Starting phenix.real_space_refine on Wed Mar 5 14:15:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tgn_10499/03_2025/6tgn_10499.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tgn_10499/03_2025/6tgn_10499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tgn_10499/03_2025/6tgn_10499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tgn_10499/03_2025/6tgn_10499.map" model { file = "/net/cci-nas-00/data/ceres_data/6tgn_10499/03_2025/6tgn_10499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tgn_10499/03_2025/6tgn_10499.cif" } resolution = 3.9 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= 1.000 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: 4 Type Number sf(0) Gaussians S 1 5.16 5 C 425 2.51 5 N 115 2.21 5 O 131 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 672 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 672 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Time building chain proxies: 1.06, per 1000 atoms: 1.58 Number of scatterers: 672 At special positions: 0 Unit cell: (38.808, 48.51, 51.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 1 16.00 O 131 8.00 N 115 7.00 C 425 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: 0.15 Conformation dependent library (CDL) restraints added in 89.5 milliseconds 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 164 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 2 sheets defined 22.7% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.859A pdb=" N GLU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.864A pdb=" N ASN A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.553A pdb=" N VAL A 17 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 14 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.553A pdb=" N VAL A 17 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 14 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 13 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 89 " --> pdb=" O SER A 13 " (cutoff:3.500A) 17 hydrogen bonds defined for protein. 42 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.12 Time building geometry restraints manager: 0.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 124 1.32 - 1.44: 153 1.44 - 1.56: 399 1.56 - 1.68: 0 1.68 - 1.80: 2 Bond restraints: 678 Sorted by residual: bond pdb=" C TYR A 58 " pdb=" O TYR A 58 " ideal model delta sigma weight residual 1.234 1.197 0.037 1.16e-02 7.43e+03 1.01e+01 bond pdb=" CA ILE A 87 " pdb=" CB ILE A 87 " ideal model delta sigma weight residual 1.537 1.505 0.032 1.26e-02 6.30e+03 6.49e+00 bond pdb=" N ALA A 5 " pdb=" CA ALA A 5 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.31e+00 bond pdb=" C LEU A 56 " pdb=" O LEU A 56 " ideal model delta sigma weight residual 1.236 1.209 0.026 1.21e-02 6.83e+03 4.72e+00 bond pdb=" C ILE A 87 " pdb=" O ILE A 87 " ideal model delta sigma weight residual 1.238 1.214 0.024 1.10e-02 8.26e+03 4.64e+00 ... (remaining 673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 622 1.53 - 3.07: 215 3.07 - 4.60: 66 4.60 - 6.13: 10 6.13 - 7.66: 3 Bond angle restraints: 916 Sorted by residual: angle pdb=" C ASN A 88 " pdb=" CA ASN A 88 " pdb=" CB ASN A 88 " ideal model delta sigma weight residual 109.53 102.18 7.35 1.65e+00 3.67e-01 1.98e+01 angle pdb=" O GLY A 15 " pdb=" C GLY A 15 " pdb=" N GLY A 16 " ideal model delta sigma weight residual 122.57 126.54 -3.97 9.10e-01 1.21e+00 1.90e+01 angle pdb=" N ILE A 87 " pdb=" CA ILE A 87 " pdb=" C ILE A 87 " ideal model delta sigma weight residual 107.75 113.41 -5.66 1.46e+00 4.69e-01 1.50e+01 angle pdb=" CA LYS A 11 " pdb=" C LYS A 11 " pdb=" O LYS A 11 " ideal model delta sigma weight residual 120.32 116.14 4.18 1.10e+00 8.26e-01 1.44e+01 angle pdb=" N LEU A 85 " pdb=" CA LEU A 85 " pdb=" CB LEU A 85 " ideal model delta sigma weight residual 110.29 105.20 5.09 1.52e+00 4.33e-01 1.12e+01 ... (remaining 911 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 10.12: 333 10.12 - 20.23: 57 20.23 - 30.34: 15 30.34 - 40.45: 4 40.45 - 50.55: 3 Dihedral angle restraints: 412 sinusoidal: 159 harmonic: 253 Sorted by residual: dihedral pdb=" CA ASP A 62 " pdb=" C ASP A 62 " pdb=" N GLY A 63 " pdb=" CA GLY A 63 " ideal model delta harmonic sigma weight residual 180.00 152.99 27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ALA A 5 " pdb=" C ALA A 5 " pdb=" N ASN A 6 " pdb=" CA ASN A 6 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" C ASN A 88 " pdb=" N ASN A 88 " pdb=" CA ASN A 88 " pdb=" CB ASN A 88 " ideal model delta harmonic sigma weight residual -122.60 -112.69 -9.91 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 409 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.058: 41 0.058 - 0.115: 36 0.115 - 0.172: 17 0.172 - 0.229: 10 0.229 - 0.286: 6 Chirality restraints: 110 Sorted by residual: chirality pdb=" CA VAL A 66 " pdb=" N VAL A 66 " pdb=" C VAL A 66 " pdb=" CB VAL A 66 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ARG A 81 " pdb=" N ARG A 81 " pdb=" C ARG A 81 " pdb=" CB ARG A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA TYR A 58 " pdb=" N TYR A 58 " pdb=" C TYR A 58 " pdb=" CB TYR A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 107 not shown) Planarity restraints: 120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 14 " 0.042 2.00e-02 2.50e+03 2.17e-02 9.38e+00 pdb=" CG TYR A 14 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 14 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 14 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 14 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 14 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 14 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 14 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 58 " -0.030 2.00e-02 2.50e+03 1.63e-02 5.33e+00 pdb=" CG TYR A 58 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 58 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 58 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 58 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 58 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 58 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 58 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 46 " 0.001 2.00e-02 2.50e+03 1.71e-02 5.12e+00 pdb=" CG PHE A 46 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 46 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 46 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 46 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 46 " -0.019 2.00e-02 2.50e+03 ... (remaining 117 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 41 2.71 - 3.26: 598 3.26 - 3.80: 901 3.80 - 4.35: 1146 4.35 - 4.90: 1881 Nonbonded interactions: 4567 Sorted by model distance: nonbonded pdb=" OD1 ASP A 60 " pdb=" N GLU A 61 " model vdw 2.161 3.120 nonbonded pdb=" N ASP A 60 " pdb=" O ASP A 60 " model vdw 2.548 2.496 nonbonded pdb=" N ARG A 19 " pdb=" O ARG A 19 " model vdw 2.602 2.496 nonbonded pdb=" N GLU A 34 " pdb=" OE1 GLU A 34 " model vdw 2.607 3.120 nonbonded pdb=" O ARG A 19 " pdb=" CA ARG A 20 " model vdw 2.627 2.776 ... (remaining 4562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.590 Find NCS groups from input model: 0.000 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:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 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 : 0.010 0.044 678 Z= 0.599 Angle : 1.727 7.656 916 Z= 1.087 Chirality : 0.118 0.286 110 Planarity : 0.008 0.022 120 Dihedral : 11.933 50.555 248 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.39 % Allowed : 2.78 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.75), residues: 86 helix: -4.95 (0.26), residues: 18 sheet: -1.43 (0.99), residues: 28 loop : -1.61 (0.75), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.008 PHE A 46 TYR 0.042 0.016 TYR A 14 ARG 0.022 0.006 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.059 Fit side-chains revert: symmetry clash REVERT: A 17 VAL cc_start: 0.9635 (t) cc_final: 0.9428 (p) REVERT: A 22 ARG cc_start: 0.9505 (mtp-110) cc_final: 0.9078 (mpt180) REVERT: A 34 GLU cc_start: 0.9286 (pm20) cc_final: 0.8982 (mp0) REVERT: A 35 MET cc_start: 0.8809 (mmm) cc_final: 0.7750 (mmm) REVERT: A 59 SER cc_start: 0.9144 (m) cc_final: 0.8752 (t) REVERT: A 62 ASP cc_start: 0.8422 (p0) cc_final: 0.8135 (p0) REVERT: A 70 ASP cc_start: 0.8954 (p0) cc_final: 0.8753 (p0) outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.1495 time to fit residues: 5.8380 Evaluate side-chains 34 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 0.0970 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 overall best weight: 4.0235 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089971 restraints weight = 1485.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.092524 restraints weight = 902.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094263 restraints weight = 638.803| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 678 Z= 0.160 Angle : 0.622 5.408 916 Z= 0.311 Chirality : 0.043 0.126 110 Planarity : 0.002 0.013 120 Dihedral : 7.154 41.780 97 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.56 % Allowed : 15.28 % Favored : 79.17 % 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: -2.57 (0.76), residues: 86 helix: -3.20 (0.77), residues: 20 sheet: -1.09 (0.99), residues: 28 loop : -1.12 (0.74), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE A 21 TYR 0.010 0.002 TYR A 58 ARG 0.001 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8170 (mmm) cc_final: 0.7184 (mmm) outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 0.1589 time to fit residues: 6.0643 Evaluate side-chains 34 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 overall best weight: 4.0988 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.107047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.092395 restraints weight = 1494.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.094798 restraints weight = 858.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.096327 restraints weight = 597.303| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 678 Z= 0.165 Angle : 0.679 8.649 916 Z= 0.320 Chirality : 0.042 0.127 110 Planarity : 0.002 0.009 120 Dihedral : 6.850 43.476 97 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.56 % Allowed : 19.44 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.89), residues: 86 helix: -2.33 (1.18), residues: 14 sheet: -0.67 (1.01), residues: 28 loop : 0.19 (0.92), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE A 46 TYR 0.010 0.001 TYR A 58 ARG 0.000 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.066 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.9129 (p90) cc_final: 0.8453 (p90) REVERT: A 35 MET cc_start: 0.8287 (mmm) cc_final: 0.7658 (mmm) REVERT: A 71 ASP cc_start: 0.8144 (t0) cc_final: 0.7891 (t0) outliers start: 4 outliers final: 2 residues processed: 35 average time/residue: 0.1573 time to fit residues: 5.8286 Evaluate side-chains 33 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 20 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.106039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091670 restraints weight = 1480.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094004 restraints weight = 872.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095650 restraints weight = 615.190| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 678 Z= 0.261 Angle : 0.725 8.971 916 Z= 0.347 Chirality : 0.042 0.118 110 Planarity : 0.002 0.009 120 Dihedral : 7.219 43.643 97 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 6.94 % Allowed : 22.22 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.99), residues: 86 helix: -1.63 (1.52), residues: 14 sheet: -0.51 (1.04), residues: 28 loop : 0.55 (1.06), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.003 PHE A 46 TYR 0.010 0.002 TYR A 58 ARG 0.000 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.8104 (mmm) cc_final: 0.7602 (mmm) REVERT: A 71 ASP cc_start: 0.8284 (t0) cc_final: 0.8040 (t0) outliers start: 5 outliers final: 4 residues processed: 34 average time/residue: 0.1645 time to fit residues: 5.9318 Evaluate side-chains 34 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 overall best weight: 6.7240 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.107123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.092629 restraints weight = 1507.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.095143 restraints weight = 829.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.096816 restraints weight = 565.665| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 678 Z= 0.215 Angle : 0.653 7.402 916 Z= 0.311 Chirality : 0.042 0.117 110 Planarity : 0.002 0.007 120 Dihedral : 7.023 44.064 97 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 6.94 % Allowed : 25.00 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.99), residues: 86 helix: -2.16 (1.40), residues: 14 sheet: -0.38 (0.96), residues: 34 loop : 1.32 (1.13), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE A 46 TYR 0.009 0.001 TYR A 58 ARG 0.001 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.074 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 34 average time/residue: 0.1661 time to fit residues: 5.9700 Evaluate side-chains 34 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 0.0030 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 overall best weight: 4.2500 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.108419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.093262 restraints weight = 1522.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095638 restraints weight = 890.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097386 restraints weight = 625.736| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.6114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 678 Z= 0.160 Angle : 0.665 6.410 916 Z= 0.307 Chirality : 0.043 0.137 110 Planarity : 0.002 0.017 120 Dihedral : 6.626 42.903 97 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.56 % Allowed : 26.39 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.97), residues: 86 helix: -2.45 (1.11), residues: 20 sheet: -0.13 (0.95), residues: 34 loop : 1.40 (1.19), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE A 46 TYR 0.010 0.001 TYR A 58 ARG 0.001 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.077 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 35 average time/residue: 0.1465 time to fit residues: 5.4695 Evaluate side-chains 36 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 0.3980 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 overall best weight: 5.8488 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.107092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.092606 restraints weight = 1510.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094960 restraints weight = 876.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096649 restraints weight = 618.228| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 678 Z= 0.205 Angle : 0.683 5.843 916 Z= 0.331 Chirality : 0.044 0.136 110 Planarity : 0.002 0.010 120 Dihedral : 4.553 12.509 93 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.56 % Allowed : 27.78 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.99), residues: 86 helix: -2.41 (1.12), residues: 20 sheet: 0.12 (0.99), residues: 34 loop : 1.30 (1.19), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE A 46 TYR 0.009 0.001 TYR A 58 ARG 0.001 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.081 Fit side-chains REVERT: A 35 MET cc_start: 0.8218 (mmm) cc_final: 0.7521 (mmm) REVERT: A 41 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8329 (tttm) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 0.1413 time to fit residues: 4.9824 Evaluate side-chains 34 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.108819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.093075 restraints weight = 1551.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095227 restraints weight = 962.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096822 restraints weight = 707.234| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.6389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 678 Z= 0.195 Angle : 0.704 6.394 916 Z= 0.340 Chirality : 0.043 0.136 110 Planarity : 0.002 0.016 120 Dihedral : 4.490 14.095 93 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 5.56 % Allowed : 27.78 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (1.01), residues: 86 helix: -2.30 (1.17), residues: 20 sheet: 0.20 (1.00), residues: 34 loop : 1.41 (1.21), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE A 46 TYR 0.009 0.001 TYR A 58 ARG 0.001 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.7963 (mmm) cc_final: 0.7371 (mmm) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 0.1427 time to fit residues: 5.0333 Evaluate side-chains 35 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 0.0070 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 overall best weight: 5.2510 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.108134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.093076 restraints weight = 1444.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095282 restraints weight = 850.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.096804 restraints weight = 617.397| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.6471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 678 Z= 0.224 Angle : 0.755 7.292 916 Z= 0.366 Chirality : 0.044 0.142 110 Planarity : 0.003 0.014 120 Dihedral : 4.484 15.884 93 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.56 % Allowed : 26.39 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (1.01), residues: 86 helix: -2.26 (1.21), residues: 20 sheet: 0.37 (1.00), residues: 34 loop : 1.43 (1.22), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE A 46 TYR 0.010 0.002 TYR A 58 ARG 0.001 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.7790 (mmm) cc_final: 0.7024 (mmm) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.1395 time to fit residues: 4.9107 Evaluate side-chains 36 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.107558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092926 restraints weight = 1451.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095272 restraints weight = 878.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096852 restraints weight = 630.073| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.6492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 678 Z= 0.243 Angle : 0.821 7.260 916 Z= 0.404 Chirality : 0.046 0.143 110 Planarity : 0.002 0.007 120 Dihedral : 4.619 16.584 93 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.56 % Allowed : 26.39 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (1.02), residues: 86 helix: -2.44 (1.13), residues: 20 sheet: 0.38 (1.00), residues: 34 loop : 1.56 (1.26), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE A 46 TYR 0.010 0.001 TYR A 58 ARG 0.001 0.000 ARG A 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.7548 (mmm) cc_final: 0.6812 (mmm) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 0.1512 time to fit residues: 5.1429 Evaluate side-chains 34 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.0060 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 overall best weight: 5.0010 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.107956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.093011 restraints weight = 1489.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095462 restraints weight = 884.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097145 restraints weight = 628.496| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.6722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 678 Z= 0.222 Angle : 0.855 7.673 916 Z= 0.398 Chirality : 0.047 0.141 110 Planarity : 0.002 0.007 120 Dihedral : 4.489 16.450 93 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.17 % Allowed : 29.17 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (1.02), residues: 86 helix: -2.48 (1.14), residues: 20 sheet: 0.42 (1.00), residues: 34 loop : 1.66 (1.27), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE A 46 TYR 0.010 0.001 TYR A 58 ARG 0.001 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 542.03 seconds wall clock time: 11 minutes 2.90 seconds (662.90 seconds total)