Starting phenix.real_space_refine on Wed Mar 5 14:17:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v49_31704/03_2025/7v49_31704.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v49_31704/03_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_31704/03_2025/7v49_31704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v49_31704/03_2025/7v49_31704.map" model { file = "/net/cci-nas-00/data/ceres_data/7v49_31704/03_2025/7v49_31704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v49_31704/03_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-5624/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: 1.12, per 1000 atoms: 0.92 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: 0.32 Conformation dependent library (CDL) restraints added in 588.5 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: 0.10 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: 0.38 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 8.150 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.790 ------------------------------------------------------------------------------- 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 : 0.120 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: 0.1222 time to fit residues: 3.4366 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 : 0.134 ------------------------------------------------------------------------------- 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: 0.7980 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.094970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.080202 restraints weight = 2116.413| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.34 r_work: 0.3625 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1303 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= 0.137 Angle : 0.799 6.688 1665 Z= 0.435 Chirality : 0.058 0.135 222 Planarity : 0.003 0.012 207 Dihedral : 6.614 18.225 180 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.41 % Favored : 77.59 % 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: -6.87 (0.37), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.23 (0.28), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.015 0.003 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 23 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.118 Fit side-chains REVERT: C 43 LYS cc_start: 0.6907 (mttt) cc_final: 0.5341 (tttt) REVERT: C 94 PHE cc_start: 0.7535 (t80) cc_final: 0.6952 (t80) REVERT: A 43 LYS cc_start: 0.6832 (mttt) cc_final: 0.5618 (tttt) REVERT: A 77 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7927 (t) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.0904 time to fit residues: 2.4910 Evaluate side-chains 22 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.1442 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.098829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.083230 restraints weight = 2118.404| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.29 r_work: 0.3684 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1227 Z= 0.114 Angle : 0.707 6.022 1665 Z= 0.384 Chirality : 0.056 0.126 222 Planarity : 0.003 0.016 207 Dihedral : 5.912 16.878 180 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.82 % Favored : 82.18 % Rotamer: Outliers : 6.50 % Allowed : 13.01 % Favored : 80.49 % 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: -6.53 (0.38), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.97 (0.29), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.011 0.003 PHE A 94 TYR 0.009 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: 8 poor density : 22 time to evaluate : 0.130 Fit side-chains REVERT: C 37 VAL cc_start: 0.8076 (p) cc_final: 0.7791 (t) REVERT: C 43 LYS cc_start: 0.6878 (mttt) cc_final: 0.5430 (tttt) REVERT: C 94 PHE cc_start: 0.7537 (t80) cc_final: 0.6965 (t80) REVERT: A 43 LYS cc_start: 0.6946 (mttt) cc_final: 0.5744 (tttt) REVERT: A 77 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.8017 (t) REVERT: B 43 LYS cc_start: 0.7072 (mttt) cc_final: 0.6692 (mptt) outliers start: 8 outliers final: 5 residues processed: 29 average time/residue: 0.0996 time to fit residues: 3.3828 Evaluate side-chains 29 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 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: 0.0270 chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.100418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.084404 restraints weight = 2123.857| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.38 r_work: 0.3707 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1227 Z= 0.110 Angle : 0.675 6.694 1665 Z= 0.369 Chirality : 0.055 0.128 222 Planarity : 0.003 0.016 207 Dihedral : 5.604 15.604 180 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.39 % Favored : 81.61 % Rotamer: Outliers : 5.69 % Allowed : 17.07 % Favored : 77.24 % 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: -6.42 (0.37), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.89 (0.28), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.011 0.002 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 25 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.128 Fit side-chains REVERT: C 43 LYS cc_start: 0.6654 (mttt) cc_final: 0.5274 (tttt) REVERT: C 94 PHE cc_start: 0.7473 (t80) cc_final: 0.6904 (t80) REVERT: A 43 LYS cc_start: 0.6901 (mttt) cc_final: 0.5632 (tttt) REVERT: B 43 LYS cc_start: 0.7005 (mttt) cc_final: 0.6628 (mptt) outliers start: 7 outliers final: 7 residues processed: 24 average time/residue: 0.1199 time to fit residues: 3.3276 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 : 0.157 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 3 optimal weight: 0.0000 chunk 17 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 overall best weight: 1.6990 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.098536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.082133 restraints weight = 2127.094| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.38 r_work: 0.3657 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 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 0.020 1227 Z= 0.137 Angle : 0.682 5.026 1665 Z= 0.375 Chirality : 0.055 0.130 222 Planarity : 0.003 0.014 207 Dihedral : 6.012 16.281 180 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.69 % Favored : 79.31 % Rotamer: Outliers : 5.69 % Allowed : 18.70 % Favored : 75.61 % 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: -6.36 (0.37), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.84 (0.29), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.010 0.002 PHE A 94 TYR 0.011 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 22 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 15 time to evaluate : 0.128 Fit side-chains REVERT: C 43 LYS cc_start: 0.6954 (mttt) cc_final: 0.5432 (tttt) REVERT: C 94 PHE cc_start: 0.7652 (t80) cc_final: 0.6976 (t80) REVERT: A 43 LYS cc_start: 0.7002 (mttt) cc_final: 0.5588 (tttt) REVERT: A 77 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7946 (t) REVERT: B 43 LYS cc_start: 0.7009 (mttt) cc_final: 0.6624 (mptt) outliers start: 7 outliers final: 6 residues processed: 22 average time/residue: 0.1218 time to fit residues: 3.1150 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 : 0.131 ------------------------------------------------------------------------------- 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=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: 3.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.094955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.079882 restraints weight = 2106.052| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 3.21 r_work: 0.3624 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1227 Z= 0.188 Angle : 0.762 5.470 1665 Z= 0.423 Chirality : 0.055 0.133 222 Planarity : 0.003 0.012 207 Dihedral : 6.683 17.177 180 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.01 % Favored : 72.99 % 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: -6.38 (0.39), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.86 (0.30), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.012 0.003 PHE A 94 TYR 0.015 0.004 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 31 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.127 Fit side-chains REVERT: C 43 LYS cc_start: 0.7273 (mttt) cc_final: 0.5740 (tttt) REVERT: C 57 GLU cc_start: 0.8164 (tp30) cc_final: 0.7630 (tp30) REVERT: C 94 PHE cc_start: 0.7865 (t80) cc_final: 0.7358 (t80) REVERT: A 43 LYS cc_start: 0.7075 (mttt) cc_final: 0.5743 (tttt) REVERT: A 77 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8078 (t) REVERT: B 43 LYS cc_start: 0.7153 (mttt) cc_final: 0.5849 (tttt) outliers start: 8 outliers final: 6 residues processed: 30 average time/residue: 0.0959 time to fit residues: 3.3635 Evaluate side-chains 27 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 0.0980 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.093616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.078789 restraints weight = 2133.364| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.24 r_work: 0.3604 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 1227 Z= 0.218 Angle : 0.823 5.907 1665 Z= 0.458 Chirality : 0.058 0.140 222 Planarity : 0.003 0.010 207 Dihedral : 7.170 18.229 180 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.89 % Favored : 70.11 % Rotamer: Outliers : 5.69 % Allowed : 21.14 % Favored : 73.17 % 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: -6.38 (0.40), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.86 (0.31), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.016 0.003 PHE A 94 TYR 0.016 0.004 TYR B 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 28 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.131 Fit side-chains REVERT: C 43 LYS cc_start: 0.7287 (mttt) cc_final: 0.5711 (tttt) REVERT: C 57 GLU cc_start: 0.8095 (tp30) cc_final: 0.7546 (tp30) REVERT: C 94 PHE cc_start: 0.7925 (t80) cc_final: 0.7382 (t80) REVERT: A 43 LYS cc_start: 0.7058 (mttt) cc_final: 0.5725 (tttt) REVERT: A 77 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8105 (t) REVERT: B 43 LYS cc_start: 0.7197 (mttt) cc_final: 0.5863 (tttt) outliers start: 7 outliers final: 6 residues processed: 27 average time/residue: 0.1095 time to fit residues: 3.4476 Evaluate side-chains 28 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 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 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: 4.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.095802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.080711 restraints weight = 2068.510| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.30 r_work: 0.3641 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1227 Z= 0.159 Angle : 0.744 5.618 1665 Z= 0.412 Chirality : 0.057 0.144 222 Planarity : 0.003 0.009 207 Dihedral : 6.523 17.268 180 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.44 % Favored : 73.56 % 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: -6.26 (0.40), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.76 (0.31), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.017 0.003 PHE A 94 TYR 0.010 0.003 TYR B 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 25 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.122 Fit side-chains REVERT: C 43 LYS cc_start: 0.7122 (mttt) cc_final: 0.5552 (tttt) REVERT: C 94 PHE cc_start: 0.7800 (t80) cc_final: 0.7171 (t80) REVERT: A 43 LYS cc_start: 0.6935 (mttt) cc_final: 0.5644 (tttt) REVERT: A 77 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8034 (t) REVERT: B 43 LYS cc_start: 0.7171 (mttt) cc_final: 0.6746 (mptt) outliers start: 7 outliers final: 6 residues processed: 24 average time/residue: 0.1033 time to fit residues: 2.9164 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 : 0.134 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.094922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.080358 restraints weight = 2108.589| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.28 r_work: 0.3652 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2445 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= 0.164 Angle : 0.758 5.673 1665 Z= 0.422 Chirality : 0.057 0.165 222 Planarity : 0.003 0.010 207 Dihedral : 6.552 16.674 180 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.59 % Favored : 72.41 % 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: -6.17 (0.41), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.70 (0.32), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.016 0.003 PHE A 94 TYR 0.011 0.003 TYR B 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 25 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.121 Fit side-chains REVERT: C 43 LYS cc_start: 0.7173 (mttt) cc_final: 0.5560 (tttt) REVERT: C 94 PHE cc_start: 0.7819 (t80) cc_final: 0.7224 (t80) REVERT: A 43 LYS cc_start: 0.6975 (mttt) cc_final: 0.5697 (tttt) REVERT: A 77 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.8102 (t) REVERT: B 43 LYS cc_start: 0.7172 (mttt) cc_final: 0.6763 (mptt) outliers start: 7 outliers final: 5 residues processed: 24 average time/residue: 0.1024 time to fit residues: 2.8973 Evaluate side-chains 24 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.100610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.084813 restraints weight = 2040.792| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.50 r_work: 0.3735 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2932 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= 0.106 Angle : 0.664 5.744 1665 Z= 0.366 Chirality : 0.057 0.175 222 Planarity : 0.002 0.008 207 Dihedral : 5.568 16.333 180 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.09 % Favored : 83.91 % Rotamer: Outliers : 5.69 % Allowed : 24.39 % Favored : 69.92 % 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: -5.95 (0.43), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.53 (0.33), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.016 0.002 PHE A 94 TYR 0.005 0.002 TYR A 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 21 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 14 time to evaluate : 0.124 Fit side-chains REVERT: C 43 LYS cc_start: 0.6841 (mttt) cc_final: 0.5308 (tttt) REVERT: C 94 PHE cc_start: 0.7398 (t80) cc_final: 0.6905 (t80) REVERT: A 43 LYS cc_start: 0.6858 (mttt) cc_final: 0.5600 (tttt) REVERT: A 77 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7927 (t) REVERT: B 43 LYS cc_start: 0.7062 (mttt) cc_final: 0.6657 (mptt) outliers start: 7 outliers final: 6 residues processed: 21 average time/residue: 0.1303 time to fit residues: 3.1568 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 : 0.126 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 0.0270 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.104556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.087713 restraints weight = 2101.349| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.60 r_work: 0.3776 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.3347 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= 0.095 Angle : 0.623 5.749 1665 Z= 0.345 Chirality : 0.055 0.150 222 Planarity : 0.002 0.010 207 Dihedral : 5.053 14.852 180 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 4.88 % Allowed : 24.39 % 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: -5.73 (0.46), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.36 (0.35), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.012 0.002 PHE A 94 TYR 0.005 0.002 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1205.93 seconds wall clock time: 21 minutes 43.37 seconds (1303.37 seconds total)