Starting phenix.real_space_refine on Mon Sep 23 12:24:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzt_24777/09_2024/7rzt_24777.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzt_24777/09_2024/7rzt_24777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzt_24777/09_2024/7rzt_24777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzt_24777/09_2024/7rzt_24777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzt_24777/09_2024/7rzt_24777.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzt_24777/09_2024/7rzt_24777.cif" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1518 2.51 5 N 426 2.21 5 O 507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2451 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "E" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Restraints were copied for chains: C, B, D, F Time building chain proxies: 1.71, per 1000 atoms: 0.70 Number of scatterers: 2451 At special positions: 0 Unit cell: (48.975, 42.445, 116.724, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 507 8.00 N 426 7.00 C 1518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 292.9 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: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 235 hydrogen bonds defined for protein. 696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.67 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 465 1.29 - 1.35: 399 1.35 - 1.42: 61 1.42 - 1.48: 365 1.48 - 1.54: 1164 Bond restraints: 2454 Sorted by residual: bond pdb=" C ILE F1179 " pdb=" O ILE F1179 " ideal model delta sigma weight residual 1.236 1.227 0.010 1.19e-02 7.06e+03 6.50e-01 bond pdb=" N VAL D1176 " pdb=" CA VAL D1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.99e-01 bond pdb=" N VAL F1176 " pdb=" CA VAL F1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.98e-01 bond pdb=" N VAL E1176 " pdb=" CA VAL E1176 " ideal model delta sigma weight residual 1.457 1.448 0.008 1.15e-02 7.56e+03 5.44e-01 bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.228 0.009 1.19e-02 7.06e+03 5.18e-01 ... (remaining 2449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.46: 2912 0.46 - 0.91: 344 0.91 - 1.37: 39 1.37 - 1.82: 11 1.82 - 2.28: 3 Bond angle restraints: 3309 Sorted by residual: angle pdb=" N ILE D1169 " pdb=" CA ILE D1169 " pdb=" C ILE D1169 " ideal model delta sigma weight residual 109.34 111.62 -2.28 2.08e+00 2.31e-01 1.20e+00 angle pdb=" N ILE E1169 " pdb=" CA ILE E1169 " pdb=" C ILE E1169 " ideal model delta sigma weight residual 109.34 111.62 -2.28 2.08e+00 2.31e-01 1.20e+00 angle pdb=" N ILE F1169 " pdb=" CA ILE F1169 " pdb=" C ILE F1169 " ideal model delta sigma weight residual 109.34 111.61 -2.27 2.08e+00 2.31e-01 1.19e+00 angle pdb=" CA ILE F1169 " pdb=" C ILE F1169 " pdb=" N SER F1170 " ideal model delta sigma weight residual 116.60 117.95 -1.35 1.45e+00 4.76e-01 8.69e-01 angle pdb=" CA ILE E1169 " pdb=" C ILE E1169 " pdb=" N SER E1170 " ideal model delta sigma weight residual 116.60 117.95 -1.35 1.45e+00 4.76e-01 8.61e-01 ... (remaining 3304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 1386 17.87 - 35.74: 120 35.74 - 53.60: 9 53.60 - 71.47: 9 71.47 - 89.34: 6 Dihedral angle restraints: 1530 sinusoidal: 594 harmonic: 936 Sorted by residual: dihedral pdb=" N LEU A 984 " pdb=" CA LEU A 984 " pdb=" CB LEU A 984 " pdb=" CG LEU A 984 " ideal model delta sinusoidal sigma weight residual -60.00 -94.67 34.67 3 1.50e+01 4.44e-03 5.89e+00 dihedral pdb=" N LEU C 984 " pdb=" CA LEU C 984 " pdb=" CB LEU C 984 " pdb=" CG LEU C 984 " ideal model delta sinusoidal sigma weight residual -60.00 -94.64 34.64 3 1.50e+01 4.44e-03 5.88e+00 dihedral pdb=" CB GLU A 918 " pdb=" CG GLU A 918 " pdb=" CD GLU A 918 " pdb=" OE1 GLU A 918 " ideal model delta sinusoidal sigma weight residual 0.00 63.30 -63.30 1 3.00e+01 1.11e-03 5.87e+00 ... (remaining 1527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 179 0.020 - 0.040: 165 0.040 - 0.060: 54 0.060 - 0.080: 10 0.080 - 0.100: 9 Chirality restraints: 417 Sorted by residual: chirality pdb=" CA ILE F1172 " pdb=" N ILE F1172 " pdb=" C ILE F1172 " pdb=" CB ILE F1172 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.52e-01 chirality pdb=" CA ILE E1172 " pdb=" N ILE E1172 " pdb=" C ILE E1172 " pdb=" CB ILE E1172 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.51e-01 chirality pdb=" CA ILE D1172 " pdb=" N ILE D1172 " pdb=" C ILE D1172 " pdb=" CB ILE D1172 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.48e-01 ... (remaining 414 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 952 " 0.003 2.00e-02 2.50e+03 6.56e-03 4.31e-01 pdb=" C VAL C 952 " -0.011 2.00e-02 2.50e+03 pdb=" O VAL C 952 " 0.004 2.00e-02 2.50e+03 pdb=" N ASN C 953 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 952 " 0.003 2.00e-02 2.50e+03 6.38e-03 4.08e-01 pdb=" C VAL B 952 " -0.011 2.00e-02 2.50e+03 pdb=" O VAL B 952 " 0.004 2.00e-02 2.50e+03 pdb=" N ASN B 953 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 952 " -0.003 2.00e-02 2.50e+03 6.37e-03 4.06e-01 pdb=" C VAL A 952 " 0.011 2.00e-02 2.50e+03 pdb=" O VAL A 952 " -0.004 2.00e-02 2.50e+03 pdb=" N ASN A 953 " -0.004 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 874 2.89 - 3.39: 2738 3.39 - 3.90: 4194 3.90 - 4.40: 4448 4.40 - 4.90: 7655 Nonbonded interactions: 19909 Sorted by model distance: nonbonded pdb=" NE2 GLN A 935 " pdb=" O ALA D1190 " model vdw 2.388 3.120 nonbonded pdb=" NE2 GLN B 935 " pdb=" O ALA E1190 " model vdw 2.388 3.120 nonbonded pdb=" NE2 GLN C 935 " pdb=" O ALA F1190 " model vdw 2.389 3.120 nonbonded pdb=" O GLY C 971 " pdb=" OG SER C 974 " model vdw 2.458 3.040 nonbonded pdb=" O GLY B 971 " pdb=" OG SER B 974 " model vdw 2.459 3.040 ... (remaining 19904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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: 0.670 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.690 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2454 Z= 0.325 Angle : 0.319 2.279 3309 Z= 0.199 Chirality : 0.032 0.100 417 Planarity : 0.002 0.007 435 Dihedral : 14.893 89.342 912 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.41), residues: 312 helix: 2.81 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -2.14 (0.61), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE C 970 ARG 0.001 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.247 Fit side-chains REVERT: A 974 SER cc_start: 0.8081 (p) cc_final: 0.7389 (p) REVERT: A 978 ASN cc_start: 0.8215 (m-40) cc_final: 0.7828 (m110) REVERT: C 979 ASP cc_start: 0.7179 (m-30) cc_final: 0.6959 (m-30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.3434 time to fit residues: 7.3602 Evaluate side-chains 19 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN E1173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2454 Z= 0.211 Angle : 0.287 2.463 3309 Z= 0.165 Chirality : 0.032 0.100 417 Planarity : 0.002 0.009 435 Dihedral : 2.956 9.582 324 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 3.90 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.97 (0.43), residues: 312 helix: 4.38 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -1.58 (0.64), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.001 0.000 ARG E1185 *********************** 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 17 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.285 Fit side-chains REVERT: A 974 SER cc_start: 0.8245 (p) cc_final: 0.7420 (p) REVERT: A 978 ASN cc_start: 0.8211 (m-40) cc_final: 0.7887 (m110) REVERT: C 979 ASP cc_start: 0.7193 (m-30) cc_final: 0.6951 (m-30) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.3745 time to fit residues: 6.8381 Evaluate side-chains 17 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 975 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 0.0040 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.0050 overall best weight: 0.3206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2454 Z= 0.138 Angle : 0.235 1.918 3309 Z= 0.139 Chirality : 0.031 0.101 417 Planarity : 0.001 0.005 435 Dihedral : 2.715 8.362 324 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 4.61 % Favored : 95.04 % 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: 5.91 (0.43), residues: 312 helix: 5.05 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -1.26 (0.68), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.000 0.000 ARG E1185 *********************** REFINEMENT MACRO_CYCLE 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 17 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.270 Fit side-chains REVERT: A 974 SER cc_start: 0.8258 (p) cc_final: 0.7442 (p) REVERT: A 978 ASN cc_start: 0.8157 (m-40) cc_final: 0.7885 (m110) REVERT: C 979 ASP cc_start: 0.7180 (m-30) cc_final: 0.6952 (m-30) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.3549 time to fit residues: 6.5229 Evaluate side-chains 17 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 975 SER 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: 0.6980 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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: 0.7433 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2454 Z= 0.189 Angle : 0.255 1.988 3309 Z= 0.149 Chirality : 0.032 0.101 417 Planarity : 0.001 0.005 435 Dihedral : 2.783 8.708 324 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.97 (0.43), residues: 312 helix: 5.09 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -1.22 (0.68), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.000 0.000 ARG 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 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.266 Fit side-chains REVERT: A 974 SER cc_start: 0.8262 (p) cc_final: 0.7407 (p) REVERT: A 978 ASN cc_start: 0.8163 (m-40) cc_final: 0.7915 (m110) REVERT: C 979 ASP cc_start: 0.7205 (m-30) cc_final: 0.6963 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3453 time to fit residues: 6.3014 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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: 0.1980 chunk 11 optimal weight: 0.3980 chunk 24 optimal weight: 0.0170 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2454 Z= 0.148 Angle : 0.236 1.932 3309 Z= 0.139 Chirality : 0.031 0.101 417 Planarity : 0.001 0.004 435 Dihedral : 2.673 8.595 324 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.03 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: 6.26 (0.42), residues: 312 helix: 5.28 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -1.08 (0.71), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.000 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 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 18 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.256 Fit side-chains REVERT: A 974 SER cc_start: 0.8256 (p) cc_final: 0.7403 (p) REVERT: A 978 ASN cc_start: 0.8145 (m-40) cc_final: 0.7907 (m110) REVERT: C 979 ASP cc_start: 0.7198 (m-30) cc_final: 0.6959 (m-30) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.3419 time to fit residues: 6.5907 Evaluate side-chains 17 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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: 0.9980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.0470 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2454 Z= 0.158 Angle : 0.240 2.112 3309 Z= 0.141 Chirality : 0.031 0.102 417 Planarity : 0.001 0.004 435 Dihedral : 2.676 8.365 324 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.23 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: 6.27 (0.42), residues: 312 helix: 5.28 (0.23), residues: 246 sheet: None (None), residues: 0 loop : -1.05 (0.70), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.000 0.000 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 18 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.298 Fit side-chains REVERT: A 978 ASN cc_start: 0.8127 (m-40) cc_final: 0.7901 (m110) REVERT: C 979 ASP cc_start: 0.7203 (m-30) cc_final: 0.6961 (m-30) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.3441 time to fit residues: 6.6498 Evaluate side-chains 17 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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: 0.5980 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 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: 0.7426 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2454 Z= 0.159 Angle : 0.241 2.103 3309 Z= 0.142 Chirality : 0.031 0.101 417 Planarity : 0.001 0.004 435 Dihedral : 2.676 8.094 324 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.67 % 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: 6.30 (0.42), residues: 312 helix: 5.30 (0.23), residues: 246 sheet: None (None), residues: 0 loop : -1.00 (0.70), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.000 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.275 Fit side-chains REVERT: A 978 ASN cc_start: 0.8140 (m-40) cc_final: 0.7899 (m110) REVERT: C 979 ASP cc_start: 0.7212 (m-30) cc_final: 0.6969 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3557 time to fit residues: 6.4586 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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: 0.0870 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2454 Z= 0.153 Angle : 0.238 1.984 3309 Z= 0.141 Chirality : 0.031 0.102 417 Planarity : 0.001 0.004 435 Dihedral : 2.654 8.083 324 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.23 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: 6.39 (0.42), residues: 312 helix: 5.35 (0.23), residues: 246 sheet: None (None), residues: 0 loop : -0.92 (0.70), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.000 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 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 18 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.251 Fit side-chains REVERT: A 978 ASN cc_start: 0.8125 (m-40) cc_final: 0.7893 (m110) REVERT: C 979 ASP cc_start: 0.7220 (m-30) cc_final: 0.6975 (m-30) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.3511 time to fit residues: 6.7589 Evaluate side-chains 17 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2454 Z= 0.208 Angle : 0.265 2.322 3309 Z= 0.153 Chirality : 0.032 0.102 417 Planarity : 0.001 0.004 435 Dihedral : 2.766 8.808 324 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.17 (0.42), residues: 312 helix: 5.18 (0.23), residues: 246 sheet: None (None), residues: 0 loop : -0.91 (0.71), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.000 0.000 ARG A 983 *********************** 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: 0 poor density : 16 time to evaluate : 0.260 Fit side-chains REVERT: A 978 ASN cc_start: 0.8100 (m-40) cc_final: 0.7834 (m110) REVERT: C 979 ASP cc_start: 0.7242 (m-30) cc_final: 0.6990 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3824 time to fit residues: 6.8976 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.7429 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2454 Z= 0.166 Angle : 0.247 2.142 3309 Z= 0.145 Chirality : 0.032 0.102 417 Planarity : 0.001 0.004 435 Dihedral : 2.692 8.340 324 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % 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: 6.34 (0.42), residues: 312 helix: 5.30 (0.23), residues: 246 sheet: None (None), residues: 0 loop : -0.87 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 940 ARG 0.000 0.000 ARG B 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.267 Fit side-chains REVERT: A 978 ASN cc_start: 0.8098 (m-40) cc_final: 0.7831 (m110) REVERT: C 979 ASP cc_start: 0.7233 (m-30) cc_final: 0.6981 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3717 time to fit residues: 6.7611 Evaluate side-chains 16 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.149100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.131238 restraints weight = 2913.606| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.98 r_work: 0.3830 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2454 Z= 0.206 Angle : 0.264 2.349 3309 Z= 0.153 Chirality : 0.032 0.101 417 Planarity : 0.001 0.004 435 Dihedral : 2.760 8.759 324 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.19 (0.42), residues: 312 helix: 5.18 (0.23), residues: 246 sheet: None (None), residues: 0 loop : -0.89 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 940 ARG 0.000 0.000 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 990.75 seconds wall clock time: 18 minutes 22.81 seconds (1102.81 seconds total)