Starting phenix.real_space_refine on Wed Jun 4 11:37:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fa2_28948/06_2025/8fa2_28948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fa2_28948/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fa2_28948/06_2025/8fa2_28948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fa2_28948/06_2025/8fa2_28948.map" model { file = "/net/cci-nas-00/data/ceres_data/8fa2_28948/06_2025/8fa2_28948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fa2_28948/06_2025/8fa2_28948.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: "E" 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: C, B, D, F Time building chain proxies: 1.76, per 1000 atoms: 0.68 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: 0.60 Conformation dependent library (CDL) restraints added in 294.4 milliseconds 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: 0.20 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: 0.64 Time building geometry restraints manager: 0.72 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.410 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.001 0.000 HIS F1159 PHE 0.006 0.001 PHE A 981 ARG 0.001 0.000 ARG D1186 Details of bonding type rmsd hydrogen bonds : bond 0.08777 ( 238) hydrogen bonds : angle 3.55639 ( 696) covalent geometry : bond 0.00624 ( 2589) covalent geometry : angle 0.54566 ( 3492) *********************** 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 : 0.295 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: 0.3824 time to fit residues: 18.6583 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 : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 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 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 = 0.141230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.126243 restraints weight = 4057.710| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.44 r_work: 0.3867 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2589 Z= 0.161 Angle : 0.389 7.889 3492 Z= 0.209 Chirality : 0.035 0.121 432 Planarity : 0.002 0.009 459 Dihedral : 3.461 11.093 342 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 11.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.43), residues: 330 helix: 2.84 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 0.20 (0.73), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 954 PHE 0.006 0.002 PHE A 970 ARG 0.001 0.000 ARG D1186 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 238) hydrogen bonds : angle 2.95055 ( 696) covalent geometry : bond 0.00332 ( 2589) covalent geometry : angle 0.38942 ( 3492) *********************** 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 43 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.291 Fit side-chains REVERT: A 965 GLN cc_start: 0.8104 (tt0) cc_final: 0.7804 (tt0) REVERT: B 970 PHE cc_start: 0.8845 (m-10) cc_final: 0.8616 (m-10) REVERT: C 954 HIS cc_start: 0.8496 (t-170) cc_final: 0.8222 (t-170) REVERT: C 973 ILE cc_start: 0.9148 (mt) cc_final: 0.8897 (mp) outliers start: 3 outliers final: 1 residues processed: 41 average time/residue: 0.4372 time to fit residues: 19.2368 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 : 0.314 ------------------------------------------------------------------------------- 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 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.139103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.123825 restraints weight = 4112.927| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.48 r_work: 0.3843 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2589 Z= 0.168 Angle : 0.391 6.933 3492 Z= 0.203 Chirality : 0.035 0.111 432 Planarity : 0.002 0.009 459 Dihedral : 3.325 9.486 342 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 11.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.63 (0.44), residues: 330 helix: 3.48 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 0.89 (0.80), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 954 PHE 0.007 0.001 PHE A 970 ARG 0.001 0.000 ARG B 983 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 238) hydrogen bonds : angle 2.91273 ( 696) covalent geometry : bond 0.00351 ( 2589) covalent geometry : angle 0.39060 ( 3492) *********************** 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 43 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.263 Fit side-chains REVERT: A 965 GLN cc_start: 0.8098 (tt0) cc_final: 0.7888 (tt0) REVERT: B 970 PHE cc_start: 0.8827 (m-10) cc_final: 0.8608 (m-10) REVERT: C 954 HIS cc_start: 0.8495 (t-170) cc_final: 0.8248 (t-170) REVERT: C 973 ILE cc_start: 0.9132 (mt) cc_final: 0.8897 (mt) outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.4327 time to fit residues: 19.0277 Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.4333 r_free = 0.4333 target = 0.142029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.125814 restraints weight = 3952.252| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.57 r_work: 0.3860 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2589 Z= 0.163 Angle : 0.378 7.718 3492 Z= 0.196 Chirality : 0.035 0.114 432 Planarity : 0.002 0.011 459 Dihedral : 3.250 9.543 342 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 12.46 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.01 (0.45), residues: 330 helix: 3.72 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.16 (0.83), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.008 0.001 PHE A 970 ARG 0.001 0.000 ARG D1186 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 238) hydrogen bonds : angle 2.85919 ( 696) covalent geometry : bond 0.00335 ( 2589) covalent geometry : angle 0.37825 ( 3492) *********************** 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 44 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.273 Fit side-chains REVERT: A 965 GLN cc_start: 0.8175 (tt0) cc_final: 0.7944 (tt0) REVERT: B 970 PHE cc_start: 0.8850 (m-10) cc_final: 0.8586 (m-10) REVERT: C 954 HIS cc_start: 0.8525 (t-170) cc_final: 0.8262 (t-170) REVERT: C 973 ILE cc_start: 0.9125 (mt) cc_final: 0.8882 (mt) outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 0.4857 time to fit residues: 22.2467 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 : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 28 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4346 r_free = 0.4346 target = 0.143117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.126876 restraints weight = 3995.152| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.59 r_work: 0.3872 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1998 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= 0.130 Angle : 0.343 6.520 3492 Z= 0.181 Chirality : 0.034 0.111 432 Planarity : 0.001 0.010 459 Dihedral : 3.149 9.119 342 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 13.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.39 (0.45), residues: 330 helix: 3.97 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.33 (0.87), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.009 0.001 PHE A 970 ARG 0.001 0.000 ARG D1186 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 238) hydrogen bonds : angle 2.71052 ( 696) covalent geometry : bond 0.00265 ( 2589) covalent geometry : angle 0.34272 ( 3492) *********************** 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 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.262 Fit side-chains REVERT: B 970 PHE cc_start: 0.8853 (m-10) cc_final: 0.8570 (m-10) REVERT: C 954 HIS cc_start: 0.8523 (t-170) cc_final: 0.8279 (t-170) REVERT: C 973 ILE cc_start: 0.9115 (mt) cc_final: 0.8867 (mt) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.4331 time to fit residues: 18.5769 Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 27 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4346 r_free = 0.4346 target = 0.143285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.126999 restraints weight = 4071.253| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.63 r_work: 0.3867 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2589 Z= 0.131 Angle : 0.363 7.596 3492 Z= 0.186 Chirality : 0.034 0.113 432 Planarity : 0.002 0.011 459 Dihedral : 3.105 8.691 342 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 5.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.57 (0.45), residues: 330 helix: 4.07 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.56 (0.89), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.009 0.001 PHE A 970 ARG 0.001 0.000 ARG D1186 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 238) hydrogen bonds : angle 2.70143 ( 696) covalent geometry : bond 0.00268 ( 2589) covalent geometry : angle 0.36345 ( 3492) *********************** 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 : 0.269 Fit side-chains REVERT: B 970 PHE cc_start: 0.8844 (m-10) cc_final: 0.8570 (m-10) REVERT: C 954 HIS cc_start: 0.8531 (t-170) cc_final: 0.8298 (t-170) REVERT: C 973 ILE cc_start: 0.9128 (mt) cc_final: 0.8891 (mt) outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.4405 time to fit residues: 19.3553 Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.0030 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 overall best weight: 0.3990 ------------------------------------------------------------------------------- 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 = 0.4370 r_free = 0.4370 target = 0.146177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.130367 restraints weight = 4023.491| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.60 r_work: 0.3896 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2589 Z= 0.108 Angle : 0.356 8.410 3492 Z= 0.177 Chirality : 0.033 0.112 432 Planarity : 0.001 0.009 459 Dihedral : 3.037 8.536 342 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 : 1.01 % Allowed : 13.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.79 (0.45), residues: 330 helix: 4.22 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.67 (0.90), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.009 0.001 PHE A 970 ARG 0.001 0.000 ARG D1186 Details of bonding type rmsd hydrogen bonds : bond 0.03014 ( 238) hydrogen bonds : angle 2.60541 ( 696) covalent geometry : bond 0.00217 ( 2589) covalent geometry : angle 0.35599 ( 3492) *********************** 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 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.292 Fit side-chains REVERT: B 966 LEU cc_start: 0.8869 (mt) cc_final: 0.8635 (mm) REVERT: B 970 PHE cc_start: 0.8795 (m-10) cc_final: 0.8538 (m-10) REVERT: C 954 HIS cc_start: 0.8514 (t-170) cc_final: 0.8256 (t-170) REVERT: C 973 ILE cc_start: 0.9103 (mt) cc_final: 0.8863 (mt) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.4688 time to fit residues: 19.6131 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 : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.0570 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 920 GLN F1174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.141998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.126371 restraints weight = 3905.983| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.51 r_work: 0.3889 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2187 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= 0.149 Angle : 0.362 6.977 3492 Z= 0.188 Chirality : 0.035 0.114 432 Planarity : 0.002 0.013 459 Dihedral : 3.075 8.611 342 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 14.14 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.63 (0.45), residues: 330 helix: 4.11 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.59 (0.89), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.010 0.001 PHE A 970 ARG 0.001 0.000 ARG D1186 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 238) hydrogen bonds : angle 2.71697 ( 696) covalent geometry : bond 0.00306 ( 2589) covalent geometry : angle 0.36178 ( 3492) *********************** 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 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.267 Fit side-chains REVERT: B 970 PHE cc_start: 0.8835 (m-10) cc_final: 0.8581 (m-10) REVERT: C 954 HIS cc_start: 0.8520 (t-170) cc_final: 0.8278 (t-170) REVERT: C 973 ILE cc_start: 0.9118 (mt) cc_final: 0.8880 (mt) outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.4320 time to fit residues: 18.5192 Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.146019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.130404 restraints weight = 3970.713| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.58 r_work: 0.3892 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2322 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= 0.114 Angle : 0.356 9.167 3492 Z= 0.179 Chirality : 0.034 0.114 432 Planarity : 0.001 0.008 459 Dihedral : 3.007 8.339 342 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 13.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.85 (0.44), residues: 330 helix: 4.27 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.62 (0.88), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.005 0.001 PHE B 970 ARG 0.001 0.000 ARG D1186 Details of bonding type rmsd hydrogen bonds : bond 0.03031 ( 238) hydrogen bonds : angle 2.59750 ( 696) covalent geometry : bond 0.00230 ( 2589) covalent geometry : angle 0.35568 ( 3492) *********************** 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 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.285 Fit side-chains REVERT: B 966 LEU cc_start: 0.8877 (mt) cc_final: 0.8656 (mm) REVERT: B 970 PHE cc_start: 0.8808 (m-10) cc_final: 0.8548 (m-10) REVERT: C 954 HIS cc_start: 0.8509 (t-170) cc_final: 0.8264 (t-170) REVERT: C 973 ILE cc_start: 0.9106 (mt) cc_final: 0.8868 (mt) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.4966 time to fit residues: 21.3093 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 : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.0470 chunk 24 optimal weight: 0.9980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.145877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.130350 restraints weight = 3876.570| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.53 r_work: 0.3896 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2589 Z= 0.118 Angle : 0.348 7.408 3492 Z= 0.181 Chirality : 0.034 0.113 432 Planarity : 0.001 0.013 459 Dihedral : 3.002 8.407 342 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 : 14.48 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.84 (0.44), residues: 330 helix: 4.27 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.60 (0.87), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.004 0.001 PHE B 970 ARG 0.001 0.000 ARG D1186 Details of bonding type rmsd hydrogen bonds : bond 0.03048 ( 238) hydrogen bonds : angle 2.61614 ( 696) covalent geometry : bond 0.00241 ( 2589) covalent geometry : angle 0.34813 ( 3492) ********************** 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: 2 poor density : 39 time to evaluate : 0.298 Fit side-chains REVERT: B 970 PHE cc_start: 0.8802 (m-10) cc_final: 0.8533 (m-10) REVERT: C 954 HIS cc_start: 0.8518 (t-170) cc_final: 0.8277 (t-170) REVERT: C 973 ILE cc_start: 0.9105 (mt) cc_final: 0.8867 (mt) outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.4496 time to fit residues: 19.3265 Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 21 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.4340 r_free = 0.4340 target = 0.141912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.125967 restraints weight = 4011.215| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.62 r_work: 0.3881 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2589 Z= 0.126 Angle : 0.361 9.060 3492 Z= 0.184 Chirality : 0.034 0.113 432 Planarity : 0.001 0.008 459 Dihedral : 3.011 8.461 342 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 14.48 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.80 (0.44), residues: 330 helix: 4.24 (0.28), residues: 270 sheet: None (None), residues: 0 loop : 1.60 (0.87), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.005 0.001 PHE B 970 ARG 0.001 0.000 ARG D1186 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 238) hydrogen bonds : angle 2.65972 ( 696) covalent geometry : bond 0.00259 ( 2589) covalent geometry : angle 0.36140 ( 3492) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1696.97 seconds wall clock time: 29 minutes 51.18 seconds (1791.18 seconds total)