Starting phenix.real_space_refine on Thu Dec 7 16:22:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzt_24777/12_2023/7rzt_24777.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzt_24777/12_2023/7rzt_24777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzt_24777/12_2023/7rzt_24777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzt_24777/12_2023/7rzt_24777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzt_24777/12_2023/7rzt_24777.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzt_24777/12_2023/7rzt_24777.pdb" } resolution = 2.35 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= 0.018 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 1518 2.51 5 N 426 2.21 5 O 507 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2451 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "D" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} 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: 1.69, per 1000 atoms: 0.69 Number of scatterers: 2451 At special positions: 0 Unit cell: (48.975, 42.445, 116.724, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 507 8.00 N 426 7.00 C 1518 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: 1.04 Conformation dependent library (CDL) restraints added in 455.4 milliseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 618 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 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: 1.12 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: 465 1.29 - 1.35: 399 1.35 - 1.42: 61 1.42 - 1.48: 365 1.48 - 1.54: 1164 Bond restraints: 2454 Sorted by residual: bond pdb=" C ILE F1179 " pdb=" O ILE F1179 " ideal model delta sigma weight residual 1.236 1.227 0.010 1.19e-02 7.06e+03 6.50e-01 bond pdb=" N VAL D1176 " pdb=" CA VAL D1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.99e-01 bond pdb=" N VAL F1176 " pdb=" CA VAL F1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.98e-01 bond pdb=" N VAL E1176 " pdb=" CA VAL E1176 " ideal model delta sigma weight residual 1.457 1.448 0.008 1.15e-02 7.56e+03 5.44e-01 bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.228 0.009 1.19e-02 7.06e+03 5.18e-01 ... (remaining 2449 not shown) Histogram of bond angle deviations from ideal: 106.94 - 110.44: 581 110.44 - 113.94: 952 113.94 - 117.45: 363 117.45 - 120.95: 891 120.95 - 124.46: 522 Bond angle restraints: 3309 Sorted by residual: angle pdb=" N ILE D1169 " pdb=" CA ILE D1169 " pdb=" C ILE D1169 " ideal model delta sigma weight residual 109.34 111.62 -2.28 2.08e+00 2.31e-01 1.20e+00 angle pdb=" N ILE E1169 " pdb=" CA ILE E1169 " pdb=" C ILE E1169 " ideal model delta sigma weight residual 109.34 111.62 -2.28 2.08e+00 2.31e-01 1.20e+00 angle pdb=" N ILE F1169 " pdb=" CA ILE F1169 " pdb=" C ILE F1169 " ideal model delta sigma weight residual 109.34 111.61 -2.27 2.08e+00 2.31e-01 1.19e+00 angle pdb=" CA ILE F1169 " pdb=" C ILE F1169 " pdb=" N SER F1170 " ideal model delta sigma weight residual 116.60 117.95 -1.35 1.45e+00 4.76e-01 8.69e-01 angle pdb=" CA ILE E1169 " pdb=" C ILE E1169 " pdb=" N SER E1170 " ideal model delta sigma weight residual 116.60 117.95 -1.35 1.45e+00 4.76e-01 8.61e-01 ... (remaining 3304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 1386 17.87 - 35.74: 120 35.74 - 53.60: 9 53.60 - 71.47: 9 71.47 - 89.34: 6 Dihedral angle restraints: 1530 sinusoidal: 594 harmonic: 936 Sorted by residual: dihedral pdb=" N LEU A 984 " pdb=" CA LEU A 984 " pdb=" CB LEU A 984 " pdb=" CG LEU A 984 " ideal model delta sinusoidal sigma weight residual -60.00 -94.67 34.67 3 1.50e+01 4.44e-03 5.89e+00 dihedral pdb=" N LEU C 984 " pdb=" CA LEU C 984 " pdb=" CB LEU C 984 " pdb=" CG LEU C 984 " ideal model delta sinusoidal sigma weight residual -60.00 -94.64 34.64 3 1.50e+01 4.44e-03 5.88e+00 dihedral pdb=" CB GLU A 918 " pdb=" CG GLU A 918 " pdb=" CD GLU A 918 " pdb=" OE1 GLU A 918 " ideal model delta sinusoidal sigma weight residual 0.00 63.30 -63.30 1 3.00e+01 1.11e-03 5.87e+00 ... (remaining 1527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 179 0.020 - 0.040: 165 0.040 - 0.060: 54 0.060 - 0.080: 10 0.080 - 0.100: 9 Chirality restraints: 417 Sorted by residual: 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 2.53 -0.10 2.00e-01 2.50e+01 2.52e-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 2.53 -0.10 2.00e-01 2.50e+01 2.51e-01 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 2.53 -0.10 2.00e-01 2.50e+01 2.48e-01 ... (remaining 414 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 952 " 0.003 2.00e-02 2.50e+03 6.56e-03 4.31e-01 pdb=" C VAL C 952 " -0.011 2.00e-02 2.50e+03 pdb=" O VAL C 952 " 0.004 2.00e-02 2.50e+03 pdb=" N ASN C 953 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 952 " 0.003 2.00e-02 2.50e+03 6.38e-03 4.08e-01 pdb=" C VAL B 952 " -0.011 2.00e-02 2.50e+03 pdb=" O VAL B 952 " 0.004 2.00e-02 2.50e+03 pdb=" N ASN B 953 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 952 " -0.003 2.00e-02 2.50e+03 6.37e-03 4.06e-01 pdb=" C VAL A 952 " 0.011 2.00e-02 2.50e+03 pdb=" O VAL A 952 " -0.004 2.00e-02 2.50e+03 pdb=" N ASN A 953 " -0.004 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 874 2.89 - 3.39: 2738 3.39 - 3.90: 4194 3.90 - 4.40: 4448 4.40 - 4.90: 7655 Nonbonded interactions: 19909 Sorted by model distance: nonbonded pdb=" NE2 GLN A 935 " pdb=" O ALA D1190 " model vdw 2.388 2.520 nonbonded pdb=" NE2 GLN B 935 " pdb=" O ALA E1190 " model vdw 2.388 2.520 nonbonded pdb=" NE2 GLN C 935 " pdb=" O ALA F1190 " model vdw 2.389 2.520 nonbonded pdb=" O GLY C 971 " pdb=" OG SER C 974 " model vdw 2.458 2.440 nonbonded pdb=" O GLY B 971 " pdb=" OG SER B 974 " model vdw 2.459 2.440 ... (remaining 19904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 11.880 Find NCS groups from input model: 0.140 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:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2454 Z= 0.325 Angle : 0.319 2.279 3309 Z= 0.199 Chirality : 0.032 0.100 417 Planarity : 0.002 0.007 435 Dihedral : 14.893 89.342 912 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.41), residues: 312 helix: 2.81 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -2.14 (0.61), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE C 970 ARG 0.001 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.3426 time to fit residues: 7.2839 Evaluate side-chains 19 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3964 ------------------------------------------------------------------------------- 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: 0.7980 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN E1173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2454 Z= 0.233 Angle : 0.287 2.510 3309 Z= 0.168 Chirality : 0.032 0.099 417 Planarity : 0.002 0.009 435 Dihedral : 2.979 8.936 324 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % 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: 4.79 (0.43), residues: 312 helix: 4.28 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -1.74 (0.62), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.248 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3566 time to fit residues: 6.4664 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4067 ------------------------------------------------------------------------------- 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: 0.5980 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.0010 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2454 Z= 0.192 Angle : 0.262 2.806 3309 Z= 0.156 Chirality : 0.032 0.101 417 Planarity : 0.001 0.006 435 Dihedral : 2.806 8.449 324 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % 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: 5.57 (0.43), residues: 312 helix: 4.82 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -1.43 (0.66), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE A 940 ARG 0.000 0.000 ARG E1185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.266 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.3958 time to fit residues: 6.7415 Evaluate side-chains 15 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.288 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.0060 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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: 0.7418 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2454 Z= 0.163 Angle : 0.249 2.812 3309 Z= 0.149 Chirality : 0.031 0.101 417 Planarity : 0.001 0.005 435 Dihedral : 2.715 8.298 324 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.96 (0.43), residues: 312 helix: 5.11 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -1.37 (0.66), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.000 0.000 ARG E1185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.294 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.3833 time to fit residues: 6.5361 Evaluate side-chains 15 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2454 Z= 0.223 Angle : 0.276 3.148 3309 Z= 0.163 Chirality : 0.033 0.100 417 Planarity : 0.001 0.005 435 Dihedral : 2.819 8.502 324 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.83 (0.43), residues: 312 helix: 4.99 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -1.27 (0.67), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE A 940 ARG 0.000 0.000 ARG E1185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.260 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3736 time to fit residues: 6.7507 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.260 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.0670 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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: 0.7420 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2454 Z= 0.159 Angle : 0.249 3.217 3309 Z= 0.150 Chirality : 0.031 0.101 417 Planarity : 0.001 0.005 435 Dihedral : 2.686 8.115 324 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 6.38 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.11 (0.42), residues: 312 helix: 5.19 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -1.18 (0.66), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.000 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.277 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 0.3626 time to fit residues: 6.5892 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.7426 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2454 Z= 0.181 Angle : 0.258 3.016 3309 Z= 0.154 Chirality : 0.032 0.101 417 Planarity : 0.001 0.005 435 Dihedral : 2.723 8.179 324 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 6.74 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.10 (0.42), residues: 312 helix: 5.17 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -1.13 (0.67), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.000 0.000 ARG E1185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.297 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.3656 time to fit residues: 6.6553 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.262 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 8 optimal weight: 0.0980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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: 0.7418 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2454 Z= 0.149 Angle : 0.247 3.145 3309 Z= 0.149 Chirality : 0.031 0.102 417 Planarity : 0.001 0.005 435 Dihedral : 2.647 7.978 324 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 6.38 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.26 (0.42), residues: 312 helix: 5.28 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -1.05 (0.68), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.000 0.000 ARG E1185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.283 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 16 average time/residue: 0.3645 time to fit residues: 6.6344 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 27 optimal weight: 0.0170 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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: 0.7417 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 0.016 2454 Z= 0.150 Angle : 0.248 3.163 3309 Z= 0.150 Chirality : 0.031 0.102 417 Planarity : 0.001 0.005 435 Dihedral : 2.641 8.009 324 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 6.74 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.33 (0.42), residues: 312 helix: 5.32 (0.23), residues: 246 sheet: None (None), residues: 0 loop : -1.00 (0.68), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.000 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.284 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.3621 time to fit residues: 6.6080 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.0020 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.0010 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- 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: 0.7411 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2454 Z= 0.136 Angle : 0.243 3.319 3309 Z= 0.148 Chirality : 0.031 0.102 417 Planarity : 0.001 0.005 435 Dihedral : 2.596 7.993 324 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 6.74 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.43 (0.42), residues: 312 helix: 5.39 (0.23), residues: 246 sheet: None (None), residues: 0 loop : -0.95 (0.69), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.000 0.000 ARG B 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.313 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.4315 time to fit residues: 7.7846 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0060 chunk 16 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.149658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.132249 restraints weight = 2913.944| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 1.96 r_work: 0.3845 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2454 Z= 0.175 Angle : 0.259 3.314 3309 Z= 0.155 Chirality : 0.032 0.102 417 Planarity : 0.001 0.005 435 Dihedral : 2.677 8.112 324 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 6.74 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.26 (0.42), residues: 312 helix: 5.27 (0.23), residues: 246 sheet: None (None), residues: 0 loop : -1.01 (0.68), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.000 0.000 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 988.59 seconds wall clock time: 18 minutes 51.07 seconds (1131.07 seconds total)