Starting phenix.real_space_refine on Sat Apr 26 14:59:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p36_17384/04_2025/8p36_17384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p36_17384/04_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_17384/04_2025/8p36_17384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p36_17384/04_2025/8p36_17384.map" model { file = "/net/cci-nas-00/data/ceres_data/8p36_17384/04_2025/8p36_17384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p36_17384/04_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-5669/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: 2.07, per 1000 atoms: 1.69 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: 0.54 Conformation dependent library (CDL) restraints added in 131.9 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: 0.12 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: 0.24 Time building geometry restraints manager: 0.41 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.940 Find NCS groups from input model: 0.010 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:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.190 ------------------------------------------------------------------------------- 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 : 0.134 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.7378 time to fit residues: 22.7142 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 : 0.137 ------------------------------------------------------------------------------- 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: 0.1980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 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 = 0.3127 r_free = 0.3127 target = 0.082174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.071071 restraints weight = 2165.195| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.34 r_work: 0.2834 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1824 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= 0.098 Angle : 0.474 5.869 1690 Z= 0.247 Chirality : 0.040 0.122 204 Planarity : 0.003 0.026 213 Dihedral : 5.982 44.207 202 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.94 % Allowed : 28.35 % 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: 0.96 (0.68), residues: 159 helix: 1.71 (0.69), residues: 55 sheet: -1.01 (0.97), residues: 26 loop : 0.62 (0.76), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.001 0.001 HIS A 54 PHE 0.003 0.001 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 0.03144 ( 58) hydrogen bonds : angle 4.38424 ( 156) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.23339 ( 2) covalent geometry : bond 0.00213 ( 1240) covalent geometry : angle 0.47403 ( 1688) Misc. bond : bond 0.00093 ( 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 : 0.130 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 27 average time/residue: 0.6774 time to fit residues: 18.7791 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 : 0.144 ------------------------------------------------------------------------------- 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: 0.9980 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3096 r_free = 0.3096 target = 0.080315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.069239 restraints weight = 2188.416| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.33 r_work: 0.2802 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1243 Z= 0.101 Angle : 0.449 4.468 1690 Z= 0.239 Chirality : 0.040 0.117 204 Planarity : 0.003 0.023 213 Dihedral : 4.912 46.108 197 Min Nonbonded Distance : 2.549 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 (0.68), residues: 159 helix: 1.82 (0.68), residues: 55 sheet: -0.90 (0.99), residues: 26 loop : 0.67 (0.76), 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 0.003 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 0.03230 ( 58) hydrogen bonds : angle 4.14854 ( 156) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.37511 ( 2) covalent geometry : bond 0.00224 ( 1240) covalent geometry : angle 0.44945 ( 1688) Misc. bond : bond 0.00169 ( 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 : 0.142 Fit side-chains REVERT: A 5 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6136 (tp30) REVERT: A 97 ASN cc_start: 0.8983 (t0) cc_final: 0.8768 (t160) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.6922 time to fit residues: 19.2121 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 : 0.142 ------------------------------------------------------------------------------- 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: 3.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 = 0.3086 r_free = 0.3086 target = 0.079774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.068865 restraints weight = 2265.301| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.33 r_work: 0.2796 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1243 Z= 0.104 Angle : 0.474 7.140 1690 Z= 0.242 Chirality : 0.040 0.117 204 Planarity : 0.003 0.022 213 Dihedral : 4.912 46.392 197 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: 1.20 (0.69), residues: 159 helix: 1.93 (0.69), residues: 55 sheet: -0.88 (1.00), residues: 26 loop : 0.75 (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 0.007 0.001 TYR A 50 ARG 0.001 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 58) hydrogen bonds : angle 4.04510 ( 156) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.32768 ( 2) covalent geometry : bond 0.00232 ( 1240) covalent geometry : angle 0.47448 ( 1688) Misc. bond : bond 0.00147 ( 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 32 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.148 Fit side-chains REVERT: A 5 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6248 (tp30) REVERT: A 78 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8858 (pt0) REVERT: A 157 ASP cc_start: 0.8756 (t0) cc_final: 0.8461 (t70) outliers start: 5 outliers final: 2 residues processed: 29 average time/residue: 0.7119 time to fit residues: 21.1670 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 : 0.142 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3062 r_free = 0.3062 target = 0.078364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.067527 restraints weight = 2199.634| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.28 r_work: 0.2769 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1243 Z= 0.120 Angle : 0.489 7.468 1690 Z= 0.249 Chirality : 0.041 0.117 204 Planarity : 0.002 0.021 213 Dihedral : 4.941 46.552 197 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.36 % Allowed : 31.50 % 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: 1.17 (0.69), residues: 159 helix: 1.88 (0.68), residues: 55 sheet: -0.92 (0.98), residues: 26 loop : 0.76 (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 1 TYR 0.007 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 58) hydrogen bonds : angle 4.10416 ( 156) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.41752 ( 2) covalent geometry : bond 0.00275 ( 1240) covalent geometry : angle 0.48936 ( 1688) Misc. bond : bond 0.00151 ( 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 30 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.153 Fit side-chains REVERT: A 5 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6220 (tp30) REVERT: A 97 ASN cc_start: 0.9050 (t0) cc_final: 0.8804 (t160) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.6835 time to fit residues: 19.6504 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 : 0.142 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.0060 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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 = 0.3084 r_free = 0.3084 target = 0.079511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.068481 restraints weight = 2175.898| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.31 r_work: 0.2787 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1243 Z= 0.105 Angle : 0.484 8.013 1690 Z= 0.244 Chirality : 0.040 0.117 204 Planarity : 0.002 0.021 213 Dihedral : 4.853 46.113 197 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.87 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: 1.17 (0.69), residues: 159 helix: 1.88 (0.69), residues: 55 sheet: -0.94 (0.97), residues: 26 loop : 0.76 (0.78), 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 0.007 0.001 TYR A 50 ARG 0.001 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 58) hydrogen bonds : angle 4.00708 ( 156) SS BOND : bond 0.00023 ( 1) SS BOND : angle 0.34686 ( 2) covalent geometry : bond 0.00239 ( 1240) covalent geometry : angle 0.48427 ( 1688) Misc. bond : bond 0.00127 ( 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: 4 poor density : 28 time to evaluate : 0.146 Fit side-chains REVERT: A 5 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6215 (tp30) REVERT: A 78 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8825 (pt0) REVERT: A 97 ASN cc_start: 0.9057 (t0) cc_final: 0.8823 (t160) outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.7362 time to fit residues: 22.6501 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 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- 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 = 0.3100 r_free = 0.3100 target = 0.080569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.069634 restraints weight = 2230.639| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.31 r_work: 0.2814 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2597 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 : 0.472 7.933 1690 Z= 0.237 Chirality : 0.039 0.120 204 Planarity : 0.002 0.021 213 Dihedral : 4.665 45.605 197 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.46 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: 1.22 (0.70), residues: 159 helix: 1.98 (0.70), residues: 55 sheet: -0.98 (0.97), residues: 26 loop : 0.78 (0.78), 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 0.02807 ( 58) hydrogen bonds : angle 3.88944 ( 156) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.27691 ( 2) covalent geometry : bond 0.00189 ( 1240) covalent geometry : angle 0.47174 ( 1688) Misc. bond : bond 0.00108 ( 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 33 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.128 Fit side-chains REVERT: A 5 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6304 (tp30) REVERT: A 78 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8818 (pt0) REVERT: A 97 ASN cc_start: 0.9012 (t0) cc_final: 0.8789 (t160) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 0.6768 time to fit residues: 21.4966 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 : 0.125 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 0.0980 chunk 12 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3032 r_free = 0.3032 target = 0.076827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.065811 restraints weight = 2232.290| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.31 r_work: 0.2737 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 1243 Z= 0.174 Angle : 0.529 8.303 1690 Z= 0.267 Chirality : 0.042 0.129 204 Planarity : 0.003 0.021 213 Dihedral : 5.087 46.813 197 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: 1.06 (0.69), residues: 159 helix: 1.74 (0.69), residues: 55 sheet: -1.07 (0.97), residues: 26 loop : 0.77 (0.78), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.002 0.001 HIS A 54 PHE 0.001 0.000 PHE A 1 TYR 0.009 0.001 TYR A 50 ARG 0.002 0.001 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 58) hydrogen bonds : angle 4.15256 ( 156) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.61979 ( 2) covalent geometry : bond 0.00410 ( 1240) covalent geometry : angle 0.52867 ( 1688) Misc. bond : bond 0.00162 ( 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 34 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.518 Fit side-chains REVERT: A 5 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6172 (tp30) REVERT: A 97 ASN cc_start: 0.9086 (t0) cc_final: 0.8845 (t160) outliers start: 5 outliers final: 3 residues processed: 32 average time/residue: 1.0044 time to fit residues: 32.7148 Evaluate side-chains 30 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 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 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: 5.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3062 r_free = 0.3062 target = 0.078410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.067370 restraints weight = 2234.907| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.36 r_work: 0.2770 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1243 Z= 0.111 Angle : 0.502 8.425 1690 Z= 0.252 Chirality : 0.041 0.119 204 Planarity : 0.003 0.020 213 Dihedral : 4.864 46.258 197 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: 1.14 (0.70), residues: 159 helix: 1.79 (0.68), residues: 55 sheet: -1.04 (1.07), residues: 24 loop : 0.79 (0.77), residues: 80 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 1 TYR 0.007 0.001 TYR A 50 ARG 0.001 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03014 ( 58) hydrogen bonds : angle 4.00769 ( 156) SS BOND : bond 0.00025 ( 1) SS BOND : angle 0.39962 ( 2) covalent geometry : bond 0.00253 ( 1240) covalent geometry : angle 0.50192 ( 1688) Misc. bond : bond 0.00131 ( 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 32 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.146 Fit side-chains REVERT: A 5 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6190 (tp30) REVERT: A 97 ASN cc_start: 0.9080 (t0) cc_final: 0.8861 (t160) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.6737 time to fit residues: 20.7535 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 5 optimal weight: 0.0370 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.079791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.068564 restraints weight = 2244.139| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.36 r_work: 0.2786 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1243 Z= 0.100 Angle : 0.497 8.507 1690 Z= 0.250 Chirality : 0.040 0.118 204 Planarity : 0.003 0.020 213 Dihedral : 4.711 45.761 197 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: 1.16 (0.70), residues: 159 helix: 1.87 (0.69), residues: 55 sheet: -1.11 (0.98), residues: 26 loop : 0.83 (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 54 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 0.02917 ( 58) hydrogen bonds : angle 3.95205 ( 156) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.34425 ( 2) covalent geometry : bond 0.00225 ( 1240) covalent geometry : angle 0.49728 ( 1688) Misc. bond : bond 0.00121 ( 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 31 residues out of total 128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.150 Fit side-chains REVERT: A 5 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6303 (tp30) REVERT: A 97 ASN cc_start: 0.9043 (t0) cc_final: 0.8795 (t160) outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.6677 time to fit residues: 19.8724 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 : 0.111 ------------------------------------------------------------------------------- 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: 0.0770 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 5 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.082236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.071182 restraints weight = 2209.126| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.34 r_work: 0.2840 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2877 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 : 0.480 8.153 1690 Z= 0.242 Chirality : 0.039 0.122 204 Planarity : 0.003 0.021 213 Dihedral : 4.479 44.995 197 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: 1.28 (0.70), residues: 159 helix: 2.00 (0.70), residues: 55 sheet: -1.04 (0.99), residues: 26 loop : 0.87 (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 0.001 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 0.02667 ( 58) hydrogen bonds : angle 3.83830 ( 156) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.21713 ( 2) covalent geometry : bond 0.00173 ( 1240) covalent geometry : angle 0.48041 ( 1688) Misc. bond : bond 0.00099 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1696.56 seconds wall clock time: 29 minutes 56.56 seconds (1796.56 seconds total)