Starting phenix.real_space_refine on Mon Sep 23 12:23:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/09_2024/7rzs_24776.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/09_2024/7rzs_24776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/09_2024/7rzs_24776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/09_2024/7rzs_24776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/09_2024/7rzs_24776.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/09_2024/7rzs_24776.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1509 2.51 5 N 426 2.21 5 O 510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2445 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 534 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: D, F, C, B Time building chain proxies: 1.84, per 1000 atoms: 0.75 Number of scatterers: 2445 At special positions: 0 Unit cell: (50.6075, 42.445, 115.908, 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 510 8.00 N 426 7.00 C 1509 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: 0.64 Conformation dependent library (CDL) restraints added in 296.7 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: 0.23 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 removed outlier: 3.569A pdb=" N LEU D1197 " --> pdb=" O ASN D1194 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.569A pdb=" N LEU E1197 " --> pdb=" O ASN E1194 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.570A pdb=" N LEU F1197 " --> pdb=" O ASN F1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1194 through 1197' 232 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: 0.68 Time building geometry restraints manager: 0.75 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 - 1.41: 63 1.41 - 1.48: 366 1.48 - 1.54: 1155 Bond restraints: 2448 Sorted by residual: bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.83e-01 bond pdb=" C ILE F1179 " pdb=" O ILE F1179 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.19e-02 7.06e+03 6.37e-01 bond pdb=" C ILE D1179 " pdb=" O ILE D1179 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.19e-02 7.06e+03 6.34e-01 bond pdb=" N VAL E1176 " pdb=" CA VAL E1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.87e-01 bond pdb=" N ILE E1179 " pdb=" CA ILE E1179 " ideal model delta sigma weight residual 1.459 1.450 0.009 1.25e-02 6.40e+03 5.42e-01 ... (remaining 2443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 3173 0.93 - 1.87: 100 1.87 - 2.80: 15 2.80 - 3.74: 6 3.74 - 4.67: 6 Bond angle restraints: 3300 Sorted by residual: angle pdb=" CA ARG B 983 " pdb=" CB ARG B 983 " pdb=" CG ARG B 983 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.46e+00 angle pdb=" CA ARG A 983 " pdb=" CB ARG A 983 " pdb=" CG ARG A 983 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.44e+00 angle pdb=" CA ARG C 983 " pdb=" CB ARG C 983 " pdb=" CG ARG C 983 " ideal model delta sigma weight residual 114.10 118.72 -4.62 2.00e+00 2.50e-01 5.34e+00 angle pdb=" C ARG C 983 " pdb=" CA ARG C 983 " pdb=" CB ARG C 983 " ideal model delta sigma weight residual 110.31 113.88 -3.57 2.09e+00 2.29e-01 2.92e+00 angle pdb=" C ARG B 983 " pdb=" CA ARG B 983 " pdb=" CB ARG B 983 " ideal model delta sigma weight residual 110.31 113.86 -3.55 2.09e+00 2.29e-01 2.89e+00 ... (remaining 3295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 1389 17.76 - 35.52: 111 35.52 - 53.28: 12 53.28 - 71.05: 9 71.05 - 88.81: 6 Dihedral angle restraints: 1527 sinusoidal: 591 harmonic: 936 Sorted by residual: dihedral pdb=" CG ARG A 983 " pdb=" CD ARG A 983 " pdb=" NE ARG A 983 " pdb=" CZ ARG A 983 " ideal model delta sinusoidal sigma weight residual -90.00 -130.02 40.02 2 1.50e+01 4.44e-03 8.82e+00 dihedral pdb=" CG ARG C 983 " pdb=" CD ARG C 983 " pdb=" NE ARG C 983 " pdb=" CZ ARG C 983 " ideal model delta sinusoidal sigma weight residual -90.00 -130.01 40.01 2 1.50e+01 4.44e-03 8.82e+00 dihedral pdb=" CG ARG B 983 " pdb=" CD ARG B 983 " pdb=" NE ARG B 983 " pdb=" CZ ARG B 983 " ideal model delta sinusoidal sigma weight residual -90.00 -130.01 40.01 2 1.50e+01 4.44e-03 8.82e+00 ... (remaining 1524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 212 0.023 - 0.046: 134 0.046 - 0.068: 53 0.068 - 0.091: 7 0.091 - 0.114: 8 Chirality restraints: 414 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 2.40 0.11 2.00e-01 2.50e+01 3.24e-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 2.40 0.11 2.00e-01 2.50e+01 3.15e-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 2.40 0.11 2.00e-01 2.50e+01 3.10e-01 ... (remaining 411 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 983 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C ARG A 983 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG A 983 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU A 984 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 983 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C ARG C 983 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG C 983 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU C 984 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 983 " -0.007 2.00e-02 2.50e+03 1.41e-02 2.00e+00 pdb=" C ARG B 983 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG B 983 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU B 984 " -0.008 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 600 2.80 - 3.32: 2636 3.32 - 3.85: 4135 3.85 - 4.37: 4614 4.37 - 4.90: 8090 Nonbonded interactions: 20075 Sorted by model distance: nonbonded pdb=" O GLY B 971 " pdb=" OG SER B 974 " model vdw 2.273 3.040 nonbonded pdb=" O GLY A 971 " pdb=" OG SER A 974 " model vdw 2.273 3.040 nonbonded pdb=" O GLY C 971 " pdb=" OG SER C 974 " model vdw 2.273 3.040 nonbonded pdb=" NE2 GLN B 935 " pdb=" O ALA E1190 " model vdw 2.506 3.120 nonbonded pdb=" NE2 GLN A 935 " pdb=" O ALA D1190 " model vdw 2.507 3.120 ... (remaining 20070 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: 0.720 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.660 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 2448 Z= 0.315 Angle : 0.461 4.674 3300 Z= 0.271 Chirality : 0.034 0.114 414 Planarity : 0.004 0.041 435 Dihedral : 14.727 88.807 909 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: 1.98 (0.43), residues: 312 helix: 2.03 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -1.53 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE B 970 ARG 0.011 0.003 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 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 980 ILE cc_start: 0.8695 (mt) cc_final: 0.8461 (mt) REVERT: C 965 GLN cc_start: 0.8146 (mm110) cc_final: 0.7903 (mm110) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.6028 time to fit residues: 20.4187 Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A 965 GLN B 935 GLN B 978 ASN C 978 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2448 Z= 0.205 Angle : 0.364 4.167 3300 Z= 0.203 Chirality : 0.034 0.096 414 Planarity : 0.002 0.024 435 Dihedral : 3.284 11.313 324 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.06 % Allowed : 7.45 % Favored : 91.49 % 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: 4.17 (0.44), residues: 312 helix: 3.62 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -0.95 (0.78), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.002 PHE C 970 ARG 0.007 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: C 965 GLN cc_start: 0.8140 (mm110) cc_final: 0.7909 (mm110) outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 0.5283 time to fit residues: 16.9172 Evaluate side-chains 30 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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: 0.7481 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2448 Z= 0.197 Angle : 0.340 5.860 3300 Z= 0.191 Chirality : 0.033 0.097 414 Planarity : 0.002 0.032 435 Dihedral : 3.090 9.972 324 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 9.57 % Favored : 90.07 % 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: 5.13 (0.44), residues: 312 helix: 4.28 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.53 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 938 ARG 0.005 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.240 Fit side-chains REVERT: B 976 VAL cc_start: 0.9021 (t) cc_final: 0.8811 (p) REVERT: C 965 GLN cc_start: 0.8137 (mm110) cc_final: 0.7892 (mm110) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.5917 time to fit residues: 16.9841 Evaluate side-chains 27 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 935 GLN C 955 ASN D1173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2448 Z= 0.207 Angle : 0.335 6.170 3300 Z= 0.186 Chirality : 0.033 0.098 414 Planarity : 0.002 0.021 435 Dihedral : 3.044 9.720 324 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 10.64 % Favored : 88.65 % 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: 5.38 (0.44), residues: 312 helix: 4.44 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.39 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE B 970 ARG 0.003 0.001 ARG A 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 29 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: B 976 VAL cc_start: 0.9006 (t) cc_final: 0.8795 (p) REVERT: B 977 LEU cc_start: 0.8943 (mt) cc_final: 0.8692 (mt) REVERT: C 965 GLN cc_start: 0.8134 (mm110) cc_final: 0.7893 (mm110) outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.5468 time to fit residues: 16.3260 Evaluate side-chains 28 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.0470 chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 0.0970 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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: 0.7467 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2448 Z= 0.157 Angle : 0.333 6.457 3300 Z= 0.178 Chirality : 0.033 0.138 414 Planarity : 0.002 0.014 435 Dihedral : 2.876 9.337 324 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 10.64 % Favored : 88.65 % 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: 5.66 (0.43), residues: 312 helix: 4.73 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.41 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE A 970 ARG 0.003 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.252 Fit side-chains REVERT: C 965 GLN cc_start: 0.8141 (mm110) cc_final: 0.7891 (mm110) outliers start: 2 outliers final: 0 residues processed: 28 average time/residue: 0.5761 time to fit residues: 17.0908 Evaluate side-chains 27 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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: 0.4980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.0020 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2448 Z= 0.207 Angle : 0.358 6.771 3300 Z= 0.189 Chirality : 0.034 0.179 414 Planarity : 0.001 0.007 435 Dihedral : 2.943 9.734 324 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 10.64 % Favored : 87.94 % 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: 5.53 (0.43), residues: 312 helix: 4.63 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.40 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE B 970 ARG 0.004 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: C 965 GLN cc_start: 0.8141 (mm110) cc_final: 0.7898 (mm110) REVERT: C 970 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7748 (m-10) outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.5507 time to fit residues: 17.5966 Evaluate side-chains 30 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.0770 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2448 Z= 0.216 Angle : 0.369 7.116 3300 Z= 0.195 Chirality : 0.034 0.169 414 Planarity : 0.002 0.013 435 Dihedral : 2.976 10.082 324 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.77 % Allowed : 10.64 % Favored : 87.59 % 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: 5.39 (0.43), residues: 312 helix: 4.52 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.44 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 938 ARG 0.005 0.001 ARG C 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 33 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: C 965 GLN cc_start: 0.8133 (mm110) cc_final: 0.7886 (mm110) REVERT: C 970 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7750 (m-10) outliers start: 5 outliers final: 3 residues processed: 31 average time/residue: 0.5308 time to fit residues: 17.5451 Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 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: 0.7483 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2448 Z= 0.205 Angle : 0.371 7.218 3300 Z= 0.195 Chirality : 0.034 0.155 414 Planarity : 0.002 0.015 435 Dihedral : 2.965 10.876 324 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 11.70 % Favored : 86.88 % 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: 5.39 (0.43), residues: 312 helix: 4.52 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.42 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 938 ARG 0.005 0.001 ARG C 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 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: C 965 GLN cc_start: 0.8139 (mm110) cc_final: 0.7893 (mm110) REVERT: C 970 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7759 (m-10) outliers start: 4 outliers final: 3 residues processed: 31 average time/residue: 0.5406 time to fit residues: 17.8182 Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 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: 0.7481 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2448 Z= 0.198 Angle : 0.379 7.431 3300 Z= 0.196 Chirality : 0.034 0.154 414 Planarity : 0.001 0.008 435 Dihedral : 2.956 11.167 324 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 11.35 % Favored : 87.23 % 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: 5.43 (0.43), residues: 312 helix: 4.53 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.35 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 938 ARG 0.005 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: C 965 GLN cc_start: 0.8135 (mm110) cc_final: 0.7893 (mm110) REVERT: C 970 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7761 (m-10) outliers start: 4 outliers final: 3 residues processed: 31 average time/residue: 0.5341 time to fit residues: 17.6382 Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.0980 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2448 Z= 0.147 Angle : 0.363 7.397 3300 Z= 0.186 Chirality : 0.033 0.154 414 Planarity : 0.002 0.030 435 Dihedral : 2.853 11.819 324 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 11.35 % Favored : 87.23 % 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: 5.67 (0.43), residues: 312 helix: 4.71 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.31 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE C 938 ARG 0.007 0.001 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: C 965 GLN cc_start: 0.8128 (mm110) cc_final: 0.7877 (mm110) REVERT: C 970 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7699 (m-10) outliers start: 4 outliers final: 3 residues processed: 31 average time/residue: 0.5641 time to fit residues: 18.6070 Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.4265 r_free = 0.4265 target = 0.141371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.126667 restraints weight = 3184.742| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.20 r_work: 0.3893 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2448 Z= 0.186 Angle : 0.371 7.492 3300 Z= 0.193 Chirality : 0.034 0.154 414 Planarity : 0.002 0.033 435 Dihedral : 2.936 12.841 324 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 12.41 % Favored : 86.17 % 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: 5.54 (0.44), residues: 312 helix: 4.61 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.31 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE C 938 ARG 0.007 0.001 ARG C 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1114.06 seconds wall clock time: 20 minutes 40.03 seconds (1240.03 seconds total)