Starting phenix.real_space_refine on Mon Feb 10 21:02:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fa2_28948/02_2025/8fa2_28948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fa2_28948/02_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_28948/02_2025/8fa2_28948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fa2_28948/02_2025/8fa2_28948.map" model { file = "/net/cci-nas-00/data/ceres_data/8fa2_28948/02_2025/8fa2_28948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fa2_28948/02_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-5592/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: 1.92, per 1000 atoms: 0.75 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: 0.70 Conformation dependent library (CDL) restraints added in 333.0 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: 0.19 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: 0.67 Time building geometry restraints manager: 0.80 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.880 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- 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= 0.398 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 *********************** 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 : 0.265 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: 0.3873 time to fit residues: 18.8147 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 : 0.306 ------------------------------------------------------------------------------- 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 = 30)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.126243 restraints weight = 4057.710| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.44 r_work: 0.3867 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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= 0.211 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 *********************** 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 : 0.307 Fit side-chains REVERT: A 965 GLN cc_start: 0.8100 (tt0) cc_final: 0.7798 (tt0) REVERT: B 970 PHE cc_start: 0.8847 (m-10) cc_final: 0.8618 (m-10) REVERT: C 954 HIS cc_start: 0.8497 (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: 0.4612 time to fit residues: 20.3518 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 : 0.275 ------------------------------------------------------------------------------- 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: 0.8980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 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 = 0.4277 r_free = 0.4277 target = 0.138670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.123412 restraints weight = 4115.584| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.48 r_work: 0.3845 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1632 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= 0.212 Angle : 0.388 7.030 3492 Z= 0.200 Chirality : 0.035 0.111 432 Planarity : 0.002 0.009 459 Dihedral : 3.304 9.233 342 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 4.24 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: 4.68 (0.44), residues: 330 helix: 3.51 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 0.93 (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 D1186 *********************** 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 : 0.308 Fit side-chains REVERT: A 965 GLN cc_start: 0.8088 (tt0) cc_final: 0.7877 (tt0) REVERT: B 970 PHE cc_start: 0.8826 (m-10) cc_final: 0.8589 (m-10) REVERT: C 954 HIS cc_start: 0.8486 (t-170) cc_final: 0.8236 (t-170) REVERT: C 973 ILE cc_start: 0.9131 (mt) cc_final: 0.8897 (mt) outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.4564 time to fit residues: 20.1027 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 : 0.301 ------------------------------------------------------------------------------- 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: 0.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.142080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.125863 restraints weight = 3950.052| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.56 r_work: 0.3861 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1880 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= 0.218 Angle : 0.383 7.933 3492 Z= 0.198 Chirality : 0.035 0.111 432 Planarity : 0.002 0.011 459 Dihedral : 3.251 9.210 342 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.82 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: 5.00 (0.45), residues: 330 helix: 3.71 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.20 (0.84), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.009 0.001 PHE A 970 ARG 0.001 0.000 ARG D1186 *********************** 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 : 0.237 Fit side-chains REVERT: A 965 GLN cc_start: 0.8166 (tt0) cc_final: 0.7945 (tt0) REVERT: B 970 PHE cc_start: 0.8850 (m-10) cc_final: 0.8592 (m-10) REVERT: C 954 HIS cc_start: 0.8522 (t-170) cc_final: 0.8294 (t-170) REVERT: C 973 ILE cc_start: 0.9140 (mt) cc_final: 0.8895 (mt) outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 0.4886 time to fit residues: 22.4087 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 : 0.285 ------------------------------------------------------------------------------- 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: 0.4980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.143637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.127451 restraints weight = 3998.882| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.60 r_work: 0.3873 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2589 Z= 0.160 Angle : 0.348 6.467 3492 Z= 0.180 Chirality : 0.034 0.111 432 Planarity : 0.001 0.009 459 Dihedral : 3.139 8.672 342 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 : 1.35 % Allowed : 12.79 % 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: 5.46 (0.45), residues: 330 helix: 4.02 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.37 (0.87), 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 *********************** 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 44 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.283 Fit side-chains REVERT: A 965 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: B 966 LEU cc_start: 0.8942 (mt) cc_final: 0.8695 (mm) REVERT: B 970 PHE cc_start: 0.8835 (m-10) cc_final: 0.8589 (m-10) REVERT: C 954 HIS cc_start: 0.8513 (t-170) cc_final: 0.8270 (t-170) REVERT: C 973 ILE cc_start: 0.9116 (mt) cc_final: 0.8866 (mt) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.4535 time to fit residues: 19.9601 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 : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 965 GLN 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: 0.1980 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 0.0170 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.142671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.126308 restraints weight = 4076.485| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.66 r_work: 0.3875 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2073 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= 0.155 Angle : 0.361 7.710 3492 Z= 0.182 Chirality : 0.034 0.112 432 Planarity : 0.001 0.011 459 Dihedral : 3.076 8.582 342 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.24 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: 5.68 (0.45), residues: 330 helix: 4.15 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.57 (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 *********************** 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 43 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.282 Fit side-chains REVERT: B 966 LEU cc_start: 0.8899 (mt) cc_final: 0.8661 (mm) REVERT: B 970 PHE cc_start: 0.8815 (m-10) cc_final: 0.8571 (m-10) REVERT: C 954 HIS cc_start: 0.8522 (t-170) cc_final: 0.8286 (t-170) REVERT: C 973 ILE cc_start: 0.9132 (mt) cc_final: 0.8890 (mt) outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.5010 time to fit residues: 21.8621 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 : 0.304 ------------------------------------------------------------------------------- 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: 0.5980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.0270 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 23 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.146124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.130316 restraints weight = 4017.770| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.62 r_work: 0.3898 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2180 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= 0.142 Angle : 0.350 8.277 3492 Z= 0.177 Chirality : 0.033 0.112 432 Planarity : 0.001 0.008 459 Dihedral : 3.007 8.550 342 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.40 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: 5.66 (0.45), residues: 330 helix: 4.20 (0.29), residues: 267 sheet: None (None), residues: 0 loop : 1.38 (0.85), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.011 0.001 PHE A 970 ARG 0.000 0.000 ARG D1186 *********************** 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 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.253 Fit side-chains REVERT: A 969 LYS cc_start: 0.8863 (tttp) cc_final: 0.8586 (ttmt) REVERT: B 970 PHE cc_start: 0.8814 (m-10) cc_final: 0.8569 (m-10) REVERT: C 954 HIS cc_start: 0.8515 (t-170) cc_final: 0.8250 (t-170) REVERT: C 973 ILE cc_start: 0.9111 (mt) cc_final: 0.8867 (mt) outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.4995 time to fit residues: 21.7608 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 : 0.267 ------------------------------------------------------------------------------- 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: 0.9980 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN B 920 GLN C 965 GLN F1174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.143711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.128396 restraints weight = 3925.273| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.41 r_work: 0.3889 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2589 Z= 0.257 Angle : 0.384 7.273 3492 Z= 0.203 Chirality : 0.036 0.114 432 Planarity : 0.002 0.014 459 Dihedral : 3.192 9.069 342 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 13.80 % 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: 5.33 (0.45), residues: 330 helix: 3.89 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.54 (0.89), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.012 0.001 PHE A 970 ARG 0.001 0.000 ARG A 983 *********************** 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 45 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.296 Fit side-chains REVERT: A 969 LYS cc_start: 0.8865 (tttp) cc_final: 0.8583 (ttmt) REVERT: B 970 PHE cc_start: 0.8790 (m-10) cc_final: 0.8523 (m-10) REVERT: C 954 HIS cc_start: 0.8547 (t-170) cc_final: 0.8321 (t-170) REVERT: C 973 ILE cc_start: 0.9088 (mt) cc_final: 0.8847 (mt) outliers start: 4 outliers final: 2 residues processed: 43 average time/residue: 0.5571 time to fit residues: 25.3928 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 : 0.301 ------------------------------------------------------------------------------- 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: 0.5980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.0060 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.145396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.129776 restraints weight = 3970.608| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.58 r_work: 0.3891 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2265 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= 0.160 Angle : 0.357 6.942 3492 Z= 0.183 Chirality : 0.034 0.114 432 Planarity : 0.001 0.008 459 Dihedral : 3.081 8.507 342 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 14.14 % 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: 5.65 (0.44), residues: 330 helix: 4.13 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.59 (0.88), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.011 0.001 PHE A 970 ARG 0.001 0.000 ARG D1186 *********************** 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 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.293 Fit side-chains REVERT: B 970 PHE cc_start: 0.8808 (m-10) cc_final: 0.8545 (m-10) REVERT: C 954 HIS cc_start: 0.8513 (t-170) cc_final: 0.8273 (t-170) REVERT: C 973 ILE cc_start: 0.9107 (mt) cc_final: 0.8861 (mt) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.4574 time to fit residues: 19.6184 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 : 0.296 ------------------------------------------------------------------------------- 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: 1.9990 chunk 3 optimal weight: 0.4980 chunk 14 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.145700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.130234 restraints weight = 3886.847| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.55 r_work: 0.3902 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2325 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= 0.144 Angle : 0.368 8.989 3492 Z= 0.183 Chirality : 0.034 0.113 432 Planarity : 0.001 0.013 459 Dihedral : 3.009 8.349 342 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 : 14.81 % Favored : 84.51 % 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: 5.88 (0.44), residues: 330 helix: 4.29 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.63 (0.87), 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 ********************** 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 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.224 Fit side-chains REVERT: B 970 PHE cc_start: 0.8781 (m-10) cc_final: 0.8529 (m-10) REVERT: C 954 HIS cc_start: 0.8507 (t-170) cc_final: 0.8269 (t-170) REVERT: C 973 ILE cc_start: 0.9092 (mt) cc_final: 0.8857 (mt) outliers start: 2 outliers final: 2 residues processed: 39 average time/residue: 0.4621 time to fit residues: 19.2489 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 : 0.290 ------------------------------------------------------------------------------- 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: 0.0670 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.0040 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 overall best weight: 0.3930 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.145965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.130313 restraints weight = 4001.519| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.59 r_work: 0.3896 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2379 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= 0.140 Angle : 0.357 7.505 3492 Z= 0.180 Chirality : 0.034 0.113 432 Planarity : 0.001 0.008 459 Dihedral : 2.975 8.278 342 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 15.15 % Favored : 84.18 % 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 (0.44), residues: 330 helix: 4.29 (0.29), residues: 267 sheet: None (None), residues: 0 loop : 1.43 (0.82), residues: 63 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1621.72 seconds wall clock time: 29 minutes 31.77 seconds (1771.77 seconds total)