Starting phenix.real_space_refine on Thu Dec 7 16:19:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzr_24775/12_2023/7rzr_24775.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzr_24775/12_2023/7rzr_24775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzr_24775/12_2023/7rzr_24775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzr_24775/12_2023/7rzr_24775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzr_24775/12_2023/7rzr_24775.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzr_24775/12_2023/7rzr_24775.pdb" } resolution = 2.27 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 1515 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 None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2448 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 535 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 535 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 535 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: 1.61, per 1000 atoms: 0.66 Number of scatterers: 2448 At special positions: 0 Unit cell: (50.6075, 42.445, 117.54, 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 1515 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: 1.08 Conformation dependent library (CDL) restraints added in 546.0 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: 0.18 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: 0.70 Time building geometry restraints manager: 1.15 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: 459 1.29 - 1.35: 399 1.35 - 1.41: 71 1.41 - 1.48: 361 1.48 - 1.54: 1161 Bond restraints: 2451 Sorted by residual: bond pdb=" CB ASN A 955 " pdb=" CG ASN A 955 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.50e-01 bond pdb=" CB ASN C 955 " pdb=" CG ASN C 955 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.32e-01 bond pdb=" CB ASN B 955 " pdb=" CG ASN B 955 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.26e-01 bond pdb=" CE1 PHE C 970 " pdb=" CZ PHE C 970 " ideal model delta sigma weight residual 1.382 1.356 0.026 3.00e-02 1.11e+03 7.53e-01 bond pdb=" C ILE D1179 " pdb=" O ILE D1179 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 7.35e-01 ... (remaining 2446 not shown) Histogram of bond angle deviations from ideal: 106.92 - 110.40: 576 110.40 - 113.88: 957 113.88 - 117.36: 321 117.36 - 120.84: 859 120.84 - 124.32: 593 Bond angle restraints: 3306 Sorted by residual: angle pdb=" CA TYR A 936 " pdb=" CB TYR A 936 " pdb=" CG TYR A 936 " ideal model delta sigma weight residual 113.90 116.03 -2.13 1.80e+00 3.09e-01 1.40e+00 angle pdb=" CA TYR C 936 " pdb=" CB TYR C 936 " pdb=" CG TYR C 936 " ideal model delta sigma weight residual 113.90 116.00 -2.10 1.80e+00 3.09e-01 1.36e+00 angle pdb=" CA TYR B 936 " pdb=" CB TYR B 936 " pdb=" CG TYR B 936 " ideal model delta sigma weight residual 113.90 115.96 -2.06 1.80e+00 3.09e-01 1.32e+00 angle pdb=" CB LEU C 984 " pdb=" CG LEU C 984 " pdb=" CD2 LEU C 984 " ideal model delta sigma weight residual 110.70 113.75 -3.05 3.00e+00 1.11e-01 1.03e+00 angle pdb=" CB LEU B 984 " pdb=" CG LEU B 984 " pdb=" CD2 LEU B 984 " ideal model delta sigma weight residual 110.70 113.75 -3.05 3.00e+00 1.11e-01 1.03e+00 ... (remaining 3301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 1404 17.88 - 35.77: 102 35.77 - 53.65: 9 53.65 - 71.53: 9 71.53 - 89.42: 6 Dihedral angle restraints: 1530 sinusoidal: 591 harmonic: 939 Sorted by residual: dihedral pdb=" CB GLU C 918 " pdb=" CG GLU C 918 " pdb=" CD GLU C 918 " pdb=" OE1 GLU C 918 " ideal model delta sinusoidal sigma weight residual 0.00 63.57 -63.57 1 3.00e+01 1.11e-03 5.92e+00 dihedral pdb=" CB GLU B 918 " pdb=" CG GLU B 918 " pdb=" CD GLU B 918 " pdb=" OE1 GLU B 918 " ideal model delta sinusoidal sigma weight residual 0.00 63.51 -63.51 1 3.00e+01 1.11e-03 5.91e+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 63.51 -63.51 1 3.00e+01 1.11e-03 5.91e+00 ... (remaining 1527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 188 0.024 - 0.048: 173 0.048 - 0.072: 41 0.072 - 0.096: 9 0.096 - 0.120: 6 Chirality restraints: 417 Sorted by residual: chirality pdb=" CA PHE C 970 " pdb=" N PHE C 970 " pdb=" C PHE C 970 " pdb=" CB PHE C 970 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA PHE A 970 " pdb=" N PHE A 970 " pdb=" C PHE A 970 " pdb=" CB PHE A 970 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA PHE B 970 " pdb=" N PHE B 970 " pdb=" C PHE B 970 " pdb=" CB PHE B 970 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 414 not shown) Planarity restraints: 432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 936 " 0.007 2.00e-02 2.50e+03 5.85e-03 6.84e-01 pdb=" CG TYR B 936 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR B 936 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 936 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 936 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 936 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 936 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 936 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 936 " 0.007 2.00e-02 2.50e+03 5.75e-03 6.61e-01 pdb=" CG TYR C 936 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR C 936 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 936 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 936 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 936 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 936 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 936 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 936 " 0.006 2.00e-02 2.50e+03 5.53e-03 6.13e-01 pdb=" CG TYR A 936 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 936 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 936 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 936 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 936 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 936 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 936 " 0.000 2.00e-02 2.50e+03 ... (remaining 429 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 968 2.93 - 3.42: 2824 3.42 - 3.91: 4147 3.91 - 4.41: 4468 4.41 - 4.90: 7504 Nonbonded interactions: 19911 Sorted by model distance: nonbonded pdb=" NE2 GLN C 935 " pdb=" O ALA F1190 " model vdw 2.436 2.520 nonbonded pdb=" NE2 GLN A 935 " pdb=" O ALA D1190 " model vdw 2.438 2.520 nonbonded pdb=" NE2 GLN B 935 " pdb=" O ALA E1190 " model vdw 2.443 2.520 nonbonded pdb=" OG SER B 943 " pdb=" OE2 GLU D1182 " model vdw 2.502 2.440 nonbonded pdb=" OD1 ASN D1173 " pdb=" N ALA D1174 " model vdw 2.508 2.520 ... (remaining 19906 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: 0.840 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: 3.350 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.780 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.007 0.027 2451 Z= 0.434 Angle : 0.400 3.183 3306 Z= 0.230 Chirality : 0.035 0.120 417 Planarity : 0.002 0.007 432 Dihedral : 14.340 89.418 912 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 2.50 (0.41), residues: 312 helix: 2.38 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -1.25 (0.78), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE A 970 TYR 0.014 0.004 TYR B 936 ARG 0.001 0.000 ARG A 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 14 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.286 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.7832 time to fit residues: 11.6631 Evaluate side-chains 14 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.218 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3016 ------------------------------------------------------------------------------- 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: 0.8980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2451 Z= 0.234 Angle : 0.300 2.425 3306 Z= 0.176 Chirality : 0.032 0.099 417 Planarity : 0.002 0.015 432 Dihedral : 3.073 9.309 327 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: 5.07 (0.43), residues: 312 helix: 4.23 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.54 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE A 970 TYR 0.013 0.003 TYR C 936 ARG 0.004 0.001 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 12 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.286 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.9042 time to fit residues: 11.5773 Evaluate side-chains 12 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3917 ------------------------------------------------------------------------------- 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: 0.8980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.0870 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2451 Z= 0.129 Angle : 0.246 2.355 3306 Z= 0.148 Chirality : 0.030 0.102 417 Planarity : 0.002 0.027 432 Dihedral : 2.732 8.724 327 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: 6.30 (0.43), residues: 312 helix: 5.08 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.01 (0.84), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE B 927 TYR 0.008 0.002 TYR C 936 ARG 0.005 0.001 ARG B 983 *********************** 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 13 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.8469 time to fit residues: 11.7280 Evaluate side-chains 13 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3929 ------------------------------------------------------------------------------- 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: 0.9980 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2451 Z= 0.279 Angle : 0.314 2.791 3306 Z= 0.180 Chirality : 0.033 0.100 417 Planarity : 0.003 0.034 432 Dihedral : 3.000 9.620 327 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 4.96 % 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: 5.84 (0.43), residues: 312 helix: 4.74 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.10 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE C 970 TYR 0.014 0.003 TYR C 936 ARG 0.004 0.001 ARG B 983 *********************** 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: 1 poor density : 14 time to evaluate : 0.272 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.7676 time to fit residues: 12.3020 Evaluate side-chains 14 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.288 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4115 ------------------------------------------------------------------------------- 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: 0.6980 chunk 11 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.7491 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 : 0.004 0.017 2451 Z= 0.222 Angle : 0.288 2.542 3306 Z= 0.167 Chirality : 0.032 0.105 417 Planarity : 0.002 0.032 432 Dihedral : 2.884 9.415 327 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 5.32 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.05 (0.43), residues: 312 helix: 4.90 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.03 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE C 970 TYR 0.010 0.002 TYR C 936 ARG 0.005 0.001 ARG C 983 *********************** 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 14 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.233 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.7839 time to fit residues: 11.7102 Evaluate side-chains 14 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.287 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3987 ------------------------------------------------------------------------------- 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: 0.5980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 21 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.7485 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2451 Z= 0.190 Angle : 0.285 2.862 3306 Z= 0.164 Chirality : 0.031 0.107 417 Planarity : 0.002 0.039 432 Dihedral : 2.836 9.290 327 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.04 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: 6.23 (0.43), residues: 312 helix: 5.02 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.02 (0.80), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE C 970 TYR 0.009 0.002 TYR C 936 ARG 0.005 0.001 ARG B 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 : 0.309 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.7129 time to fit residues: 12.9318 Evaluate side-chains 17 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3897 ------------------------------------------------------------------------------- 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: 0.8980 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2451 Z= 0.240 Angle : 0.323 3.556 3306 Z= 0.182 Chirality : 0.032 0.108 417 Planarity : 0.001 0.012 432 Dihedral : 2.930 9.605 327 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 6.74 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.06 (0.43), residues: 312 helix: 4.89 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.03 (0.80), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE C 970 TYR 0.010 0.002 TYR C 936 ARG 0.002 0.000 ARG B 983 *********************** 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 18 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.317 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 17 average time/residue: 0.7127 time to fit residues: 13.0205 Evaluate side-chains 17 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.242 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3515 ------------------------------------------------------------------------------- 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: 0.7980 chunk 22 optimal weight: 0.0050 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.0870 chunk 25 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 24 optimal weight: 0.0770 chunk 17 optimal weight: 0.5980 overall best weight: 0.1328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.020 2451 Z= 0.088 Angle : 0.271 3.524 3306 Z= 0.158 Chirality : 0.031 0.112 417 Planarity : 0.002 0.045 432 Dihedral : 2.638 12.041 327 Min Nonbonded Distance : 2.271 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: 6.77 (0.42), residues: 312 helix: 5.42 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.14 (0.80), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE B 927 TYR 0.005 0.001 TYR C 936 ARG 0.008 0.001 ARG B 983 *********************** 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 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.331 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.7453 time to fit residues: 12.7892 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.245 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3579 ------------------------------------------------------------------------------- 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: 0.0980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.7475 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2451 Z= 0.194 Angle : 0.294 3.434 3306 Z= 0.168 Chirality : 0.032 0.109 417 Planarity : 0.001 0.010 432 Dihedral : 2.784 10.875 327 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 7.09 % Favored : 92.55 % 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: 6.50 (0.42), residues: 312 helix: 5.20 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.15 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE C 970 TYR 0.009 0.002 TYR C 936 ARG 0.001 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 : 0.281 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.7369 time to fit residues: 12.5576 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.263 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3335 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2451 Z= 0.221 Angle : 0.299 2.983 3306 Z= 0.172 Chirality : 0.032 0.111 417 Planarity : 0.001 0.009 432 Dihedral : 2.861 10.647 327 Min Nonbonded Distance : 2.279 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: 6.30 (0.42), residues: 312 helix: 5.05 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.14 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE C 970 TYR 0.010 0.002 TYR C 936 ARG 0.002 0.000 ARG C 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 : 0.274 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.7372 time to fit residues: 12.5807 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.270 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3933 ------------------------------------------------------------------------------- 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: 0.0870 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.146997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.132161 restraints weight = 2921.108| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.73 r_work: 0.3880 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2451 Z= 0.148 Angle : 0.305 6.267 3306 Z= 0.175 Chirality : 0.032 0.119 417 Planarity : 0.003 0.049 432 Dihedral : 2.841 15.700 327 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.44 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: 6.52 (0.42), residues: 312 helix: 5.21 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.20 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.000 PHE B 927 TYR 0.007 0.002 TYR C 936 ARG 0.013 0.001 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1032.30 seconds wall clock time: 19 minutes 39.38 seconds (1179.38 seconds total)