Starting phenix.real_space_refine on Wed Jan 17 11:25:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzq_24774/01_2024/7rzq_24774.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzq_24774/01_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_24774/01_2024/7rzq_24774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzq_24774/01_2024/7rzq_24774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzq_24774/01_2024/7rzq_24774.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzq_24774/01_2024/7rzq_24774.pdb" } 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 Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 1.65, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 487.8 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: 0.64 Time building geometry restraints manager: 1.16 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: 106.83 - 110.35: 516 110.35 - 113.87: 1005 113.87 - 117.39: 335 117.39 - 120.91: 874 120.91 - 124.43: 534 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 2.440 nonbonded pdb=" O GLY B 971 " pdb=" OG SER B 974 " model vdw 2.340 2.440 nonbonded pdb=" O GLY C 971 " pdb=" OG SER C 974 " model vdw 2.340 2.440 nonbonded pdb=" OG SER B 943 " pdb=" OE2 GLU D1182 " model vdw 2.354 2.440 nonbonded pdb=" OG SER C 943 " pdb=" OE2 GLU E1182 " model vdw 2.354 2.440 ... (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 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: 0.740 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: 0.000 Extract box with map and model: 3.370 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.850 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.210 ------------------------------------------------------------------------------- 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 : 0.284 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.6668 time to fit residues: 16.9750 Evaluate side-chains 24 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.0010 chunk 8 optimal weight: 0.5980 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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: 0.7508 moved from start: 0.1111 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= 0.186 Angle : 0.293 2.821 3264 Z= 0.172 Chirality : 0.031 0.104 414 Planarity : 0.002 0.014 429 Dihedral : 2.943 8.487 322 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 3.57 % 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: 4.70 (0.44), residues: 310 helix: 4.05 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.89 (0.75), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE C 970 ARG 0.005 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 21 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.251 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 20 average time/residue: 0.7264 time to fit residues: 15.3441 Evaluate side-chains 20 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 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: 0.7521 moved from start: 0.1414 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= 0.218 Angle : 0.301 2.690 3264 Z= 0.175 Chirality : 0.032 0.109 414 Planarity : 0.002 0.007 429 Dihedral : 2.953 9.700 322 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 3.57 % 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: 5.33 (0.44), residues: 310 helix: 4.47 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.55 (0.79), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE C 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 25 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.253 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.5602 time to fit residues: 13.7570 Evaluate side-chains 25 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER 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: 0.5980 chunk 13 optimal weight: 0.0000 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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: 0.7503 moved from start: 0.1564 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= 0.159 Angle : 0.257 2.109 3264 Z= 0.154 Chirality : 0.031 0.107 414 Planarity : 0.001 0.017 429 Dihedral : 2.773 9.466 322 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 3.93 % Favored : 95.00 % 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: 5.99 (0.44), residues: 310 helix: 4.95 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.38 (0.78), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 927 ARG 0.003 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 26 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.287 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.5257 time to fit residues: 13.5390 Evaluate side-chains 25 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.4980 chunk 11 optimal weight: 0.1980 chunk 24 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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: 0.7503 moved from start: 0.1673 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= 0.158 Angle : 0.261 2.130 3264 Z= 0.154 Chirality : 0.031 0.108 414 Planarity : 0.001 0.007 429 Dihedral : 2.729 9.174 322 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 5.36 % 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: 6.17 (0.44), residues: 310 helix: 5.07 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.31 (0.78), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE C 970 ARG 0.001 0.000 ARG A 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 27 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.280 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.5257 time to fit residues: 14.0999 Evaluate side-chains 27 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 981 LEU 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: 0.5980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7519 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2421 Z= 0.222 Angle : 0.286 2.297 3264 Z= 0.167 Chirality : 0.032 0.110 414 Planarity : 0.001 0.007 429 Dihedral : 2.855 9.487 322 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.30 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: 5.98 (0.44), residues: 310 helix: 4.92 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.25 (0.78), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE C 970 ARG 0.001 0.000 ARG A 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 25 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.283 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.5862 time to fit residues: 14.4014 Evaluate side-chains 24 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER 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: 0.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 0.0670 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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: 0.7508 moved from start: 0.1797 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= 0.177 Angle : 0.259 2.239 3264 Z= 0.154 Chirality : 0.031 0.108 414 Planarity : 0.001 0.006 429 Dihedral : 2.748 9.130 322 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.43 % Allowed : 5.71 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.19 (0.43), residues: 310 helix: 5.06 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.20 (0.78), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 927 ARG 0.001 0.000 ARG A 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 26 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.266 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 24 average time/residue: 0.5662 time to fit residues: 14.5151 Evaluate side-chains 24 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER 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: 0.6980 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 25 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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: 0.7502 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2421 Z= 0.159 Angle : 0.249 2.235 3264 Z= 0.150 Chirality : 0.031 0.108 414 Planarity : 0.001 0.006 429 Dihedral : 2.692 8.982 322 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 6.07 % Favored : 92.86 % 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: 6.07 (0.44), residues: 310 helix: 4.71 (0.27), residues: 255 sheet: None (None), residues: 0 loop : -0.04 (0.80), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE C 970 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 : 0.280 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.5523 time to fit residues: 14.1936 Evaluate side-chains 25 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.0070 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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: 0.7513 moved from start: 0.1861 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= 0.197 Angle : 0.270 2.197 3264 Z= 0.159 Chirality : 0.032 0.109 414 Planarity : 0.001 0.016 429 Dihedral : 2.775 8.963 322 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.30 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: 5.88 (0.44), residues: 310 helix: 4.58 (0.27), residues: 255 sheet: None (None), residues: 0 loop : -0.10 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE C 970 ARG 0.002 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 26 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.276 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.5476 time to fit residues: 14.0995 Evaluate side-chains 25 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 0.0770 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.0570 chunk 17 optimal weight: 1.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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: 0.7497 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2421 Z= 0.143 Angle : 0.245 2.267 3264 Z= 0.148 Chirality : 0.031 0.108 414 Planarity : 0.001 0.008 429 Dihedral : 2.669 8.988 322 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 6.43 % Favored : 92.86 % 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: 6.18 (0.44), residues: 310 helix: 4.79 (0.27), residues: 255 sheet: None (None), residues: 0 loop : -0.00 (0.80), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE C 970 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 24 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.284 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.5882 time to fit residues: 13.8581 Evaluate side-chains 24 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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: 0.5980 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.145336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.127634 restraints weight = 2935.870| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 1.65 r_work: 0.4076 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3912 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1905 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= 0.191 Angle : 0.266 2.254 3264 Z= 0.157 Chirality : 0.032 0.109 414 Planarity : 0.001 0.008 429 Dihedral : 2.750 8.953 322 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 6.07 % Favored : 92.86 % 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: 5.98 (0.44), residues: 310 helix: 4.65 (0.27), residues: 255 sheet: None (None), residues: 0 loop : -0.06 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE C 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: 1098.77 seconds wall clock time: 22 minutes 10.02 seconds (1330.02 seconds total)