000 atoms: 0.82 Number of scatterers: 2421 At special positions: 0 Unit cell: (44.8938, 51.4238, 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 506 8.00 N 424 7.00 C 1491 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: 0.58 Conformation dependent library (CDL) restraints added in 291.4 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 614 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 83.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 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 Processing helix chain 'E' and resid 1179 through 1193 Processing helix 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 235 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: 0.61 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 461 1.29 - 1.35: 397 1.35 - 1.42: 53 1.42 - 1.48: 358 1.48 - 1.54: 1152 Bond restraints: 2421 Sorted by residual: bond pdb=" C ILE F1179 " pdb=" O ILE F1179 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.98e-01 bond pdb=" C ILE D1179 " pdb=" O ILE D1179 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.29e-01 bond pdb=" CA ASN E1178 " pdb=" CB ASN E1178 " ideal model delta sigma weight residual 1.526 1.511 0.015 1.70e-02 3.46e+03 8.23e-01 bond pdb=" N ILE F1179 " pdb=" CA ILE F1179 " ideal model delta sigma weight residual 1.459 1.448 0.011 1.25e-02 6.40e+03 8.17e-01 bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.226 0.011 1.19e-02 7.06e+03 7.98e-01 ... (remaining 2416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.67: 3048 0.67 - 1.34: 169 1.34 - 2.00: 35 2.00 - 2.67: 6 2.67 - 3.34: 6 Bond angle restraints: 3264 Sorted by residual: angle pdb=" N ILE F1169 " pdb=" CA ILE F1169 " pdb=" C ILE F1169 " ideal model delta sigma weight residual 113.20 111.55 1.65 9.60e-01 1.09e+00 2.96e+00 angle pdb=" N ILE D1169 " pdb=" CA ILE D1169 " pdb=" C ILE D1169 " ideal model delta sigma weight residual 113.20 111.56 1.64 9.60e-01 1.09e+00 2.93e+00 angle pdb=" N ILE E1169 " pdb=" CA ILE E1169 " pdb=" C ILE E1169 " ideal model delta sigma weight residual 113.20 111.57 1.63 9.60e-01 1.09e+00 2.87e+00 angle pdb=" CA ARG A 983 " pdb=" CB ARG A 983 " pdb=" CG ARG A 983 " ideal model delta sigma weight residual 114.10 117.44 -3.34 2.00e+00 2.50e-01 2.79e+00 angle pdb=" CA ARG C 983 " pdb=" CB ARG C 983 " pdb=" CG ARG C 983 " ideal model delta sigma weight residual 114.10 117.39 -3.29 2.00e+00 2.50e-01 2.71e+00 ... (remaining 3259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 1400 16.80 - 33.60: 88 33.60 - 50.40: 15 50.40 - 67.21: 6 67.21 - 84.01: 9 Dihedral angle restraints: 1518 sinusoidal: 588 harmonic: 930 Sorted by residual: dihedral pdb=" CG ARG B 983 " pdb=" CD ARG B 983 " pdb=" NE ARG B 983 " pdb=" CZ ARG B 983 " ideal model delta sinusoidal sigma weight residual -180.00 -137.17 -42.83 2 1.50e+01 4.44e-03 9.86e+00 dihedral pdb=" CG ARG C 983 " pdb=" CD ARG C 983 " pdb=" NE ARG C 983 " pdb=" CZ ARG C 983 " ideal model delta sinusoidal sigma weight residual 180.00 -137.20 -42.80 2 1.50e+01 4.44e-03 9.85e+00 dihedral pdb=" CG ARG A 983 " pdb=" CD ARG A 983 " pdb=" NE ARG A 983 " pdb=" CZ ARG A 983 " ideal model delta sinusoidal sigma weight residual 180.00 -137.21 -42.79 2 1.50e+01 4.44e-03 9.85e+00 ... (remaining 1515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 175 0.021 - 0.043: 156 0.043 - 0.064: 66 0.064 - 0.085: 11 0.085 - 0.106: 6 Chirality restraints: 414 Sorted by residual: chirality pdb=" CA ILE D1172 " pdb=" N ILE D1172 " pdb=" C ILE D1172 " pdb=" CB ILE D1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.83e-01 chirality pdb=" CA ILE E1172 " pdb=" N ILE E1172 " pdb=" C ILE E1172 " pdb=" CB ILE E1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.74e-01 chirality pdb=" CA ILE F1172 " pdb=" N ILE F1172 " pdb=" C ILE F1172 " pdb=" CB ILE F1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.70e-01 ... (remaining 411 not shown) Planarity restraints: 429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 983 " -0.100 9.50e-02 1.11e+02 4.50e-02 1.49e+00 pdb=" NE ARG B 983 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 983 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 983 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 983 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 983 " 0.099 9.50e-02 1.11e+02 4.47e-02 1.46e+00 pdb=" NE ARG C 983 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG C 983 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 983 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 983 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 983 " -0.098 9.50e-02 1.11e+02 4.43e-02 1.43e+00 pdb=" NE ARG A 983 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 983 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 983 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 983 " -0.001 2.00e-02 2.50e+03 ... (remaining 426 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 818 2.85 - 3.36: 2698 3.36 - 3.88: 4086 3.88 - 4.39: 4441 4.39 - 4.90: 7889 Nonbonded interactions: 19932 Sorted by model distance: nonbonded pdb=" O GLY A 971 " pdb=" OG SER A 974 " model vdw 2.339 3.040 nonbonded pdb=" O GLY B 971 " pdb=" OG SER B 974 " model vdw 2.340 3.040 nonbonded pdb=" O GLY C 971 " pdb=" OG SER C 974 " model vdw 2.340 3.040 nonbonded pdb=" OG SER B 943 " pdb=" OE2 GLU D1182 " model vdw 2.354 3.040 nonbonded pdb=" OG SER C 943 " pdb=" OE2 GLU E1182 " model vdw 2.354 3.040 ... (remaining 19927 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' and resid 1166 through 1200) selection = (chain 'F' and resid 1166 through 1200) } 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: 0.710 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.580 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:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2421 Z= 0.399 Angle : 0.396 3.339 3264 Z= 0.240 Chirality : 0.034 0.106 414 Planarity : 0.004 0.045 429 Dihedral : 14.232 84.007 904 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.43), residues: 310 helix: 2.17 (0.28), residues: 246 sheet: None (None), residues: 0 loop : -1.64 (0.77), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 970 ARG 0.009 0.002 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.263 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.6163 time to fit residues: 15.7023 Evaluate side-chains 24 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 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 949 GLN B 949 GLN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2421 Z= 0.200 Angle : 0.317 2.790 3264 Z= 0.184 Chirality : 0.032 0.103 414 Planarity : 0.002 0.014 429 Dihedral : 2.991 9.155 322 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.36 % Allowed : 3.93 % Favored : 95.71 % 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: 4.68 (0.45), residues: 310 helix: 4.01 (0.28), residues: 243 sheet: None (None), residues: 0 loop : -0.83 (0.77), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE C 970 ARG 0.003 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.286 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.7309 time to fit residues: 15.4918 Evaluate side-chains 19 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.0060 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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: 0.7510 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2421 Z= 0.161 Angle : 0.275 2.268 3264 Z= 0.162 Chirality : 0.031 0.107 414 Planarity : 0.001 0.006 429 Dihedral : 2.802 9.393 322 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.36 % Allowed : 4.29 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.63 (0.44), residues: 310 helix: 4.66 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.35 (0.84), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 970 ARG 0.002 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.257 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.6222 time to fit residues: 14.5875 Evaluate side-chains 23 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.0170 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.0670 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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: 0.7504 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2421 Z= 0.147 Angle : 0.266 2.850 3264 Z= 0.160 Chirality : 0.031 0.107 414 Planarity : 0.001 0.012 429 Dihedral : 2.702 9.176 322 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 5.00 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.05 (0.44), residues: 310 helix: 4.96 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.23 (0.82), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 970 ARG 0.004 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.267 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.5399 time to fit residues: 13.8913 Evaluate side-chains 24 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7529 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2421 Z= 0.238 Angle : 0.307 2.284 3264 Z= 0.177 Chirality : 0.033 0.110 414 Planarity : 0.001 0.008 429 Dihedral : 2.886 9.373 322 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 5.71 % Favored : 93.21 % 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: 5.71 (0.44), residues: 310 helix: 4.70 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.25 (0.79), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 927 ARG 0.002 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.263 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.5349 time to fit residues: 13.7520 Evaluate side-chains 25 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 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: 0.7518 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2421 Z= 0.190 Angle : 0.284 3.029 3264 Z= 0.168 Chirality : 0.032 0.108 414 Planarity : 0.002 0.020 429 Dihedral : 2.795 8.990 322 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 5.71 % Favored : 93.57 % 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: 5.92 (0.43), residues: 310 helix: 4.84 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.13 (0.79), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 970 ARG 0.002 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.269 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.5656 time to fit residues: 15.2283 Evaluate side-chains 25 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7525 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2421 Z= 0.214 Angle : 0.293 2.511 3264 Z= 0.172 Chirality : 0.033 0.109 414 Planarity : 0.001 0.007 429 Dihedral : 2.852 10.270 322 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 6.79 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.81 (0.43), residues: 310 helix: 4.75 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.13 (0.79), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 970 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.259 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 0.5068 time to fit residues: 14.1335 Evaluate side-chains 25 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2421 Z= 0.195 Angle : 0.290 3.337 3264 Z= 0.173 Chirality : 0.032 0.108 414 Planarity : 0.001 0.006 429 Dihedral : 2.813 9.980 322 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 7.14 % Favored : 91.79 % 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: 5.60 (0.44), residues: 310 helix: 4.34 (0.27), residues: 255 sheet: None (None), residues: 0 loop : 0.06 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 927 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.256 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.5121 time to fit residues: 13.1710 Evaluate side-chains 25 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7537 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2421 Z= 0.271 Angle : 0.322 2.528 3264 Z= 0.186 Chirality : 0.034 0.111 414 Planarity : 0.002 0.007 429 Dihedral : 2.963 10.152 322 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 7.50 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.33 (0.44), residues: 310 helix: 4.14 (0.28), residues: 255 sheet: None (None), residues: 0 loop : 0.02 (0.81), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 927 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.275 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.5983 time to fit residues: 14.0442 Evaluate side-chains 23 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7524 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2421 Z= 0.202 Angle : 0.294 3.437 3264 Z= 0.175 Chirality : 0.033 0.109 414 Planarity : 0.001 0.006 429 Dihedral : 2.857 10.057 322 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 7.86 % Favored : 91.07 % 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: 5.56 (0.44), residues: 310 helix: 4.30 (0.27), residues: 255 sheet: None (None), residues: 0 loop : 0.12 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 927 ARG 0.001 0.000 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.343 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.5462 time to fit residues: 13.5254 Evaluate side-chains 24 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0070 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 29 optimal weight: 0.2980 chunk 1 optimal weight: 0.0370 chunk 28 optimal weight: 0.9990 overall best weight: 0.2676 ------------------------------------------------------------------------------- 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 = 0.4436 r_free = 0.4436 target = 0.144338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.125735 restraints weight = 2938.039| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 1.69 r_work: 0.4041 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2421 Z= 0.113 Angle : 0.246 2.512 3264 Z= 0.150 Chirality : 0.031 0.106 414 Planarity : 0.001 0.006 429 Dihedral : 2.626 9.651 322 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 7.50 % Favored : 91.79 % 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: 6.40 (0.43), residues: 310 helix: 5.16 (0.25), residues: 243 sheet: None (None), residues: 0 loop : 0.11 (0.82), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 970 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: 1089.72 seconds wall clock time: 20 minutes 20.61 seconds (1220.61 seconds total)