Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:49:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzr_24775/11_2022/7rzr_24775.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzr_24775/11_2022/7rzr_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_24775/11_2022/7rzr_24775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzr_24775/11_2022/7rzr_24775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzr_24775/11_2022/7rzr_24775.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzr_24775/11_2022/7rzr_24775.pdb" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 1.74, per 1000 atoms: 0.71 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: 1.10 Conformation dependent library (CDL) restraints added in 411.6 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: 0.06 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: 1.17 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 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. 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: 0.590 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: 3.100 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 12.180 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 % 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 *********************** 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 : 0.295 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.7123 time to fit residues: 10.7591 Evaluate side-chains 14 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4359 ------------------------------------------------------------------------------- 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: 0.6980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 8 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: A 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1046 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= 0.221 Angle : 0.294 2.578 3306 Z= 0.173 Chirality : 0.032 0.100 417 Planarity : 0.002 0.015 432 Dihedral : 3.047 9.197 327 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.17 (0.43), residues: 312 helix: 4.31 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.53 (0.81), residues: 66 *********************** 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 : 0.226 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.8079 time to fit residues: 10.3555 Evaluate side-chains 12 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.292 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4189 ------------------------------------------------------------------------------- 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: 0.8980 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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: 0.7974 moved from start: 0.1332 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= 0.232 Angle : 0.295 2.408 3306 Z= 0.171 Chirality : 0.032 0.099 417 Planarity : 0.002 0.016 432 Dihedral : 2.955 9.692 327 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.80 (0.43), residues: 312 helix: 4.70 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.05 (0.84), residues: 66 *********************** 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 : 0.292 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.8292 time to fit residues: 11.5080 Evaluate side-chains 13 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4173 ------------------------------------------------------------------------------- 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: 0.5980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 28 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.0370 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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: 0.7952 moved from start: 0.1489 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= 0.142 Angle : 0.252 2.437 3306 Z= 0.151 Chirality : 0.030 0.102 417 Planarity : 0.002 0.030 432 Dihedral : 2.729 8.809 327 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.35 % 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: 6.42 (0.43), residues: 312 helix: 5.18 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.02 (0.81), residues: 66 *********************** 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 14 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.266 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.6832 time to fit residues: 10.2704 Evaluate side-chains 13 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.260 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3780 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 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: C 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1552 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= 0.224 Angle : 0.288 2.986 3306 Z= 0.167 Chirality : 0.032 0.105 417 Planarity : 0.002 0.042 432 Dihedral : 2.874 8.931 327 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.19 (0.43), residues: 312 helix: 4.98 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.04 (0.81), residues: 66 *********************** 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 15 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.295 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.6895 time to fit residues: 11.1599 Evaluate side-chains 15 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.296 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4260 ------------------------------------------------------------------------------- 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: 0.7980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 chunk 27 optimal weight: 0.0020 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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: 0.7954 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.013 2451 Z= 0.163 Angle : 0.282 3.180 3306 Z= 0.159 Chirality : 0.031 0.107 417 Planarity : 0.002 0.034 432 Dihedral : 2.748 8.682 327 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.35 % 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: 6.46 (0.43), residues: 312 helix: 5.17 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.15 (0.81), residues: 66 *********************** 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 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.288 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.6809 time to fit residues: 11.6757 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.285 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4032 ------------------------------------------------------------------------------- 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: 0.9990 chunk 24 optimal weight: 0.0070 chunk 28 optimal weight: 0.0770 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 overall best weight: 0.3356 ------------------------------------------------------------------------------- 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: 0.7947 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 2451 Z= 0.145 Angle : 0.265 2.471 3306 Z= 0.157 Chirality : 0.031 0.109 417 Planarity : 0.002 0.028 432 Dihedral : 2.699 8.492 327 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.59 (0.43), residues: 312 helix: 5.25 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.25 (0.82), residues: 66 *********************** 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 17 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.290 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 16 average time/residue: 0.6743 time to fit residues: 11.6087 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.288 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4134 ------------------------------------------------------------------------------- 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: 0.6980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 25 optimal weight: 0.0050 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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: 0.7948 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 2451 Z= 0.159 Angle : 0.284 3.276 3306 Z= 0.164 Chirality : 0.031 0.109 417 Planarity : 0.001 0.008 432 Dihedral : 2.741 10.560 327 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.56 (0.42), residues: 312 helix: 5.23 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.24 (0.82), residues: 66 *********************** 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 : 0.316 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 16 average time/residue: 0.6720 time to fit residues: 11.5780 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4231 ------------------------------------------------------------------------------- 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: 0.6980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 2451 Z= 0.206 Angle : 0.300 3.625 3306 Z= 0.173 Chirality : 0.032 0.110 417 Planarity : 0.002 0.017 432 Dihedral : 2.831 10.618 327 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.35 % 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: 6.35 (0.42), residues: 312 helix: 5.08 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.20 (0.82), residues: 66 *********************** 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 : 0.296 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.6787 time to fit residues: 11.6459 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.260 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3744 ------------------------------------------------------------------------------- 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: 0.3980 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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: 0.7949 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 2451 Z= 0.170 Angle : 0.325 5.982 3306 Z= 0.181 Chirality : 0.032 0.123 417 Planarity : 0.002 0.024 432 Dihedral : 2.850 15.765 327 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.35 % 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: 5.13 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.22 (0.81), residues: 66 ********************** 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 15 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.280 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.7330 time to fit residues: 11.7780 Evaluate side-chains 15 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.257 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3935 ------------------------------------------------------------------------------- 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: 0.0270 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 overall best weight: 0.3638 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.146217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.131377 restraints weight = 2912.437| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.74 r_work: 0.4008 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3994 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work: 0.3979 rms_B_bonded: 1.61 restraints_weight: 0.1250 r_work: 0.3963 rms_B_bonded: 1.74 restraints_weight: 0.0625 r_work: 0.3945 rms_B_bonded: 1.92 restraints_weight: 0.0312 r_work: 0.3926 rms_B_bonded: 2.16 restraints_weight: 0.0156 r_work: 0.3904 rms_B_bonded: 2.44 restraints_weight: 0.0078 r_work: 0.3880 rms_B_bonded: 2.77 restraints_weight: 0.0039 r_work: 0.3852 rms_B_bonded: 3.16 restraints_weight: 0.0020 r_work: 0.3821 rms_B_bonded: 3.63 restraints_weight: 0.0010 r_work: 0.3785 rms_B_bonded: 4.17 restraints_weight: 0.0005 r_work: 0.3744 rms_B_bonded: 4.81 restraints_weight: 0.0002 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.003 0.023 2451 Z= 0.157 Angle : 0.297 5.154 3306 Z= 0.170 Chirality : 0.031 0.112 417 Planarity : 0.003 0.046 432 Dihedral : 2.807 14.905 327 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.35 % 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: 6.55 (0.42), residues: 312 helix: 5.23 (0.24), residues: 246 sheet: None (None), residues: 0 loop : 0.23 (0.81), residues: 66 =============================================================================== Job complete usr+sys time: 962.12 seconds wall clock time: 18 minutes 43.98 seconds (1123.98 seconds total)