Starting phenix.real_space_refine on Fri Aug 22 12:56:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fa2_28948/08_2025/8fa2_28948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fa2_28948/08_2025/8fa2_28948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fa2_28948/08_2025/8fa2_28948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fa2_28948/08_2025/8fa2_28948.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fa2_28948/08_2025/8fa2_28948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fa2_28948/08_2025/8fa2_28948.map" } resolution = 2.82 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= 0.021 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 1590 2.51 5 N 453 2.21 5 O 534 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2577 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "D" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 323 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Restraints were copied for chains: B, C, E, F Time building chain proxies: 0.66, per 1000 atoms: 0.26 Number of scatterers: 2577 At special positions: 0 Unit cell: (48.975, 57.9538, 118.356, 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 534 8.00 N 453 7.00 C 1590 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: 0.22 Conformation dependent library (CDL) restraints added in 65.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 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: 12 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 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 1169 through 1173 Processing helix chain 'D' and resid 1180 through 1194 Processing helix chain 'D' and resid 1195 through 1197 No H-bonds generated for 'chain 'D' and resid 1195 through 1197' Processing helix chain 'E' and resid 1169 through 1173 Processing helix chain 'E' and resid 1180 through 1194 Processing helix chain 'E' and resid 1195 through 1197 No H-bonds generated for 'chain 'E' and resid 1195 through 1197' Processing helix chain 'F' and resid 1169 through 1173 Processing helix chain 'F' and resid 1180 through 1194 Processing helix chain 'F' and resid 1195 through 1197 No H-bonds generated for 'chain 'F' and resid 1195 through 1197' 238 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: 0.40 Time building geometry restraints manager: 0.25 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: 483 1.29 - 1.35: 426 1.35 - 1.41: 71 1.41 - 1.48: 400 1.48 - 1.54: 1209 Bond restraints: 2589 Sorted by residual: bond pdb=" CA LEU A 966 " pdb=" C LEU A 966 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.29e-02 6.01e+03 1.01e+00 bond pdb=" CA LEU B 966 " pdb=" C LEU B 966 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.29e-02 6.01e+03 9.67e-01 bond pdb=" CA ILE A 980 " pdb=" C ILE A 980 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.18e-02 7.18e+03 8.96e-01 bond pdb=" N PHE B 970 " pdb=" CA PHE B 970 " ideal model delta sigma weight residual 1.459 1.448 0.012 1.23e-02 6.61e+03 8.75e-01 bond pdb=" CA ILE C 980 " pdb=" C ILE C 980 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.18e-02 7.18e+03 8.69e-01 ... (remaining 2584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 3350 1.18 - 2.37: 127 2.37 - 3.55: 4 3.55 - 4.73: 8 4.73 - 5.91: 3 Bond angle restraints: 3492 Sorted by residual: angle pdb=" N ILE F1170 " pdb=" CA ILE F1170 " pdb=" C ILE F1170 " ideal model delta sigma weight residual 109.34 113.14 -3.80 2.08e+00 2.31e-01 3.33e+00 angle pdb=" N ILE E1170 " pdb=" CA ILE E1170 " pdb=" C ILE E1170 " ideal model delta sigma weight residual 109.34 113.13 -3.79 2.08e+00 2.31e-01 3.32e+00 angle pdb=" N ILE D1170 " pdb=" CA ILE D1170 " pdb=" C ILE D1170 " ideal model delta sigma weight residual 109.34 113.12 -3.78 2.08e+00 2.31e-01 3.31e+00 angle pdb=" CA LEU C 962 " pdb=" CB LEU C 962 " pdb=" CG LEU C 962 " ideal model delta sigma weight residual 116.30 122.21 -5.91 3.50e+00 8.16e-02 2.86e+00 angle pdb=" CA LEU B 962 " pdb=" CB LEU B 962 " pdb=" CG LEU B 962 " ideal model delta sigma weight residual 116.30 122.20 -5.90 3.50e+00 8.16e-02 2.84e+00 ... (remaining 3487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 1455 15.00 - 29.99: 111 29.99 - 44.99: 24 44.99 - 59.98: 6 59.98 - 74.98: 9 Dihedral angle restraints: 1605 sinusoidal: 621 harmonic: 984 Sorted by residual: dihedral pdb=" N GLN C 957 " pdb=" CA GLN C 957 " pdb=" CB GLN C 957 " pdb=" CG GLN C 957 " ideal model delta sinusoidal sigma weight residual -60.00 -119.75 59.75 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN A 957 " pdb=" CA GLN A 957 " pdb=" CB GLN A 957 " pdb=" CG GLN A 957 " ideal model delta sinusoidal sigma weight residual -60.00 -119.72 59.72 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN B 957 " pdb=" CA GLN B 957 " pdb=" CB GLN B 957 " pdb=" CG GLN B 957 " ideal model delta sinusoidal sigma weight residual -60.00 -119.68 59.68 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 196 0.021 - 0.043: 123 0.043 - 0.064: 73 0.064 - 0.086: 24 0.086 - 0.107: 16 Chirality restraints: 432 Sorted by residual: chirality pdb=" CA ILE F1173 " pdb=" N ILE F1173 " pdb=" C ILE F1173 " pdb=" CB ILE F1173 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.87e-01 chirality pdb=" CA ILE D1173 " pdb=" N ILE D1173 " pdb=" C ILE D1173 " pdb=" CB ILE D1173 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.71e-01 chirality pdb=" CA ILE D1199 " pdb=" N ILE D1199 " pdb=" C ILE D1199 " pdb=" CB ILE D1199 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.70e-01 ... (remaining 429 not shown) Planarity restraints: 459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 926 " -0.005 2.00e-02 2.50e+03 9.12e-03 8.32e-01 pdb=" C GLN A 926 " 0.016 2.00e-02 2.50e+03 pdb=" O GLN A 926 " -0.006 2.00e-02 2.50e+03 pdb=" N PHE A 927 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 926 " 0.004 2.00e-02 2.50e+03 8.87e-03 7.86e-01 pdb=" C GLN C 926 " -0.015 2.00e-02 2.50e+03 pdb=" O GLN C 926 " 0.006 2.00e-02 2.50e+03 pdb=" N PHE C 927 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 926 " -0.004 2.00e-02 2.50e+03 8.83e-03 7.80e-01 pdb=" C GLN B 926 " 0.015 2.00e-02 2.50e+03 pdb=" O GLN B 926 " -0.006 2.00e-02 2.50e+03 pdb=" N PHE B 927 " -0.005 2.00e-02 2.50e+03 ... (remaining 456 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 726 2.82 - 3.34: 2718 3.34 - 3.86: 4380 3.86 - 4.38: 4822 4.38 - 4.90: 8131 Nonbonded interactions: 20777 Sorted by model distance: nonbonded pdb=" OD1 ASN D1174 " pdb=" N ALA D1175 " model vdw 2.297 3.120 nonbonded pdb=" OD1 ASN F1174 " pdb=" N ALA F1175 " model vdw 2.297 3.120 nonbonded pdb=" OD1 ASN E1174 " pdb=" N ALA E1175 " model vdw 2.297 3.120 nonbonded pdb=" NZ LYS C 969 " pdb=" O GLY E1168 " model vdw 2.497 3.120 nonbonded pdb=" NZ LYS A 969 " pdb=" O GLY F1168 " model vdw 2.497 3.120 ... (remaining 20772 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: 0.01 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: 1.260 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.030 Process input model: 4.050 Find NCS groups from input model: 0.020 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:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 : 0.006 0.029 2589 Z= 0.324 Angle : 0.546 5.914 3492 Z= 0.326 Chirality : 0.039 0.107 432 Planarity : 0.002 0.009 459 Dihedral : 13.542 74.977 957 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % 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: -0.12 (0.39), residues: 330 helix: 0.33 (0.26), residues: 270 sheet: None (None), residues: 0 loop : -1.52 (0.68), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1186 PHE 0.006 0.001 PHE A 981 HIS 0.001 0.000 HIS F1159 Details of bonding type rmsd covalent geometry : bond 0.00624 ( 2589) covalent geometry : angle 0.54566 ( 3492) hydrogen bonds : bond 0.08777 ( 238) hydrogen bonds : angle 3.55639 ( 696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.113 Fit side-chains REVERT: B 970 PHE cc_start: 0.8964 (m-10) cc_final: 0.8760 (m-10) REVERT: C 954 HIS cc_start: 0.8541 (t-170) cc_final: 0.8237 (t-170) REVERT: C 980 ILE cc_start: 0.9080 (mt) cc_final: 0.8863 (mt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.2066 time to fit residues: 9.9279 Evaluate side-chains 44 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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: 0.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.0040 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.141263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.126261 restraints weight = 4023.303| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.42 r_work: 0.3868 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2589 Z= 0.157 Angle : 0.391 8.089 3492 Z= 0.208 Chirality : 0.035 0.120 432 Planarity : 0.002 0.009 459 Dihedral : 3.464 11.198 342 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 10.77 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.61 (0.43), residues: 330 helix: 2.84 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 0.16 (0.73), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1186 PHE 0.006 0.001 PHE A 970 HIS 0.002 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 2589) covalent geometry : angle 0.39062 ( 3492) hydrogen bonds : bond 0.03320 ( 238) hydrogen bonds : angle 2.93771 ( 696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.071 Fit side-chains REVERT: A 965 GLN cc_start: 0.8094 (tt0) cc_final: 0.7789 (tt0) REVERT: B 970 PHE cc_start: 0.8844 (m-10) cc_final: 0.8581 (m-10) REVERT: C 954 HIS cc_start: 0.8492 (t-170) cc_final: 0.8218 (t-170) REVERT: C 973 ILE cc_start: 0.9145 (mt) cc_final: 0.8925 (mt) outliers start: 4 outliers final: 1 residues processed: 42 average time/residue: 0.2063 time to fit residues: 9.2141 Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.140093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.124345 restraints weight = 4170.073| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.53 r_work: 0.3852 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2589 Z= 0.131 Angle : 0.373 7.095 3492 Z= 0.191 Chirality : 0.034 0.113 432 Planarity : 0.002 0.010 459 Dihedral : 3.231 9.101 342 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.34 % Allowed : 12.12 % Favored : 87.54 % 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 (0.44), residues: 330 helix: 3.69 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 0.78 (0.79), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1186 PHE 0.008 0.001 PHE A 970 HIS 0.001 0.000 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 2589) covalent geometry : angle 0.37301 ( 3492) hydrogen bonds : bond 0.03142 ( 238) hydrogen bonds : angle 2.77610 ( 696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.106 Fit side-chains REVERT: A 965 GLN cc_start: 0.8076 (tt0) cc_final: 0.7860 (tt0) REVERT: B 970 PHE cc_start: 0.8823 (m-10) cc_final: 0.8570 (m-10) REVERT: C 954 HIS cc_start: 0.8470 (t-170) cc_final: 0.8224 (t-170) REVERT: C 973 ILE cc_start: 0.9112 (mt) cc_final: 0.8880 (mt) outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.1796 time to fit residues: 7.3407 Evaluate side-chains 39 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU 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 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 920 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.142324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.126070 restraints weight = 4007.853| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.59 r_work: 0.3862 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2589 Z= 0.160 Angle : 0.378 7.761 3492 Z= 0.195 Chirality : 0.035 0.111 432 Planarity : 0.002 0.010 459 Dihedral : 3.237 9.541 342 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.34 % Allowed : 12.46 % Favored : 87.21 % 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: 5.10 (0.45), residues: 330 helix: 3.82 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 0.99 (0.83), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1186 PHE 0.009 0.001 PHE A 970 HIS 0.001 0.000 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 2589) covalent geometry : angle 0.37752 ( 3492) hydrogen bonds : bond 0.03148 ( 238) hydrogen bonds : angle 2.83950 ( 696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.102 Fit side-chains REVERT: B 970 PHE cc_start: 0.8847 (m-10) cc_final: 0.8585 (m-10) REVERT: C 954 HIS cc_start: 0.8515 (t-170) cc_final: 0.8282 (t-170) REVERT: C 973 ILE cc_start: 0.9138 (mt) cc_final: 0.8894 (mt) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.2106 time to fit residues: 9.1310 Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.142208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.125764 restraints weight = 4004.102| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.60 r_work: 0.3862 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2589 Z= 0.158 Angle : 0.364 6.645 3492 Z= 0.192 Chirality : 0.035 0.113 432 Planarity : 0.002 0.008 459 Dihedral : 3.206 9.235 342 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 13.47 % Favored : 85.86 % 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: 5.22 (0.45), residues: 330 helix: 3.88 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.13 (0.86), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1186 PHE 0.007 0.001 PHE A 970 HIS 0.001 0.000 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2589) covalent geometry : angle 0.36385 ( 3492) hydrogen bonds : bond 0.03121 ( 238) hydrogen bonds : angle 2.78919 ( 696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.112 Fit side-chains REVERT: B 970 PHE cc_start: 0.8829 (m-10) cc_final: 0.8572 (m-10) REVERT: C 954 HIS cc_start: 0.8515 (t-170) cc_final: 0.8279 (t-170) REVERT: C 973 ILE cc_start: 0.9133 (mt) cc_final: 0.8885 (mt) outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.2409 time to fit residues: 10.4978 Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN F1174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.142139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.125960 restraints weight = 3950.942| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.57 r_work: 0.3863 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2589 Z= 0.142 Angle : 0.366 7.535 3492 Z= 0.189 Chirality : 0.034 0.114 432 Planarity : 0.002 0.012 459 Dihedral : 3.182 8.921 342 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 13.47 % Favored : 85.86 % 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: 5.36 (0.45), residues: 330 helix: 3.97 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.24 (0.87), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1186 PHE 0.009 0.001 PHE A 970 HIS 0.001 0.000 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 2589) covalent geometry : angle 0.36600 ( 3492) hydrogen bonds : bond 0.03087 ( 238) hydrogen bonds : angle 2.74986 ( 696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.105 Fit side-chains REVERT: B 970 PHE cc_start: 0.8831 (m-10) cc_final: 0.8563 (m-10) REVERT: C 954 HIS cc_start: 0.8522 (t-170) cc_final: 0.8256 (t-170) REVERT: C 973 ILE cc_start: 0.9146 (mt) cc_final: 0.8901 (mt) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.2269 time to fit residues: 9.6563 Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.0060 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4370 r_free = 0.4370 target = 0.146170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.130775 restraints weight = 3952.877| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.47 r_work: 0.3912 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2589 Z= 0.117 Angle : 0.359 8.341 3492 Z= 0.181 Chirality : 0.034 0.113 432 Planarity : 0.001 0.008 459 Dihedral : 3.060 8.540 342 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.34 % Allowed : 13.47 % Favored : 86.20 % 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: 5.64 (0.45), residues: 330 helix: 4.16 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.36 (0.88), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1186 PHE 0.004 0.001 PHE B 970 HIS 0.001 0.000 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 2589) covalent geometry : angle 0.35907 ( 3492) hydrogen bonds : bond 0.03044 ( 238) hydrogen bonds : angle 2.62386 ( 696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.062 Fit side-chains REVERT: B 970 PHE cc_start: 0.8783 (m-10) cc_final: 0.8536 (m-10) REVERT: C 954 HIS cc_start: 0.8483 (t-170) cc_final: 0.8244 (t-170) REVERT: C 973 ILE cc_start: 0.9077 (mt) cc_final: 0.8846 (mt) outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.2113 time to fit residues: 8.5041 Evaluate side-chains 39 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN C 965 GLN F1174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.145700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.130254 restraints weight = 3977.613| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.49 r_work: 0.3903 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2589 Z= 0.126 Angle : 0.341 6.745 3492 Z= 0.179 Chirality : 0.034 0.114 432 Planarity : 0.002 0.013 459 Dihedral : 3.080 8.532 342 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 12.79 % Favored : 86.20 % 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: 5.61 (0.45), residues: 330 helix: 4.13 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.44 (0.89), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1186 PHE 0.004 0.001 PHE B 927 HIS 0.001 0.000 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 2589) covalent geometry : angle 0.34136 ( 3492) hydrogen bonds : bond 0.03032 ( 238) hydrogen bonds : angle 2.65792 ( 696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.118 Fit side-chains REVERT: B 970 PHE cc_start: 0.8763 (m-10) cc_final: 0.8495 (m-10) REVERT: C 954 HIS cc_start: 0.8498 (t-170) cc_final: 0.8262 (t-170) REVERT: C 973 ILE cc_start: 0.9070 (mt) cc_final: 0.8838 (mt) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.2414 time to fit residues: 10.2282 Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.0470 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.145720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.130285 restraints weight = 4005.270| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.50 r_work: 0.3908 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2589 Z= 0.117 Angle : 0.358 8.640 3492 Z= 0.179 Chirality : 0.034 0.114 432 Planarity : 0.001 0.008 459 Dihedral : 3.040 8.445 342 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 13.47 % Favored : 85.86 % 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: 5.73 (0.45), residues: 330 helix: 4.21 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.46 (0.88), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1186 PHE 0.004 0.001 PHE B 970 HIS 0.001 0.000 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 2589) covalent geometry : angle 0.35835 ( 3492) hydrogen bonds : bond 0.03009 ( 238) hydrogen bonds : angle 2.62055 ( 696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.107 Fit side-chains REVERT: B 970 PHE cc_start: 0.8762 (m-10) cc_final: 0.8513 (m-10) REVERT: C 954 HIS cc_start: 0.8497 (t-170) cc_final: 0.8266 (t-170) REVERT: C 973 ILE cc_start: 0.9081 (mt) cc_final: 0.8852 (mt) outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.2277 time to fit residues: 9.1695 Evaluate side-chains 39 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.144947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.129566 restraints weight = 3959.417| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.46 r_work: 0.3896 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2589 Z= 0.161 Angle : 0.368 7.125 3492 Z= 0.193 Chirality : 0.035 0.114 432 Planarity : 0.002 0.013 459 Dihedral : 3.117 8.806 342 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.34 % Allowed : 14.14 % Favored : 85.52 % 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: 5.45 (0.45), residues: 330 helix: 4.01 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.40 (0.87), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1186 PHE 0.004 0.001 PHE A 970 HIS 0.001 0.000 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 2589) covalent geometry : angle 0.36812 ( 3492) hydrogen bonds : bond 0.03102 ( 238) hydrogen bonds : angle 2.78713 ( 696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.102 Fit side-chains REVERT: B 970 PHE cc_start: 0.8781 (m-10) cc_final: 0.8518 (m-10) REVERT: C 954 HIS cc_start: 0.8514 (t-170) cc_final: 0.8284 (t-170) REVERT: C 973 ILE cc_start: 0.9092 (mt) cc_final: 0.8857 (mt) outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.2246 time to fit residues: 9.5293 Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.145107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.129469 restraints weight = 3992.731| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.48 r_work: 0.3896 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2589 Z= 0.154 Angle : 0.372 7.062 3492 Z= 0.191 Chirality : 0.035 0.114 432 Planarity : 0.001 0.008 459 Dihedral : 3.103 8.817 342 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 13.80 % Favored : 85.52 % 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 (0.44), residues: 330 helix: 4.02 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.41 (0.87), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1186 PHE 0.004 0.001 PHE A 927 HIS 0.001 0.000 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2589) covalent geometry : angle 0.37197 ( 3492) hydrogen bonds : bond 0.03095 ( 238) hydrogen bonds : angle 2.74808 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 855.17 seconds wall clock time: 15 minutes 19.49 seconds (919.49 seconds total)