Starting phenix.real_space_refine on Mon Feb 10 20:55:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8czi_27098/02_2025/8czi_27098.cif Found real_map, /net/cci-nas-00/data/ceres_data/8czi_27098/02_2025/8czi_27098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8czi_27098/02_2025/8czi_27098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8czi_27098/02_2025/8czi_27098.map" model { file = "/net/cci-nas-00/data/ceres_data/8czi_27098/02_2025/8czi_27098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8czi_27098/02_2025/8czi_27098.cif" } resolution = 2.22 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 1566 2.51 5 N 447 2.21 5 O 537 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-5592/modules/chem_data/mon_lib" Total number of atoms: 2550 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "E" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Restraints were copied for chains: C, B, D, F Time building chain proxies: 2.01, per 1000 atoms: 0.79 Number of scatterers: 2550 At special positions: 0 Unit cell: (45.71, 49.7913, 117.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 537 8.00 N 447 7.00 C 1566 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: 0.65 Conformation dependent library (CDL) restraints added in 314.2 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 235 hydrogen bonds defined for protein. 696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.66 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: 1.23 - 1.29: 486 1.29 - 1.35: 420 1.35 - 1.42: 83 1.42 - 1.48: 361 1.48 - 1.54: 1206 Bond restraints: 2556 Sorted by residual: bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.19e-02 7.06e+03 5.84e-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 5.77e-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 5.77e-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 5.75e-01 bond pdb=" N VAL D1176 " pdb=" CA VAL D1176 " ideal model delta sigma weight residual 1.457 1.449 0.008 1.15e-02 7.56e+03 4.95e-01 ... (remaining 2551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.58: 3212 0.58 - 1.17: 199 1.17 - 1.75: 35 1.75 - 2.33: 1 2.33 - 2.92: 6 Bond angle restraints: 3453 Sorted by residual: angle pdb=" C ASP F1165 " pdb=" CA ASP F1165 " pdb=" CB ASP F1165 " ideal model delta sigma weight residual 110.19 111.68 -1.49 1.62e+00 3.81e-01 8.49e-01 angle pdb=" C ASP D1165 " pdb=" CA ASP D1165 " pdb=" CB ASP D1165 " ideal model delta sigma weight residual 110.19 111.67 -1.48 1.62e+00 3.81e-01 8.39e-01 angle pdb=" C ASP E1165 " pdb=" CA ASP E1165 " pdb=" CB ASP E1165 " ideal model delta sigma weight residual 110.19 111.67 -1.48 1.62e+00 3.81e-01 8.35e-01 angle pdb=" CA PRO D1162 " pdb=" CB PRO D1162 " pdb=" CG PRO D1162 " ideal model delta sigma weight residual 104.50 106.22 -1.72 1.90e+00 2.77e-01 8.19e-01 angle pdb=" CA PRO E1162 " pdb=" CB PRO E1162 " pdb=" CG PRO E1162 " ideal model delta sigma weight residual 104.50 106.21 -1.71 1.90e+00 2.77e-01 8.14e-01 ... (remaining 3448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 1461 17.82 - 35.64: 114 35.64 - 53.46: 9 53.46 - 71.28: 9 71.28 - 89.10: 6 Dihedral angle restraints: 1599 sinusoidal: 618 harmonic: 981 Sorted by residual: dihedral pdb=" N ASN D1187 " pdb=" CA ASN D1187 " pdb=" CB ASN D1187 " pdb=" CG ASN D1187 " ideal model delta sinusoidal sigma weight residual -60.00 -97.03 37.03 3 1.50e+01 4.44e-03 6.45e+00 dihedral pdb=" N ASN E1187 " pdb=" CA ASN E1187 " pdb=" CB ASN E1187 " pdb=" CG ASN E1187 " ideal model delta sinusoidal sigma weight residual -60.00 -97.02 37.02 3 1.50e+01 4.44e-03 6.44e+00 dihedral pdb=" N ASN F1187 " pdb=" CA ASN F1187 " pdb=" CB ASN F1187 " pdb=" CG ASN F1187 " ideal model delta sinusoidal sigma weight residual -60.00 -97.02 37.02 3 1.50e+01 4.44e-03 6.44e+00 ... (remaining 1596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 214 0.021 - 0.041: 148 0.041 - 0.062: 59 0.062 - 0.083: 2 0.083 - 0.103: 12 Chirality restraints: 435 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 2.54 -0.10 2.00e-01 2.50e+01 2.67e-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 2.54 -0.10 2.00e-01 2.50e+01 2.60e-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 2.54 -0.10 2.00e-01 2.50e+01 2.60e-01 ... (remaining 432 not shown) Planarity restraints: 456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D1161 " -0.012 5.00e-02 4.00e+02 1.79e-02 5.13e-01 pdb=" N PRO D1162 " 0.031 5.00e-02 4.00e+02 pdb=" CA PRO D1162 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO D1162 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F1161 " 0.012 5.00e-02 4.00e+02 1.78e-02 5.09e-01 pdb=" N PRO F1162 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO F1162 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO F1162 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E1161 " 0.012 5.00e-02 4.00e+02 1.76e-02 4.97e-01 pdb=" N PRO E1162 " -0.030 5.00e-02 4.00e+02 pdb=" CA PRO E1162 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO E1162 " 0.010 5.00e-02 4.00e+02 ... (remaining 453 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 903 2.89 - 3.39: 2866 3.39 - 3.89: 4324 3.89 - 4.40: 4612 4.40 - 4.90: 7926 Nonbonded interactions: 20631 Sorted by model distance: nonbonded pdb=" ND2 ASN C 978 " pdb=" OD1 ASP F1163 " model vdw 2.382 3.120 nonbonded pdb=" ND2 ASN A 978 " pdb=" OD1 ASP D1163 " model vdw 2.383 3.120 nonbonded pdb=" ND2 ASN B 978 " pdb=" OD1 ASP E1163 " model vdw 2.384 3.120 nonbonded pdb=" NE2 GLN B 935 " pdb=" O ALA E1190 " model vdw 2.396 3.120 nonbonded pdb=" NE2 GLN C 935 " pdb=" O ALA F1190 " model vdw 2.397 3.120 ... (remaining 20626 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.130 Find NCS groups from input model: 0.050 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:14.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.004 0.026 2556 Z= 0.276 Angle : 0.333 2.918 3453 Z= 0.199 Chirality : 0.031 0.103 435 Planarity : 0.002 0.018 456 Dihedral : 14.483 89.102 951 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.90 (0.41), residues: 327 helix: 3.03 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -1.90 (0.56), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D1159 PHE 0.007 0.001 PHE A 970 ARG 0.001 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.270 Fit side-chains REVERT: B 973 ILE cc_start: 0.8582 (mt) cc_final: 0.8253 (mt) REVERT: C 964 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7962 (ttmt) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.4533 time to fit residues: 14.2467 Evaluate side-chains 27 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.141437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.124743 restraints weight = 3274.074| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.62 r_work: 0.3797 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2556 Z= 0.215 Angle : 0.322 2.872 3453 Z= 0.184 Chirality : 0.032 0.098 435 Planarity : 0.002 0.016 456 Dihedral : 2.831 8.899 339 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 5.05 % Favored : 94.28 % 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: 4.71 (0.43), residues: 327 helix: 4.45 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -1.39 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.295 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.3497 time to fit residues: 9.7516 Evaluate side-chains 26 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.140651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.124102 restraints weight = 3315.577| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.61 r_work: 0.3779 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2556 Z= 0.272 Angle : 0.329 3.187 3453 Z= 0.189 Chirality : 0.033 0.103 435 Planarity : 0.002 0.017 456 Dihedral : 2.915 9.552 339 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 5.39 % Favored : 93.27 % 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: 5.09 (0.43), residues: 327 helix: 4.67 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -1.06 (0.62), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E1159 PHE 0.009 0.001 PHE C 970 ARG 0.001 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.279 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 0.2799 time to fit residues: 9.7863 Evaluate side-chains 32 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain E residue 1173 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.140412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.124275 restraints weight = 3314.678| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.57 r_work: 0.3788 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2556 Z= 0.256 Angle : 0.333 2.953 3453 Z= 0.190 Chirality : 0.033 0.102 435 Planarity : 0.002 0.017 456 Dihedral : 2.872 9.696 339 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 7.07 % Favored : 91.58 % 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: 5.19 (0.43), residues: 327 helix: 4.73 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.96 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.297 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.3134 time to fit residues: 10.2173 Evaluate side-chains 33 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain E residue 1173 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.0870 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.141197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.124533 restraints weight = 3308.893| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.62 r_work: 0.3791 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2556 Z= 0.180 Angle : 0.304 3.107 3453 Z= 0.174 Chirality : 0.032 0.104 435 Planarity : 0.002 0.015 456 Dihedral : 2.700 9.050 339 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 6.73 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.59 (0.43), residues: 327 helix: 5.02 (0.24), residues: 243 sheet: None (None), residues: 0 loop : -0.80 (0.65), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.004 0.001 PHE C 970 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.267 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 0.2178 time to fit residues: 7.3765 Evaluate side-chains 30 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.0980 chunk 15 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.140641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.124314 restraints weight = 3324.750| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.59 r_work: 0.3794 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2556 Z= 0.180 Angle : 0.320 4.397 3453 Z= 0.178 Chirality : 0.032 0.104 435 Planarity : 0.001 0.016 456 Dihedral : 2.666 9.210 339 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 7.41 % Favored : 91.58 % 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: 5.75 (0.43), residues: 327 helix: 5.14 (0.24), residues: 243 sheet: None (None), residues: 0 loop : -0.76 (0.65), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.004 0.001 PHE C 970 ARG 0.001 0.000 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.233 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 0.2138 time to fit residues: 6.9832 Evaluate side-chains 29 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1166 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.140379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.123993 restraints weight = 3389.850| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.61 r_work: 0.3787 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2556 Z= 0.223 Angle : 0.324 3.542 3453 Z= 0.183 Chirality : 0.032 0.104 435 Planarity : 0.002 0.015 456 Dihedral : 2.733 9.437 339 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 6.73 % Favored : 91.58 % 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: 5.64 (0.43), residues: 327 helix: 5.05 (0.24), residues: 243 sheet: None (None), residues: 0 loop : -0.76 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.273 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.2259 time to fit residues: 7.3489 Evaluate side-chains 34 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain E residue 1173 ASN Chi-restraints excluded: chain F residue 1166 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 5 optimal weight: 0.9990 chunk 32 optimal weight: 0.0070 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.133555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.114423 restraints weight = 3394.209| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.79 r_work: 0.3764 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2556 Z= 0.194 Angle : 0.324 3.720 3453 Z= 0.185 Chirality : 0.032 0.117 435 Planarity : 0.001 0.015 456 Dihedral : 2.700 9.265 339 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 6.73 % Favored : 91.58 % 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: 327 helix: 5.06 (0.24), residues: 243 sheet: None (None), residues: 0 loop : -0.73 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.288 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.2244 time to fit residues: 7.3418 Evaluate side-chains 32 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain E residue 1173 ASN Chi-restraints excluded: chain F residue 1166 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.0060 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.133266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.114223 restraints weight = 3395.678| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.78 r_work: 0.3763 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2556 Z= 0.213 Angle : 0.354 6.700 3453 Z= 0.194 Chirality : 0.033 0.115 435 Planarity : 0.002 0.016 456 Dihedral : 2.734 9.320 339 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 7.07 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.57 (0.43), residues: 327 helix: 4.98 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.73 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.267 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.2334 time to fit residues: 7.0733 Evaluate side-chains 30 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain E residue 1173 ASN Chi-restraints excluded: chain F residue 1166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 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 = 0.4210 r_free = 0.4210 target = 0.140587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.124348 restraints weight = 3308.626| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.58 r_work: 0.3791 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2556 Z= 0.211 Angle : 0.348 6.075 3453 Z= 0.193 Chirality : 0.033 0.112 435 Planarity : 0.002 0.014 456 Dihedral : 2.728 9.332 339 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 6.73 % Favored : 91.58 % 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: 5.58 (0.43), residues: 327 helix: 4.98 (0.24), residues: 243 sheet: None (None), residues: 0 loop : -0.71 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG A 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.298 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.2294 time to fit residues: 6.9842 Evaluate side-chains 30 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain E residue 1173 ASN Chi-restraints excluded: chain F residue 1166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 11 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.132399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.114402 restraints weight = 3334.124| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.72 r_work: 0.3773 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2556 Z= 0.192 Angle : 0.341 5.648 3453 Z= 0.190 Chirality : 0.032 0.110 435 Planarity : 0.002 0.014 456 Dihedral : 2.702 9.241 339 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 7.07 % Favored : 91.58 % 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: 5.65 (0.43), residues: 327 helix: 5.03 (0.24), residues: 243 sheet: None (None), residues: 0 loop : -0.67 (0.68), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.004 0.001 PHE C 970 ARG 0.001 0.000 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2149.59 seconds wall clock time: 38 minutes 33.29 seconds (2313.29 seconds total)