Starting phenix.real_space_refine on Fri May 9 12:42:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p36_17384/05_2025/8p36_17384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p36_17384/05_2025/8p36_17384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p36_17384/05_2025/8p36_17384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p36_17384/05_2025/8p36_17384.map" model { file = "/net/cci-nas-00/data/ceres_data/8p36_17384/05_2025/8p36_17384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p36_17384/05_2025/8p36_17384.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 4 5.16 5 C 760 2.51 5 N 209 2.21 5 O 249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 1223 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1197 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'B6D': 1, 'G3P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.11, per 1000 atoms: 2.54 Number of scatterers: 1223 At special positions: 0 Unit cell: (45.57, 45.57, 96.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 P 1 15.00 O 249 8.00 N 209 7.00 C 760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 154 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 135.9 milliseconds 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 302 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 2 sheets defined 44.7% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 Processing helix chain 'A' and resid 23 through 43 removed outlier: 3.726A pdb=" N TYR A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.507A pdb=" N GLY A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.657A pdb=" N LYS A 101 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.933A pdb=" N ARG A 155 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 83 Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125 58 hydrogen bonds defined for protein. 156 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: 0.33 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 402 1.34 - 1.45: 146 1.45 - 1.57: 685 1.57 - 1.69: 1 1.69 - 1.80: 6 Bond restraints: 1240 Sorted by residual: bond pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " ideal model delta sigma weight residual 1.726 1.608 0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" C3 B6D A 202 " pdb=" O3 B6D A 202 " ideal model delta sigma weight residual 1.404 1.433 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" CA ILE A 72 " pdb=" CB ILE A 72 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.32e+00 bond pdb=" C1 B6D A 202 " pdb=" O5 B6D A 202 " ideal model delta sigma weight residual 1.405 1.427 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" O3P G3P A 201 " pdb=" P G3P A 201 " ideal model delta sigma weight residual 1.526 1.507 0.019 2.00e-02 2.50e+03 9.19e-01 ... (remaining 1235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 1653 1.82 - 3.65: 27 3.65 - 5.47: 4 5.47 - 7.29: 3 7.29 - 9.12: 1 Bond angle restraints: 1688 Sorted by residual: angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 100.65 109.77 -9.12 3.00e+00 1.11e-01 9.24e+00 angle pdb=" N GLY A 121 " pdb=" CA GLY A 121 " pdb=" C GLY A 121 " ideal model delta sigma weight residual 111.42 114.92 -3.50 1.51e+00 4.39e-01 5.39e+00 angle pdb=" O2P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 115.71 109.88 5.83 3.00e+00 1.11e-01 3.78e+00 angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O3P G3P A 201 " ideal model delta sigma weight residual 104.20 109.93 -5.73 3.00e+00 1.11e-01 3.65e+00 angle pdb=" O3P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 115.20 109.53 5.67 3.00e+00 1.11e-01 3.57e+00 ... (remaining 1683 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.09: 638 16.09 - 32.17: 77 32.17 - 48.25: 27 48.25 - 64.33: 15 64.33 - 80.41: 3 Dihedral angle restraints: 760 sinusoidal: 293 harmonic: 467 Sorted by residual: dihedral pdb=" CG ARG A 126 " pdb=" CD ARG A 126 " pdb=" NE ARG A 126 " pdb=" CZ ARG A 126 " ideal model delta sinusoidal sigma weight residual 180.00 135.42 44.58 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB LYS A 73 " pdb=" CG LYS A 73 " pdb=" CD LYS A 73 " pdb=" CE LYS A 73 " ideal model delta sinusoidal sigma weight residual 60.00 118.13 -58.13 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLU A 41 " pdb=" CB GLU A 41 " pdb=" CG GLU A 41 " pdb=" CD GLU A 41 " ideal model delta sinusoidal sigma weight residual -60.00 -115.07 55.07 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 757 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.042: 151 0.042 - 0.083: 40 0.083 - 0.125: 12 0.125 - 0.166: 0 0.166 - 0.207: 1 Chirality restraints: 204 Sorted by residual: chirality pdb=" C4 B6D A 202 " pdb=" C3 B6D A 202 " pdb=" C5 B6D A 202 " pdb=" N4 B6D A 202 " both_signs ideal model delta sigma weight residual False -2.31 -2.52 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA VAL A 82 " pdb=" N VAL A 82 " pdb=" C VAL A 82 " pdb=" CB VAL A 82 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.22e-01 chirality pdb=" CA VAL A 80 " pdb=" N VAL A 80 " pdb=" C VAL A 80 " pdb=" CB VAL A 80 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 ... (remaining 201 not shown) Planarity restraints: 213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 B6D A 202 " -0.019 2.00e-02 2.50e+03 1.57e-02 3.09e+00 pdb=" C7 B6D A 202 " 0.005 2.00e-02 2.50e+03 pdb=" C8 B6D A 202 " -0.015 2.00e-02 2.50e+03 pdb=" N2 B6D A 202 " 0.025 2.00e-02 2.50e+03 pdb=" O7 B6D A 202 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 122 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO A 123 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 21 " 0.012 5.00e-02 4.00e+02 1.85e-02 5.48e-01 pdb=" N PRO A 22 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.010 5.00e-02 4.00e+02 ... (remaining 210 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 118 2.74 - 3.28: 1170 3.28 - 3.82: 2098 3.82 - 4.36: 2468 4.36 - 4.90: 4247 Nonbonded interactions: 10101 Sorted by model distance: nonbonded pdb=" O1 G3P A 201 " pdb=" O1P G3P A 201 " model vdw 2.195 3.040 nonbonded pdb=" O LYS A 44 " pdb=" OG1 THR A 48 " model vdw 2.285 3.040 nonbonded pdb=" NZ LYS A 110 " pdb=" O ALA A 160 " model vdw 2.379 3.120 nonbonded pdb=" NZ LYS A 140 " pdb=" OD2 ASP A 143 " model vdw 2.425 3.120 nonbonded pdb=" O LEU A 39 " pdb=" NE2 GLN A 43 " model vdw 2.453 3.120 ... (remaining 10096 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 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: 1.740 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: 0.020 Process input model: 10.810 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 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 : 0.005 0.118 1243 Z= 0.294 Angle : 0.632 9.119 1690 Z= 0.291 Chirality : 0.042 0.207 204 Planarity : 0.003 0.028 213 Dihedral : 18.623 80.410 455 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.51 % Allowed : 29.92 % Favored : 64.57 % 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: 1.15 (0.68), residues: 159 helix: 1.85 (0.71), residues: 49 sheet: -1.23 (0.95), residues: 24 loop : 0.92 (0.74), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 108 HIS 0.001 0.001 HIS A 54 PHE 0.005 0.001 PHE A 119 TYR 0.006 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.16582 ( 58) hydrogen bonds : angle 6.49601 ( 156) SS BOND : bond 0.00190 ( 1) SS BOND : angle 0.52809 ( 2) covalent geometry : bond 0.00496 ( 1240) covalent geometry : angle 0.63251 ( 1688) Misc. bond : bond 0.04374 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.146 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.7241 time to fit residues: 22.2673 Evaluate side-chains 25 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.0770 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.082027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.070891 restraints weight = 2165.759| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.34 r_work: 0.2831 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1243 Z= 0.097 Angle : 0.473 5.869 1690 Z= 0.247 Chirality : 0.040 0.119 204 Planarity : 0.003 0.025 213 Dihedral : 6.064 44.205 202 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.94 % Allowed : 27.56 % Favored : 68.50 % 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 (0.68), residues: 159 helix: 1.72 (0.69), residues: 55 sheet: -1.01 (0.97), residues: 26 loop : 0.63 (0.76), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.001 HIS A 149 PHE 0.002 0.000 PHE A 119 TYR 0.005 0.001 TYR A 50 ARG 0.002 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 58) hydrogen bonds : angle 4.39759 ( 156) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.25941 ( 2) covalent geometry : bond 0.00213 ( 1240) covalent geometry : angle 0.47331 ( 1688) Misc. bond : bond 0.00121 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.172 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 27 average time/residue: 0.6816 time to fit residues: 18.9025 Evaluate side-chains 24 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.079921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.068925 restraints weight = 2189.123| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.31 r_work: 0.2797 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1243 Z= 0.108 Angle : 0.455 4.529 1690 Z= 0.241 Chirality : 0.040 0.117 204 Planarity : 0.003 0.022 213 Dihedral : 4.933 46.199 197 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.36 % Allowed : 29.13 % Favored : 68.50 % 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: 1.08 (0.69), residues: 159 helix: 1.84 (0.69), residues: 55 sheet: -0.91 (0.99), residues: 26 loop : 0.66 (0.76), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.001 HIS A 54 PHE 0.002 0.000 PHE A 119 TYR 0.006 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 58) hydrogen bonds : angle 4.17013 ( 156) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.45925 ( 2) covalent geometry : bond 0.00243 ( 1240) covalent geometry : angle 0.45485 ( 1688) Misc. bond : bond 0.00189 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.140 Fit side-chains REVERT: A 5 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6132 (tp30) REVERT: A 97 ASN cc_start: 0.8991 (t0) cc_final: 0.8782 (t160) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.7038 time to fit residues: 19.5053 Evaluate side-chains 27 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3039 r_free = 0.3039 target = 0.076974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.065976 restraints weight = 2269.916| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.34 r_work: 0.2732 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 1243 Z= 0.166 Angle : 0.516 6.996 1690 Z= 0.263 Chirality : 0.042 0.117 204 Planarity : 0.002 0.020 213 Dihedral : 5.234 47.268 197 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.15 % Allowed : 29.92 % Favored : 66.93 % 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: 1.06 (0.69), residues: 159 helix: 1.75 (0.68), residues: 55 sheet: -0.91 (1.00), residues: 26 loop : 0.70 (0.78), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.001 HIS A 54 PHE 0.001 0.000 PHE A 119 TYR 0.008 0.001 TYR A 50 ARG 0.002 0.001 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 58) hydrogen bonds : angle 4.28026 ( 156) SS BOND : bond 0.00109 ( 1) SS BOND : angle 0.54398 ( 2) covalent geometry : bond 0.00385 ( 1240) covalent geometry : angle 0.51600 ( 1688) Misc. bond : bond 0.00180 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.148 Fit side-chains REVERT: A 5 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6207 (tp30) outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 0.7976 time to fit residues: 22.8311 Evaluate side-chains 28 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.0050 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.081773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.070838 restraints weight = 2175.025| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.33 r_work: 0.2831 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1243 Z= 0.081 Angle : 0.470 7.711 1690 Z= 0.238 Chirality : 0.040 0.120 204 Planarity : 0.002 0.020 213 Dihedral : 4.787 45.687 197 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.94 % Allowed : 29.92 % Favored : 66.14 % 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: 1.28 (0.70), residues: 159 helix: 2.06 (0.69), residues: 55 sheet: -0.84 (1.07), residues: 24 loop : 0.69 (0.76), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.001 0.000 PHE A 1 TYR 0.005 0.001 TYR A 50 ARG 0.000 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.02792 ( 58) hydrogen bonds : angle 3.98752 ( 156) SS BOND : bond 0.00000 ( 1) SS BOND : angle 0.25339 ( 2) covalent geometry : bond 0.00174 ( 1240) covalent geometry : angle 0.46979 ( 1688) Misc. bond : bond 0.00122 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.148 Fit side-chains REVERT: A 5 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6304 (tp30) REVERT: A 78 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8944 (pt0) REVERT: A 97 ASN cc_start: 0.9020 (t0) cc_final: 0.8790 (t160) outliers start: 5 outliers final: 2 residues processed: 32 average time/residue: 0.7905 time to fit residues: 25.8628 Evaluate side-chains 32 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 12 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 chunk 9 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.079666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.068820 restraints weight = 2211.952| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.31 r_work: 0.2802 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1243 Z= 0.092 Angle : 0.478 7.680 1690 Z= 0.242 Chirality : 0.040 0.118 204 Planarity : 0.003 0.021 213 Dihedral : 4.755 45.718 197 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.36 % Allowed : 30.71 % Favored : 66.93 % 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: 1.28 (0.70), residues: 159 helix: 2.02 (0.69), residues: 55 sheet: -0.93 (1.06), residues: 24 loop : 0.77 (0.78), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.001 0.000 PHE A 1 TYR 0.006 0.001 TYR A 50 ARG 0.001 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.02892 ( 58) hydrogen bonds : angle 3.95477 ( 156) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.33244 ( 2) covalent geometry : bond 0.00208 ( 1240) covalent geometry : angle 0.47840 ( 1688) Misc. bond : bond 0.00121 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.143 Fit side-chains REVERT: A 5 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6308 (tp30) REVERT: A 97 ASN cc_start: 0.9048 (t0) cc_final: 0.8801 (t160) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.7267 time to fit residues: 22.3223 Evaluate side-chains 29 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 2 optimal weight: 0.0050 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.080177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.069412 restraints weight = 2279.546| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.30 r_work: 0.2806 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1243 Z= 0.086 Angle : 0.475 7.702 1690 Z= 0.240 Chirality : 0.040 0.119 204 Planarity : 0.003 0.021 213 Dihedral : 4.646 45.299 197 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.72 % Allowed : 28.35 % Favored : 66.93 % 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: 1.25 (0.70), residues: 159 helix: 2.04 (0.69), residues: 55 sheet: -1.02 (0.98), residues: 26 loop : 0.79 (0.79), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.002 0.000 PHE A 1 TYR 0.005 0.001 TYR A 50 ARG 0.000 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 58) hydrogen bonds : angle 3.85750 ( 156) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.28131 ( 2) covalent geometry : bond 0.00188 ( 1240) covalent geometry : angle 0.47495 ( 1688) Misc. bond : bond 0.00107 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.147 Fit side-chains REVERT: A 5 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6224 (tp30) REVERT: A 97 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8772 (t160) outliers start: 6 outliers final: 3 residues processed: 31 average time/residue: 0.6704 time to fit residues: 21.3406 Evaluate side-chains 31 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 2 optimal weight: 0.0040 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.069062 restraints weight = 2232.254| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.26 r_work: 0.2806 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1243 Z= 0.094 Angle : 0.490 8.080 1690 Z= 0.248 Chirality : 0.040 0.118 204 Planarity : 0.003 0.021 213 Dihedral : 4.646 45.456 197 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.15 % Allowed : 29.92 % Favored : 66.93 % 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: 1.30 (0.70), residues: 159 helix: 2.02 (0.69), residues: 55 sheet: -1.09 (0.97), residues: 26 loop : 0.90 (0.79), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.002 0.000 PHE A 1 TYR 0.006 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.02909 ( 58) hydrogen bonds : angle 3.86906 ( 156) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.32046 ( 2) covalent geometry : bond 0.00207 ( 1240) covalent geometry : angle 0.48987 ( 1688) Misc. bond : bond 0.00106 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.129 Fit side-chains REVERT: A 5 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6334 (tp30) REVERT: A 78 GLN cc_start: 0.9199 (pt0) cc_final: 0.8926 (pt0) REVERT: A 97 ASN cc_start: 0.9029 (t0) cc_final: 0.8786 (t160) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.6941 time to fit residues: 21.3457 Evaluate side-chains 31 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 9 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.077626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.066567 restraints weight = 2264.139| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.36 r_work: 0.2748 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1243 Z= 0.135 Angle : 0.521 8.370 1690 Z= 0.264 Chirality : 0.041 0.118 204 Planarity : 0.003 0.021 213 Dihedral : 4.901 46.081 197 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.94 % Allowed : 29.13 % Favored : 66.93 % 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: 1.13 (0.69), residues: 159 helix: 1.80 (0.68), residues: 55 sheet: -1.17 (0.96), residues: 26 loop : 0.88 (0.79), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.001 0.001 HIS A 54 PHE 0.001 0.000 PHE A 1 TYR 0.008 0.001 TYR A 50 ARG 0.002 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 58) hydrogen bonds : angle 4.06597 ( 156) SS BOND : bond 0.00021 ( 1) SS BOND : angle 0.47822 ( 2) covalent geometry : bond 0.00314 ( 1240) covalent geometry : angle 0.52140 ( 1688) Misc. bond : bond 0.00133 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.144 Fit side-chains REVERT: A 5 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6188 (tp30) REVERT: A 41 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6000 (pt0) REVERT: A 97 ASN cc_start: 0.9081 (OUTLIER) cc_final: 0.8853 (t160) outliers start: 5 outliers final: 3 residues processed: 31 average time/residue: 0.6376 time to fit residues: 20.3164 Evaluate side-chains 33 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 5 optimal weight: 0.0470 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.079591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.068443 restraints weight = 2273.463| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.37 r_work: 0.2786 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1243 Z= 0.096 Angle : 0.502 8.342 1690 Z= 0.254 Chirality : 0.040 0.120 204 Planarity : 0.003 0.020 213 Dihedral : 4.678 45.437 197 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.15 % Allowed : 29.13 % Favored : 67.72 % 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: 1.20 (0.69), residues: 159 helix: 1.87 (0.68), residues: 55 sheet: -1.12 (0.98), residues: 26 loop : 0.90 (0.79), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.001 0.001 HIS A 149 PHE 0.001 0.000 PHE A 1 TYR 0.006 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 58) hydrogen bonds : angle 3.91974 ( 156) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.32535 ( 2) covalent geometry : bond 0.00212 ( 1240) covalent geometry : angle 0.50192 ( 1688) Misc. bond : bond 0.00111 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.150 Fit side-chains REVERT: A 5 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6321 (tp30) REVERT: A 97 ASN cc_start: 0.9031 (t0) cc_final: 0.8789 (t160) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.6370 time to fit residues: 19.6240 Evaluate side-chains 32 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.0060 chunk 5 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.082061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.070932 restraints weight = 2243.249| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.38 r_work: 0.2836 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1243 Z= 0.082 Angle : 0.490 8.307 1690 Z= 0.248 Chirality : 0.040 0.121 204 Planarity : 0.003 0.020 213 Dihedral : 4.428 44.606 197 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.15 % Allowed : 29.13 % Favored : 67.72 % 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: 1.34 (0.70), residues: 159 helix: 2.04 (0.69), residues: 55 sheet: -1.07 (0.98), residues: 26 loop : 0.96 (0.79), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.001 0.000 PHE A 1 TYR 0.005 0.001 TYR A 50 ARG 0.000 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.02712 ( 58) hydrogen bonds : angle 3.75917 ( 156) SS BOND : bond 0.00021 ( 1) SS BOND : angle 0.24600 ( 2) covalent geometry : bond 0.00173 ( 1240) covalent geometry : angle 0.49004 ( 1688) Misc. bond : bond 0.00094 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1593.53 seconds wall clock time: 28 minutes 12.48 seconds (1692.48 seconds total)