Starting phenix.real_space_refine on Wed Jul 1 20:44:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7og6_12879/07_2026/7og6_12879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7og6_12879/07_2026/7og6_12879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7og6_12879/07_2026/7og6_12879.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7og6_12879/07_2026/7og6_12879.cif" model { file = "/net/cci-nas-00/data/ceres_data/7og6_12879/07_2026/7og6_12879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7og6_12879/07_2026/7og6_12879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7og6_12879/07_2026/7og6_12879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7og6_12879/07_2026/7og6_12879.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.018 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 5 5.49 5 S 4 5.16 5 C 996 2.51 5 N 265 2.21 5 O 332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1602 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1502 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 183} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Time building chain proxies: 0.59, per 1000 atoms: 0.37 Number of scatterers: 1602 At special positions: 0 Unit cell: (69.225, 71.355, 68.16, 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 5 15.00 O 332 8.00 N 265 7.00 C 996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.14 Conformation dependent library (CDL) restraints added in 66.5 milliseconds 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 382 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 0 sheets defined 43.7% alpha, 0.0% beta 0 base pairs and 1 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 31 through 40 removed outlier: 3.613A pdb=" N ALA A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 63 removed outlier: 3.713A pdb=" N ALA A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 94 through 111 removed outlier: 3.776A pdb=" N PHE A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 3.715A pdb=" N ASN A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 removed outlier: 3.853A pdb=" N LYS A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE A 130 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.556A pdb=" N VAL A 139 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 175 removed outlier: 3.521A pdb=" N VAL A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) 45 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 1 stacking parallelities Total time for adding SS restraints: 0.18 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 484 1.33 - 1.45: 276 1.45 - 1.57: 871 1.57 - 1.69: 9 1.69 - 1.81: 6 Bond restraints: 1646 Sorted by residual: bond pdb=" C ASN A 141 " pdb=" O ASN A 141 " ideal model delta sigma weight residual 1.249 1.234 0.015 8.50e-03 1.38e+04 3.16e+00 bond pdb=" C MET A 145 " pdb=" N GLN A 146 " ideal model delta sigma weight residual 1.339 1.248 0.092 5.57e-02 3.22e+02 2.71e+00 bond pdb=" CA LYS A 89 " pdb=" CB LYS A 89 " ideal model delta sigma weight residual 1.526 1.503 0.023 1.51e-02 4.39e+03 2.24e+00 bond pdb=" C LYS A 125 " pdb=" N PRO A 126 " ideal model delta sigma weight residual 1.335 1.319 0.016 1.19e-02 7.06e+03 1.82e+00 bond pdb=" CG GLU A 120 " pdb=" CD GLU A 120 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.76e+00 ... (remaining 1641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 2160 1.72 - 3.44: 94 3.44 - 5.15: 13 5.15 - 6.87: 0 6.87 - 8.59: 1 Bond angle restraints: 2268 Sorted by residual: angle pdb=" N GLN A 173 " pdb=" CA GLN A 173 " pdb=" C GLN A 173 " ideal model delta sigma weight residual 114.62 106.03 8.59 1.14e+00 7.69e-01 5.68e+01 angle pdb=" N VAL A 84 " pdb=" CA VAL A 84 " pdb=" C VAL A 84 " ideal model delta sigma weight residual 111.45 107.42 4.03 9.30e-01 1.16e+00 1.88e+01 angle pdb=" N GLU A 140 " pdb=" CA GLU A 140 " pdb=" C GLU A 140 " ideal model delta sigma weight residual 113.21 108.38 4.83 1.15e+00 7.56e-01 1.76e+01 angle pdb=" N ASN A 14 " pdb=" CA ASN A 14 " pdb=" C ASN A 14 " ideal model delta sigma weight residual 114.31 109.25 5.06 1.29e+00 6.01e-01 1.54e+01 angle pdb=" N ILE A 200 " pdb=" CA ILE A 200 " pdb=" C ILE A 200 " ideal model delta sigma weight residual 113.43 109.17 4.26 1.09e+00 8.42e-01 1.53e+01 ... (remaining 2263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 852 17.04 - 34.08: 93 34.08 - 51.12: 26 51.12 - 68.16: 9 68.16 - 85.21: 5 Dihedral angle restraints: 985 sinusoidal: 403 harmonic: 582 Sorted by residual: dihedral pdb=" CA PRO A 198 " pdb=" C PRO A 198 " pdb=" N THR A 199 " pdb=" CA THR A 199 " ideal model delta harmonic sigma weight residual 180.00 148.52 31.48 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA PHE A 172 " pdb=" C PHE A 172 " pdb=" N GLN A 173 " pdb=" CA GLN A 173 " ideal model delta harmonic sigma weight residual 180.00 163.69 16.31 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA PHE A 5 " pdb=" C PHE A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta harmonic sigma weight residual -180.00 -164.48 -15.52 0 5.00e+00 4.00e-02 9.63e+00 ... (remaining 982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 130 0.027 - 0.055: 84 0.055 - 0.082: 39 0.082 - 0.109: 11 0.109 - 0.137: 6 Chirality restraints: 270 Sorted by residual: chirality pdb=" CA PRO A 6 " pdb=" N PRO A 6 " pdb=" C PRO A 6 " pdb=" CB PRO A 6 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA PRO A 126 " pdb=" N PRO A 126 " pdb=" C PRO A 126 " pdb=" CB PRO A 126 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA PHE A 135 " pdb=" N PHE A 135 " pdb=" C PHE A 135 " pdb=" CB PHE A 135 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 267 not shown) Planarity restraints: 284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 197 " 0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO A 198 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 198 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 198 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 147 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 148 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 148 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 148 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 135 " 0.009 2.00e-02 2.50e+03 8.99e-03 1.42e+00 pdb=" CG PHE A 135 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 135 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 135 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 135 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 135 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 135 " 0.000 2.00e-02 2.50e+03 ... (remaining 281 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 618 2.84 - 3.35: 1561 3.35 - 3.87: 2505 3.87 - 4.38: 2985 4.38 - 4.90: 4693 Nonbonded interactions: 12362 Sorted by model distance: nonbonded pdb=" O ALA A 90 " pdb=" OG SER A 91 " model vdw 2.325 3.040 nonbonded pdb=" O ASP A 61 " pdb=" ND2 ASN A 118 " model vdw 2.329 3.120 nonbonded pdb=" O SER A 185 " pdb=" OG1 THR A 189 " model vdw 2.332 3.040 nonbonded pdb=" NH2 ARG A 96 " pdb=" OP2 U R 44 " model vdw 2.356 3.120 nonbonded pdb=" N ASP A 134 " pdb=" OD1 ASP A 134 " model vdw 2.402 3.120 ... (remaining 12357 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.450 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.260 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 0.008 0.092 1646 Z= 0.375 Angle : 0.816 8.590 2268 Z= 0.540 Chirality : 0.044 0.137 270 Planarity : 0.006 0.081 284 Dihedral : 17.328 85.206 603 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 6.10 % Allowed : 20.12 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.47 (0.46), residues: 197 helix: -3.17 (0.38), residues: 88 sheet: None (None), residues: 0 loop : -2.84 (0.49), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 160 TYR 0.012 0.003 TYR A 67 PHE 0.021 0.002 PHE A 135 TRP 0.004 0.001 TRP A 107 HIS 0.001 0.001 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.38 ( 1646) covalent geometry : angle 0.81640 / 0.54 ( 2268) hydrogen bonds : bond 0.24238 / 14.43 ( 45) hydrogen bonds : angle 10.28088 / 6.95 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 15 time to evaluate : 0.065 Fit side-chains REVERT: A 43 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8498 (t) outliers start: 10 outliers final: 3 residues processed: 25 average time/residue: 0.0215 time to fit residues: 0.6974 Evaluate side-chains 11 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 196 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 40.0000 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN A 30 GLN A 83 GLN A 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.045357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.039185 restraints weight = 15321.785| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 4.02 r_work: 0.3042 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1646 Z= 0.135 Angle : 0.597 6.226 2268 Z= 0.309 Chirality : 0.042 0.135 270 Planarity : 0.006 0.076 284 Dihedral : 11.454 79.227 268 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.27 % Allowed : 20.12 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.54), residues: 197 helix: -1.96 (0.51), residues: 87 sheet: None (None), residues: 0 loop : -2.14 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 96 TYR 0.006 0.001 TYR A 60 PHE 0.015 0.001 PHE A 135 TRP 0.005 0.001 TRP A 107 HIS 0.000 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 1646) covalent geometry : angle 0.59745 / 0.31 ( 2268) hydrogen bonds : bond 0.03680 / 2.19 ( 45) hydrogen bonds : angle 6.39179 / 4.49 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.059 Fit side-chains REVERT: A 54 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8664 (mm-30) REVERT: A 196 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8040 (p0) outliers start: 7 outliers final: 4 residues processed: 16 average time/residue: 0.0311 time to fit residues: 0.6751 Evaluate side-chains 12 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 7 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 196 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 50.0000 chunk 15 optimal weight: 50.0000 chunk 8 optimal weight: 50.0000 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 18 optimal weight: 0.0010 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 overall best weight: 4.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.044380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.038295 restraints weight = 15287.528| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.91 r_work: 0.3033 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1646 Z= 0.121 Angle : 0.546 5.111 2268 Z= 0.284 Chirality : 0.040 0.123 270 Planarity : 0.006 0.068 284 Dihedral : 10.715 75.201 267 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.66 % Allowed : 23.17 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.57), residues: 197 helix: -1.23 (0.56), residues: 86 sheet: None (None), residues: 0 loop : -1.75 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 96 TYR 0.006 0.001 TYR A 60 PHE 0.012 0.001 PHE A 135 TRP 0.003 0.001 TRP A 119 HIS 0.001 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 1646) covalent geometry : angle 0.54621 / 0.28 ( 2268) hydrogen bonds : bond 0.03470 / 2.00 ( 45) hydrogen bonds : angle 5.60257 / 3.98 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 8 time to evaluate : 0.062 Fit side-chains REVERT: A 196 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8062 (p0) outliers start: 6 outliers final: 4 residues processed: 14 average time/residue: 0.0364 time to fit residues: 0.6972 Evaluate side-chains 11 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 196 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 11 optimal weight: 20.0000 chunk 5 optimal weight: 30.0000 chunk 10 optimal weight: 8.9990 chunk 8 optimal weight: 30.0000 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 7 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.044295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.038113 restraints weight = 14995.298| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.90 r_work: 0.3015 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 1646 Z= 0.160 Angle : 0.545 4.717 2268 Z= 0.286 Chirality : 0.042 0.134 270 Planarity : 0.005 0.067 284 Dihedral : 10.714 75.186 267 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.88 % Allowed : 23.17 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.61), residues: 197 helix: -0.89 (0.57), residues: 87 sheet: None (None), residues: 0 loop : -1.39 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 160 TYR 0.006 0.001 TYR A 60 PHE 0.014 0.001 PHE A 172 TRP 0.003 0.001 TRP A 119 HIS 0.000 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 1646) covalent geometry : angle 0.54540 / 0.29 ( 2268) hydrogen bonds : bond 0.03620 / 2.13 ( 45) hydrogen bonds : angle 5.06284 / 3.66 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 9 time to evaluate : 0.077 Fit side-chains REVERT: A 196 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.8016 (p0) outliers start: 8 outliers final: 5 residues processed: 17 average time/residue: 0.0522 time to fit residues: 1.1031 Evaluate side-chains 13 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 7 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 196 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 0.0470 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 GLN A 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.045033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.038695 restraints weight = 14999.100| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.98 r_work: 0.3031 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1646 Z= 0.114 Angle : 0.561 5.901 2268 Z= 0.290 Chirality : 0.041 0.142 270 Planarity : 0.005 0.064 284 Dihedral : 10.474 73.591 267 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.66 % Allowed : 25.61 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.62), residues: 197 helix: -0.54 (0.59), residues: 87 sheet: None (None), residues: 0 loop : -1.25 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 96 TYR 0.007 0.001 TYR A 60 PHE 0.013 0.001 PHE A 135 TRP 0.003 0.001 TRP A 119 HIS 0.001 0.001 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.11 ( 1646) covalent geometry : angle 0.56058 / 0.29 ( 2268) hydrogen bonds : bond 0.03365 / 2.06 ( 45) hydrogen bonds : angle 4.82636 / 3.52 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.063 Fit side-chains REVERT: A 196 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.8005 (p0) outliers start: 6 outliers final: 5 residues processed: 15 average time/residue: 0.0530 time to fit residues: 0.9946 Evaluate side-chains 14 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 8 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 196 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 50.0000 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 0.0470 chunk 7 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 overall best weight: 6.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 118 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.044418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.038192 restraints weight = 15126.747| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.92 r_work: 0.3021 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1646 Z= 0.136 Angle : 0.552 6.029 2268 Z= 0.288 Chirality : 0.041 0.144 270 Planarity : 0.005 0.064 284 Dihedral : 10.458 73.056 267 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.49 % Allowed : 23.17 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.63), residues: 197 helix: -0.40 (0.60), residues: 87 sheet: None (None), residues: 0 loop : -1.07 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 160 TYR 0.007 0.001 TYR A 60 PHE 0.015 0.001 PHE A 172 TRP 0.003 0.001 TRP A 119 HIS 0.000 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 1646) covalent geometry : angle 0.55187 / 0.29 ( 2268) hydrogen bonds : bond 0.03405 / 2.03 ( 45) hydrogen bonds : angle 4.74082 / 3.48 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 8 time to evaluate : 0.054 Fit side-chains REVERT: A 196 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7947 (p0) outliers start: 9 outliers final: 5 residues processed: 17 average time/residue: 0.0481 time to fit residues: 1.0243 Evaluate side-chains 12 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 6 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 196 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 40.0000 chunk 17 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 50.0000 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.044521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.038251 restraints weight = 14786.704| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.87 r_work: 0.3014 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1646 Z= 0.129 Angle : 0.567 6.257 2268 Z= 0.293 Chirality : 0.041 0.141 270 Planarity : 0.005 0.063 284 Dihedral : 10.373 72.154 267 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.66 % Allowed : 27.44 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.63), residues: 197 helix: -0.27 (0.60), residues: 87 sheet: None (None), residues: 0 loop : -0.97 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 96 TYR 0.007 0.001 TYR A 60 PHE 0.015 0.001 PHE A 172 TRP 0.003 0.001 TRP A 119 HIS 0.001 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 1646) covalent geometry : angle 0.56703 / 0.29 ( 2268) hydrogen bonds : bond 0.03181 / 1.87 ( 45) hydrogen bonds : angle 4.61915 / 3.39 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 7 time to evaluate : 0.063 Fit side-chains REVERT: A 196 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7947 (p0) outliers start: 6 outliers final: 4 residues processed: 13 average time/residue: 0.0460 time to fit residues: 0.7732 Evaluate side-chains 12 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 7 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 196 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 40.0000 chunk 16 optimal weight: 10.0000 chunk 2 optimal weight: 30.0000 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 9 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 overall best weight: 7.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.043589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.037546 restraints weight = 15239.131| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.78 r_work: 0.3002 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 1646 Z= 0.151 Angle : 0.573 6.804 2268 Z= 0.298 Chirality : 0.042 0.141 270 Planarity : 0.005 0.064 284 Dihedral : 10.488 72.760 267 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.66 % Allowed : 28.05 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.63), residues: 197 helix: -0.07 (0.59), residues: 87 sheet: None (None), residues: 0 loop : -0.83 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 160 TYR 0.007 0.001 TYR A 60 PHE 0.016 0.001 PHE A 172 TRP 0.003 0.001 TRP A 119 HIS 0.000 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 ( 1646) covalent geometry : angle 0.57301 / 0.30 ( 2268) hydrogen bonds : bond 0.03380 / 1.96 ( 45) hydrogen bonds : angle 4.71610 / 3.50 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 6 time to evaluate : 0.066 Fit side-chains REVERT: A 11 GLU cc_start: 0.9420 (mp0) cc_final: 0.9188 (pp20) REVERT: A 196 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.7951 (p0) outliers start: 6 outliers final: 4 residues processed: 12 average time/residue: 0.0256 time to fit residues: 0.4717 Evaluate side-chains 10 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 5 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 196 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 30.0000 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 40.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.043876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.037778 restraints weight = 15117.287| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.78 r_work: 0.2996 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 1646 Z= 0.147 Angle : 0.579 6.226 2268 Z= 0.297 Chirality : 0.042 0.136 270 Planarity : 0.005 0.064 284 Dihedral : 10.486 72.978 267 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.44 % Allowed : 29.27 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.64), residues: 197 helix: 0.34 (0.61), residues: 85 sheet: None (None), residues: 0 loop : -0.69 (0.64), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 96 TYR 0.007 0.001 TYR A 60 PHE 0.014 0.001 PHE A 172 TRP 0.003 0.001 TRP A 119 HIS 0.000 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 1646) covalent geometry : angle 0.57873 / 0.30 ( 2268) hydrogen bonds : bond 0.03384 / 2.01 ( 45) hydrogen bonds : angle 4.63387 / 3.44 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.067 Fit side-chains REVERT: A 11 GLU cc_start: 0.9417 (mp0) cc_final: 0.9193 (pp20) REVERT: A 196 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.7911 (p0) outliers start: 4 outliers final: 3 residues processed: 11 average time/residue: 0.0382 time to fit residues: 0.5881 Evaluate side-chains 10 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 6 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 196 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 0.0070 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.043647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.037639 restraints weight = 15332.529| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.76 r_work: 0.3010 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1646 Z= 0.130 Angle : 0.589 8.287 2268 Z= 0.302 Chirality : 0.041 0.135 270 Planarity : 0.005 0.064 284 Dihedral : 10.359 71.781 267 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.44 % Allowed : 29.27 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.63), residues: 197 helix: 0.31 (0.61), residues: 85 sheet: None (None), residues: 0 loop : -0.60 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 160 TYR 0.007 0.001 TYR A 60 PHE 0.013 0.001 PHE A 135 TRP 0.003 0.001 TRP A 119 HIS 0.001 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 1646) covalent geometry : angle 0.58935 / 0.30 ( 2268) hydrogen bonds : bond 0.03250 / 1.92 ( 45) hydrogen bonds : angle 4.62884 / 3.44 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 6 time to evaluate : 0.057 Fit side-chains REVERT: A 11 GLU cc_start: 0.9407 (mp0) cc_final: 0.9168 (mp0) REVERT: A 196 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7891 (p0) outliers start: 4 outliers final: 3 residues processed: 10 average time/residue: 0.0331 time to fit residues: 0.4785 Evaluate side-chains 10 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 6 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 196 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 13 optimal weight: 0.0970 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 50.0000 chunk 17 optimal weight: 6.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.043949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.037860 restraints weight = 15251.260| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.81 r_work: 0.3004 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1646 Z= 0.129 Angle : 0.576 7.707 2268 Z= 0.296 Chirality : 0.041 0.128 270 Planarity : 0.005 0.064 284 Dihedral : 10.244 70.068 267 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.44 % Allowed : 29.27 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.64), residues: 197 helix: -0.06 (0.59), residues: 91 sheet: None (None), residues: 0 loop : -0.54 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 96 TYR 0.008 0.001 TYR A 60 PHE 0.012 0.001 PHE A 135 TRP 0.003 0.001 TRP A 119 HIS 0.000 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 ( 1646) covalent geometry : angle 0.57585 / 0.30 ( 2268) hydrogen bonds : bond 0.03169 / 1.86 ( 45) hydrogen bonds : angle 4.49151 / 3.34 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 624.72 seconds wall clock time: 11 minutes 46.00 seconds (706.00 seconds total)