Starting phenix.real_space_refine on Wed Sep 17 03:07:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8czi_27098/09_2025/8czi_27098.cif Found real_map, /net/cci-nas-00/data/ceres_data/8czi_27098/09_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_27098/09_2025/8czi_27098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8czi_27098/09_2025/8czi_27098.map" model { file = "/net/cci-nas-00/data/ceres_data/8czi_27098/09_2025/8czi_27098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8czi_27098/09_2025/8czi_27098.cif" } resolution = 2.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: "D" 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: B, C, E, F Time building chain proxies: 0.68, per 1000 atoms: 0.27 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: 0.20 Conformation dependent library (CDL) restraints added in 102.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 235 hydrogen bonds defined for protein. 696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.42 Time building geometry restraints manager: 0.28 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: 0.00 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: 1.490 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.550 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:9.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.270 ------------------------------------------------------------------------------- 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= 0.197 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG B 983 PHE 0.007 0.001 PHE A 970 HIS 0.000 0.000 HIS D1159 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 2556) covalent geometry : angle 0.33337 ( 3453) hydrogen bonds : bond 0.07520 ( 235) hydrogen bonds : angle 2.48261 ( 696) *********************** 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 : 0.102 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: 0.2276 time to fit residues: 7.0586 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 : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.0170 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.4018 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.142308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.125655 restraints weight = 3295.075| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.62 r_work: 0.3808 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2556 Z= 0.120 Angle : 0.306 2.823 3453 Z= 0.176 Chirality : 0.032 0.099 435 Planarity : 0.002 0.015 456 Dihedral : 2.736 8.470 339 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 4.38 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.87 (0.43), residues: 327 helix: 4.59 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -1.41 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 983 PHE 0.004 0.001 PHE C 970 HIS 0.001 0.000 HIS E1159 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 2556) covalent geometry : angle 0.30630 ( 3453) hydrogen bonds : bond 0.03262 ( 235) hydrogen bonds : angle 2.32560 ( 696) *********************** 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 : 0.105 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.1418 time to fit residues: 3.9316 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 : 0.093 ------------------------------------------------------------------------------- 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 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.139140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.122014 restraints weight = 3342.625| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.68 r_work: 0.3775 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1361 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= 0.174 Angle : 0.325 3.160 3453 Z= 0.188 Chirality : 0.033 0.102 435 Planarity : 0.002 0.015 456 Dihedral : 2.895 9.641 339 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 5.05 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.18 (0.43), residues: 327 helix: 4.76 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -1.10 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 983 PHE 0.009 0.001 PHE C 970 HIS 0.001 0.000 HIS E1159 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 2556) covalent geometry : angle 0.32545 ( 3453) hydrogen bonds : bond 0.03461 ( 235) hydrogen bonds : angle 2.38335 ( 696) *********************** 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 32 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.076 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.1297 time to fit residues: 4.0272 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 : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU 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 14 optimal weight: 0.0070 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 2 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 = 0.4181 r_free = 0.4181 target = 0.133963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.116196 restraints weight = 3311.417| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.69 r_work: 0.3778 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1483 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= 0.132 Angle : 0.299 2.874 3453 Z= 0.173 Chirality : 0.032 0.103 435 Planarity : 0.002 0.015 456 Dihedral : 2.718 9.153 339 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 6.73 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.55 (0.43), residues: 327 helix: 5.01 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.92 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1185 PHE 0.005 0.001 PHE C 970 HIS 0.000 0.000 HIS E1159 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2556) covalent geometry : angle 0.29873 ( 3453) hydrogen bonds : bond 0.03362 ( 235) hydrogen bonds : angle 2.29576 ( 696) *********************** 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 32 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.108 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 30 average time/residue: 0.1087 time to fit residues: 3.7084 Evaluate side-chains 31 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.140574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.124358 restraints weight = 3331.676| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.59 r_work: 0.3793 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1567 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= 0.149 Angle : 0.327 3.189 3453 Z= 0.185 Chirality : 0.033 0.103 435 Planarity : 0.002 0.015 456 Dihedral : 2.751 9.450 339 Min Nonbonded Distance : 2.373 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.52 (0.43), residues: 327 helix: 4.97 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.83 (0.65), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 983 PHE 0.004 0.001 PHE C 970 HIS 0.000 0.000 HIS E1159 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 2556) covalent geometry : angle 0.32679 ( 3453) hydrogen bonds : bond 0.03425 ( 235) hydrogen bonds : angle 2.35560 ( 696) *********************** 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 : 0.095 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 0.1424 time to fit residues: 4.6116 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 : 0.095 ------------------------------------------------------------------------------- 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 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 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 = 0.140570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.124382 restraints weight = 3341.160| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.60 r_work: 0.3790 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1629 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= 0.153 Angle : 0.326 3.658 3453 Z= 0.184 Chirality : 0.033 0.103 435 Planarity : 0.002 0.017 456 Dihedral : 2.761 9.462 339 Min Nonbonded Distance : 2.467 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.52 (0.43), residues: 327 helix: 4.95 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.76 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 983 PHE 0.005 0.001 PHE C 970 HIS 0.000 0.000 HIS E1159 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 2556) covalent geometry : angle 0.32626 ( 3453) hydrogen bonds : bond 0.03421 ( 235) hydrogen bonds : angle 2.36222 ( 696) *********************** 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 : 0.075 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.0922 time to fit residues: 2.9104 Evaluate side-chains 30 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain E residue 1173 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.139978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.123585 restraints weight = 3346.030| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.60 r_work: 0.3786 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1665 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= 0.157 Angle : 0.326 3.445 3453 Z= 0.185 Chirality : 0.033 0.104 435 Planarity : 0.002 0.016 456 Dihedral : 2.757 9.499 339 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.50 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.53 (0.43), residues: 327 helix: 4.95 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.72 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 983 PHE 0.006 0.001 PHE C 970 HIS 0.000 0.000 HIS F1159 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2556) covalent geometry : angle 0.32625 ( 3453) hydrogen bonds : bond 0.03430 ( 235) hydrogen bonds : angle 2.36734 ( 696) *********************** 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 34 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.152 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.1016 time to fit residues: 3.4088 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 : 0.111 ------------------------------------------------------------------------------- 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 31 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.132754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.113691 restraints weight = 3433.854| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.78 r_work: 0.3752 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.004 0.022 2556 Z= 0.196 Angle : 0.367 5.304 3453 Z= 0.201 Chirality : 0.034 0.103 435 Planarity : 0.002 0.017 456 Dihedral : 2.876 9.945 339 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 7.41 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.32 (0.43), residues: 327 helix: 4.77 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.72 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 983 PHE 0.006 0.001 PHE C 970 HIS 0.000 0.000 HIS E1159 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 2556) covalent geometry : angle 0.36698 ( 3453) hydrogen bonds : bond 0.03547 ( 235) hydrogen bonds : angle 2.44767 ( 696) *********************** 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 34 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.099 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 30 average time/residue: 0.1363 time to fit residues: 4.5407 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 : 0.091 ------------------------------------------------------------------------------- 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 29 optimal weight: 0.0060 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.133146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.114117 restraints weight = 3458.757| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.79 r_work: 0.3758 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.004 0.020 2556 Z= 0.164 Angle : 0.349 4.021 3453 Z= 0.198 Chirality : 0.033 0.128 435 Planarity : 0.002 0.018 456 Dihedral : 2.805 9.566 339 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 7.74 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.41 (0.43), residues: 327 helix: 4.83 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.66 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 983 PHE 0.005 0.001 PHE C 970 HIS 0.000 0.000 HIS F1159 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 2556) covalent geometry : angle 0.34901 ( 3453) hydrogen bonds : bond 0.03501 ( 235) hydrogen bonds : angle 2.48138 ( 696) *********************** 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 33 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.090 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.1396 time to fit residues: 4.3198 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 : 0.097 ------------------------------------------------------------------------------- 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 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.132823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.114242 restraints weight = 3443.675| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.76 r_work: 0.3762 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1767 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= 0.151 Angle : 0.342 3.666 3453 Z= 0.196 Chirality : 0.033 0.121 435 Planarity : 0.002 0.022 456 Dihedral : 2.761 9.385 339 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 7.41 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.47 (0.43), residues: 327 helix: 4.87 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.63 (0.68), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1185 PHE 0.005 0.001 PHE C 970 HIS 0.000 0.000 HIS F1159 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 2556) covalent geometry : angle 0.34250 ( 3453) hydrogen bonds : bond 0.03464 ( 235) hydrogen bonds : angle 2.48880 ( 696) ********************** 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 33 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.107 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.1110 time to fit residues: 3.5358 Evaluate side-chains 31 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.068 ------------------------------------------------------------------------------- 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 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 chunk 3 optimal weight: 0.0370 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.132804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.114090 restraints weight = 3408.898| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.77 r_work: 0.3763 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1778 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= 0.161 Angle : 0.366 7.406 3453 Z= 0.202 Chirality : 0.033 0.120 435 Planarity : 0.002 0.020 456 Dihedral : 2.785 9.500 339 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 7.41 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.42 (0.43), residues: 327 helix: 4.83 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.64 (0.68), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 983 PHE 0.005 0.001 PHE C 970 HIS 0.000 0.000 HIS F1159 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 2556) covalent geometry : angle 0.36630 ( 3453) hydrogen bonds : bond 0.03474 ( 235) hydrogen bonds : angle 2.48990 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1122.41 seconds wall clock time: 19 minutes 55.31 seconds (1195.31 seconds total)