Starting phenix.real_space_refine on Mon Feb 10 19:26:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v49_31704/02_2025/7v49_31704.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v49_31704/02_2025/7v49_31704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v49_31704/02_2025/7v49_31704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v49_31704/02_2025/7v49_31704.map" model { file = "/net/cci-nas-00/data/ceres_data/7v49_31704/02_2025/7v49_31704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v49_31704/02_2025/7v49_31704.cif" } resolution = 3.4 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= 0.000 sd= 0.005 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 765 2.51 5 N 210 2.21 5 O 246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 1221 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 407 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Restraints were copied for chains: C, B Time building chain proxies: 0.99, per 1000 atoms: 0.81 Number of scatterers: 1221 At special positions: 0 Unit cell: (78.44, 65.72, 28.62, 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 246 8.00 N 210 7.00 C 765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 688.2 milliseconds 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 300 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 1 sheets defined 0.0% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 88 through 89 removed outlier: 6.281A pdb=" N ILE C 88 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 No hydrogen bonds 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: 0.01 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 213 1.29 - 1.35: 192 1.35 - 1.42: 54 1.42 - 1.48: 207 1.48 - 1.54: 561 Bond restraints: 1227 Sorted by residual: bond pdb=" CB VAL A 82 " pdb=" CG1 VAL A 82 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.11e+00 bond pdb=" CB VAL B 82 " pdb=" CG1 VAL B 82 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.11e+00 bond pdb=" CB VAL C 82 " pdb=" CG1 VAL C 82 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 bond pdb=" CB VAL C 37 " pdb=" CG1 VAL C 37 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.96e-01 bond pdb=" CB VAL B 37 " pdb=" CG1 VAL B 37 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.70e-01 ... (remaining 1222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 1467 1.54 - 3.08: 177 3.08 - 4.61: 18 4.61 - 6.15: 0 6.15 - 7.69: 3 Bond angle restraints: 1665 Sorted by residual: angle pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " pdb=" CG LEU C 38 " ideal model delta sigma weight residual 116.30 123.99 -7.69 3.50e+00 8.16e-02 4.83e+00 angle pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " pdb=" CG LEU A 38 " ideal model delta sigma weight residual 116.30 123.98 -7.68 3.50e+00 8.16e-02 4.81e+00 angle pdb=" CA LEU B 38 " pdb=" CB LEU B 38 " pdb=" CG LEU B 38 " ideal model delta sigma weight residual 116.30 123.97 -7.67 3.50e+00 8.16e-02 4.80e+00 angle pdb=" N ILE B 88 " pdb=" CA ILE B 88 " pdb=" C ILE B 88 " ideal model delta sigma weight residual 106.61 110.32 -3.71 1.78e+00 3.16e-01 4.34e+00 angle pdb=" N ILE C 88 " pdb=" CA ILE C 88 " pdb=" C ILE C 88 " ideal model delta sigma weight residual 106.61 110.28 -3.67 1.78e+00 3.16e-01 4.25e+00 ... (remaining 1660 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 9.48: 557 9.48 - 18.94: 91 18.94 - 28.41: 36 28.41 - 37.88: 3 37.88 - 47.34: 15 Dihedral angle restraints: 702 sinusoidal: 222 harmonic: 480 Sorted by residual: dihedral pdb=" CA THR B 81 " pdb=" C THR B 81 " pdb=" N VAL B 82 " pdb=" CA VAL B 82 " ideal model delta harmonic sigma weight residual 180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA THR A 81 " pdb=" C THR A 81 " pdb=" N VAL A 82 " pdb=" CA VAL A 82 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR C 81 " pdb=" C THR C 81 " pdb=" N VAL C 82 " pdb=" CA VAL C 82 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 68 0.028 - 0.055: 77 0.055 - 0.082: 43 0.082 - 0.109: 19 0.109 - 0.136: 15 Chirality restraints: 222 Sorted by residual: chirality pdb=" CA VAL C 40 " pdb=" N VAL C 40 " pdb=" C VAL C 40 " pdb=" CB VAL C 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL B 40 " pdb=" N VAL B 40 " pdb=" C VAL B 40 " pdb=" CB VAL B 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL A 40 " pdb=" N VAL A 40 " pdb=" C VAL A 40 " pdb=" CB VAL A 40 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 219 not shown) Planarity restraints: 207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 70 " -0.005 2.00e-02 2.50e+03 9.63e-03 9.27e-01 pdb=" C VAL B 70 " 0.017 2.00e-02 2.50e+03 pdb=" O VAL B 70 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL B 71 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 70 " -0.005 2.00e-02 2.50e+03 9.44e-03 8.90e-01 pdb=" C VAL A 70 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL A 70 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL A 71 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 70 " -0.005 2.00e-02 2.50e+03 9.16e-03 8.39e-01 pdb=" C VAL C 70 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL C 70 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL C 71 " -0.005 2.00e-02 2.50e+03 ... (remaining 204 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 356 2.80 - 3.33: 1111 3.33 - 3.85: 1702 3.85 - 4.38: 1838 4.38 - 4.90: 3934 Nonbonded interactions: 8941 Sorted by model distance: nonbonded pdb=" O SER A 42 " pdb=" OG SER A 42 " model vdw 2.279 3.040 nonbonded pdb=" O SER B 42 " pdb=" OG SER B 42 " model vdw 2.279 3.040 nonbonded pdb=" O SER C 42 " pdb=" OG SER C 42 " model vdw 2.280 3.040 nonbonded pdb=" O LYS B 80 " pdb=" OG1 THR B 81 " model vdw 2.498 3.040 nonbonded pdb=" O LYS C 80 " pdb=" OG1 THR C 81 " model vdw 2.499 3.040 ... (remaining 8936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.960 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 : 0.007 0.048 1227 Z= 0.293 Angle : 1.014 7.691 1665 Z= 0.570 Chirality : 0.057 0.136 222 Planarity : 0.004 0.010 207 Dihedral : 13.695 47.342 402 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 39.66 % Favored : 60.34 % Rotamer: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % 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: -7.67 (0.34), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.84 (0.26), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 50 PHE 0.007 0.002 PHE A 94 TYR 0.014 0.004 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.129 Fit side-chains REVERT: C 43 LYS cc_start: 0.7224 (mttt) cc_final: 0.5716 (tttt) REVERT: C 94 PHE cc_start: 0.7455 (t80) cc_final: 0.6889 (t80) REVERT: A 43 LYS cc_start: 0.7146 (mttt) cc_final: 0.5842 (tttt) REVERT: A 57 GLU cc_start: 0.7923 (tp30) cc_final: 0.7141 (tp30) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1101 time to fit residues: 3.1128 Evaluate side-chains 13 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.094166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.079625 restraints weight = 2132.113| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.30 r_work: 0.3616 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1227 Z= 0.146 Angle : 0.816 6.839 1665 Z= 0.444 Chirality : 0.059 0.138 222 Planarity : 0.003 0.013 207 Dihedral : 6.755 18.327 180 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.56 % Favored : 76.44 % Rotamer: Outliers : 2.44 % Allowed : 16.26 % Favored : 81.30 % 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: -6.91 (0.36), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.26 (0.28), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.016 0.004 PHE B 94 TYR 0.008 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.131 Fit side-chains REVERT: C 43 LYS cc_start: 0.6954 (mttt) cc_final: 0.5384 (tttt) REVERT: C 94 PHE cc_start: 0.7517 (t80) cc_final: 0.6904 (t80) REVERT: A 43 LYS cc_start: 0.6892 (mttt) cc_final: 0.5658 (tttt) REVERT: A 77 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.8008 (t) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.0941 time to fit residues: 2.8185 Evaluate side-chains 23 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.0770 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.6944 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.094826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.080503 restraints weight = 2046.645| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.20 r_work: 0.3641 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1227 Z= 0.139 Angle : 0.768 6.362 1665 Z= 0.418 Chirality : 0.057 0.123 222 Planarity : 0.003 0.014 207 Dihedral : 6.449 17.724 180 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.69 % Favored : 79.31 % Rotamer: Outliers : 4.88 % Allowed : 17.07 % Favored : 78.05 % 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: -6.59 (0.38), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.02 (0.29), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 50 PHE 0.013 0.003 PHE A 94 TYR 0.010 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.135 Fit side-chains REVERT: C 43 LYS cc_start: 0.6914 (mttt) cc_final: 0.5318 (tttt) REVERT: C 94 PHE cc_start: 0.7578 (t80) cc_final: 0.7015 (t80) REVERT: A 43 LYS cc_start: 0.6993 (mttt) cc_final: 0.5739 (tttt) REVERT: B 43 LYS cc_start: 0.7082 (mttt) cc_final: 0.5766 (tttt) outliers start: 6 outliers final: 5 residues processed: 30 average time/residue: 0.1059 time to fit residues: 3.7306 Evaluate side-chains 26 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.096943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.082515 restraints weight = 2056.816| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.20 r_work: 0.3682 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1227 Z= 0.124 Angle : 0.721 6.789 1665 Z= 0.395 Chirality : 0.056 0.128 222 Planarity : 0.003 0.016 207 Dihedral : 5.989 16.503 180 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.97 % Favored : 81.03 % Rotamer: Outliers : 6.50 % Allowed : 17.07 % Favored : 76.42 % 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: -6.44 (0.38), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.91 (0.29), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 50 PHE 0.012 0.003 PHE A 94 TYR 0.009 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.128 Fit side-chains REVERT: C 43 LYS cc_start: 0.6975 (mttt) cc_final: 0.5522 (tttt) REVERT: C 94 PHE cc_start: 0.7637 (t80) cc_final: 0.7101 (t80) REVERT: A 43 LYS cc_start: 0.6970 (mttt) cc_final: 0.5654 (tttt) REVERT: A 62 GLN cc_start: 0.7420 (pt0) cc_final: 0.7210 (tt0) REVERT: A 77 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8070 (t) REVERT: B 43 LYS cc_start: 0.7017 (mttt) cc_final: 0.5727 (tttt) outliers start: 8 outliers final: 6 residues processed: 26 average time/residue: 0.1127 time to fit residues: 3.3982 Evaluate side-chains 24 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.098215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.081922 restraints weight = 2122.599| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.39 r_work: 0.3645 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1227 Z= 0.138 Angle : 0.722 6.278 1665 Z= 0.398 Chirality : 0.056 0.127 222 Planarity : 0.003 0.014 207 Dihedral : 6.108 16.742 180 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.54 % Favored : 80.46 % Rotamer: Outliers : 8.13 % Allowed : 17.07 % Favored : 74.80 % 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: -6.37 (0.38), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.85 (0.29), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.015 0.003 PHE A 94 TYR 0.010 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 14 time to evaluate : 0.133 Fit side-chains REVERT: C 43 LYS cc_start: 0.7041 (mttt) cc_final: 0.5596 (tttt) REVERT: C 94 PHE cc_start: 0.7698 (t80) cc_final: 0.7052 (t80) REVERT: A 43 LYS cc_start: 0.6893 (mttt) cc_final: 0.5577 (tttt) REVERT: A 77 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7991 (t) REVERT: B 43 LYS cc_start: 0.7002 (mttt) cc_final: 0.5683 (tttt) outliers start: 10 outliers final: 7 residues processed: 23 average time/residue: 0.1181 time to fit residues: 3.1562 Evaluate side-chains 21 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 13 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.091996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.077399 restraints weight = 2123.645| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.13 r_work: 0.3575 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 1227 Z= 0.255 Angle : 0.875 6.092 1665 Z= 0.487 Chirality : 0.058 0.138 222 Planarity : 0.004 0.011 207 Dihedral : 7.498 19.757 180 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 31.03 % Favored : 68.97 % Rotamer: Outliers : 4.07 % Allowed : 24.39 % Favored : 71.54 % 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: -6.52 (0.40), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.97 (0.30), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS A 50 PHE 0.015 0.003 PHE A 94 TYR 0.019 0.005 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.132 Fit side-chains REVERT: C 37 VAL cc_start: 0.8205 (p) cc_final: 0.7901 (t) REVERT: C 43 LYS cc_start: 0.7359 (mttt) cc_final: 0.5771 (tttt) REVERT: C 57 GLU cc_start: 0.8139 (tp30) cc_final: 0.7637 (tp30) REVERT: C 94 PHE cc_start: 0.7916 (t80) cc_final: 0.7384 (t80) REVERT: A 43 LYS cc_start: 0.6998 (mttt) cc_final: 0.5747 (tttt) REVERT: B 43 LYS cc_start: 0.7175 (mttt) cc_final: 0.5805 (tttt) outliers start: 5 outliers final: 5 residues processed: 23 average time/residue: 0.1235 time to fit residues: 3.3087 Evaluate side-chains 23 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 0.0000 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.100431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.083961 restraints weight = 2135.127| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.60 r_work: 0.3701 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1227 Z= 0.105 Angle : 0.680 5.336 1665 Z= 0.372 Chirality : 0.057 0.153 222 Planarity : 0.002 0.015 207 Dihedral : 5.718 18.089 180 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % Rotamer: Outliers : 5.69 % Allowed : 21.95 % Favored : 72.36 % 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: -6.22 (0.39), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.74 (0.30), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.017 0.003 PHE A 94 TYR 0.006 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 15 time to evaluate : 0.133 Fit side-chains REVERT: C 43 LYS cc_start: 0.6789 (mttt) cc_final: 0.5288 (tttt) REVERT: C 94 PHE cc_start: 0.7516 (t80) cc_final: 0.6974 (t80) REVERT: A 43 LYS cc_start: 0.6813 (mttt) cc_final: 0.5614 (tttt) REVERT: A 77 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7837 (t) REVERT: B 43 LYS cc_start: 0.7010 (mttt) cc_final: 0.6570 (mptt) outliers start: 7 outliers final: 6 residues processed: 22 average time/residue: 0.1192 time to fit residues: 3.0583 Evaluate side-chains 20 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.0170 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.104617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.087224 restraints weight = 2043.305| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.61 r_work: 0.3751 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1227 Z= 0.098 Angle : 0.639 5.418 1665 Z= 0.352 Chirality : 0.056 0.142 222 Planarity : 0.002 0.013 207 Dihedral : 5.157 14.693 180 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.09 % Favored : 83.91 % Rotamer: Outliers : 6.50 % Allowed : 21.95 % Favored : 71.54 % 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: -6.07 (0.40), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.62 (0.30), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.013 0.002 PHE A 94 TYR 0.005 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 14 time to evaluate : 0.129 Fit side-chains REVERT: C 43 LYS cc_start: 0.6612 (mttt) cc_final: 0.5216 (tttt) REVERT: C 94 PHE cc_start: 0.7414 (t80) cc_final: 0.6862 (t80) REVERT: A 43 LYS cc_start: 0.6867 (mttt) cc_final: 0.5574 (tttt) REVERT: A 77 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7772 (t) REVERT: B 43 LYS cc_start: 0.7010 (mttt) cc_final: 0.6677 (mptt) outliers start: 8 outliers final: 7 residues processed: 22 average time/residue: 0.1085 time to fit residues: 2.7897 Evaluate side-chains 21 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 13 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.099159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.083075 restraints weight = 2005.636| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.54 r_work: 0.3690 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1227 Z= 0.121 Angle : 0.661 5.598 1665 Z= 0.368 Chirality : 0.055 0.166 222 Planarity : 0.002 0.011 207 Dihedral : 5.618 15.364 180 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.69 % Favored : 79.31 % Rotamer: Outliers : 6.50 % Allowed : 21.95 % Favored : 71.54 % 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: -5.99 (0.41), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.32), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.011 0.002 PHE A 94 TYR 0.009 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 12 time to evaluate : 0.135 Fit side-chains REVERT: C 43 LYS cc_start: 0.6811 (mttt) cc_final: 0.5267 (tttt) REVERT: C 94 PHE cc_start: 0.7564 (t80) cc_final: 0.6982 (t80) REVERT: A 43 LYS cc_start: 0.6832 (mttt) cc_final: 0.5578 (tttt) REVERT: A 77 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7914 (t) REVERT: B 43 LYS cc_start: 0.7074 (mttt) cc_final: 0.6737 (mptt) outliers start: 8 outliers final: 7 residues processed: 20 average time/residue: 0.1335 time to fit residues: 3.1314 Evaluate side-chains 20 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 12 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.095080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.079510 restraints weight = 2063.014| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.40 r_work: 0.3628 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1227 Z= 0.175 Angle : 0.746 5.759 1665 Z= 0.417 Chirality : 0.056 0.164 222 Planarity : 0.003 0.010 207 Dihedral : 6.449 17.119 180 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.01 % Favored : 72.99 % Rotamer: Outliers : 5.69 % Allowed : 23.58 % Favored : 70.73 % 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: -5.91 (0.44), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.50 (0.34), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.011 0.002 PHE A 94 TYR 0.013 0.003 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 15 time to evaluate : 0.134 Fit side-chains REVERT: C 43 LYS cc_start: 0.6958 (mttt) cc_final: 0.5423 (tttt) REVERT: C 61 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7333 (mp0) REVERT: C 94 PHE cc_start: 0.7853 (t80) cc_final: 0.7263 (t80) REVERT: A 43 LYS cc_start: 0.6828 (mttt) cc_final: 0.5551 (tttt) REVERT: A 57 GLU cc_start: 0.7909 (tp30) cc_final: 0.7290 (tp30) REVERT: A 77 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7918 (t) REVERT: B 43 LYS cc_start: 0.7112 (mttt) cc_final: 0.6686 (mptt) outliers start: 7 outliers final: 6 residues processed: 22 average time/residue: 0.1322 time to fit residues: 3.3776 Evaluate side-chains 21 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 14 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 0.3980 chunk 11 optimal weight: 20.0000 chunk 15 optimal weight: 0.1980 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.100696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.084168 restraints weight = 2125.754| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.45 r_work: 0.3704 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1227 Z= 0.116 Angle : 0.663 5.666 1665 Z= 0.368 Chirality : 0.055 0.158 222 Planarity : 0.002 0.008 207 Dihedral : 5.693 15.838 180 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % Rotamer: Outliers : 5.69 % Allowed : 25.20 % Favored : 69.11 % 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 (0.45), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.34), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.014 0.003 PHE A 94 TYR 0.008 0.002 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1250.60 seconds wall clock time: 23 minutes 25.93 seconds (1405.93 seconds total)