Starting phenix.real_space_refine on Thu Sep 10 19:47:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7og6_12879/09_2026/7og6_12879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7og6_12879/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7og6_12879/09_2026/7og6_12879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7og6_12879/09_2026/7og6_12879.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7og6_12879/09_2026/7og6_12879.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7og6_12879/09_2026/7og6_12879.cif" model { file = "/net/cci-nas-00/data/ceres_data/7og6_12879/09_2026/7og6_12879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7og6_12879/09_2026/7og6_12879.cif" } 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-2.2.1-6174/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: {'RNAv2': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Time building chain proxies: 0.44, per 1000 atoms: 0.27 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: 0.09 Conformation dependent library (CDL) restraints added in 35.1 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: 0.13 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: 0.09 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: 2144 1.72 - 3.44: 106 3.44 - 5.15: 17 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: 842 17.04 - 34.08: 101 34.08 - 51.12: 25 51.12 - 68.16: 12 68.16 - 85.21: 5 Dihedral angle restraints: 985 sinusoidal: 403 harmonic: 582 Sorted by residual: dihedral pdb=" C4' U R 44 " pdb=" C3' U R 44 " pdb=" C2' U R 44 " pdb=" C1' U R 44 " ideal model delta sinusoidal sigma weight residual 36.34 -36.42 72.76 1 3.10e+00 1.04e-01 7.03e+02 dihedral pdb=" O4' U R 44 " pdb=" C4' U R 44 " pdb=" C3' U R 44 " pdb=" C2' U R 44 " ideal model delta sinusoidal sigma weight residual -35.15 23.07 -58.21 1 4.00e+00 6.25e-02 2.84e+02 dihedral pdb=" O4' U R 44 " pdb=" C2' U R 44 " pdb=" C1' U R 44 " pdb=" C3' U R 44 " ideal model delta sinusoidal sigma weight residual -94.41 -38.33 -56.08 3 3.80e+00 6.93e-02 1.46e+02 ... (remaining 982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 207 0.056 - 0.111: 50 0.111 - 0.167: 6 0.167 - 0.222: 2 0.222 - 0.277: 5 Chirality restraints: 270 Sorted by residual: chirality pdb=" C2' U R 44 " pdb=" C3' U R 44 " pdb=" O2' U R 44 " pdb=" C1' U R 44 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" P U R 42 " pdb=" OP1 U R 42 " pdb=" OP2 U R 42 " pdb=" O5' U R 42 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" P U R 45 " pdb=" OP1 U R 45 " pdb=" OP2 U R 45 " pdb=" O5' U R 45 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (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: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.470 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.720 ------------------------------------------------------------------------------- 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 : 0.861 8.590 2268 Z= 0.545 Chirality : 0.059 0.277 270 Planarity : 0.006 0.081 284 Dihedral : 17.937 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 0.00770 / 0.37 ( 1646) covalent geometry : angle 0.86073 / 0.55 ( 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 : 0.034 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: 0.0187 time to fit residues: 0.6094 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 : 0.032 ------------------------------------------------------------------------------- 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: 5.9990 chunk 15 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.045877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.039808 restraints weight = 15206.041| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.89 r_work: 0.3062 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2050 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= 0.143 Angle : 0.670 5.798 2268 Z= 0.325 Chirality : 0.049 0.261 270 Planarity : 0.006 0.076 284 Dihedral : 13.290 139.527 268 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.08 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: -3.14 (0.54), residues: 197 helix: -1.97 (0.51), residues: 87 sheet: None (None), residues: 0 loop : -2.22 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.005 0.001 TYR A 60 PHE 0.015 0.001 PHE A 135 TRP 0.004 0.001 TRP A 107 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 0.66977 / 0.32 ( 2268) hydrogen bonds : bond 0.03979 / 2.34 ( 45) hydrogen bonds : angle 6.53829 / 4.57 ( 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 : 0.058 Fit side-chains REVERT: A 196 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8093 (p0) outliers start: 7 outliers final: 4 residues processed: 16 average time/residue: 0.0307 time to fit residues: 0.6719 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 : 0.054 ------------------------------------------------------------------------------- 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: 30.0000 chunk 8 optimal weight: 30.0000 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 40.0000 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 overall best weight: 6.5188 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.044666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.038647 restraints weight = 15039.353| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.83 r_work: 0.3056 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2699 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= 0.144 Angle : 0.632 4.773 2268 Z= 0.309 Chirality : 0.050 0.291 270 Planarity : 0.006 0.068 284 Dihedral : 12.239 133.190 267 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.66 % Allowed : 22.56 % Favored : 73.78 % 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: -2.30 (0.58), residues: 197 helix: -1.29 (0.55), residues: 86 sheet: None (None), residues: 0 loop : -1.72 (0.58), 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 0.000 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 ( 1646) covalent geometry : angle 0.63176 / 0.31 ( 2268) hydrogen bonds : bond 0.03659 / 2.06 ( 45) hydrogen bonds : angle 5.66639 / 4.03 ( 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 16 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.033 Fit side-chains REVERT: A 196 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8095 (p0) outliers start: 6 outliers final: 4 residues processed: 16 average time/residue: 0.0290 time to fit residues: 0.5775 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 : 0.033 ------------------------------------------------------------------------------- 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: 30.0000 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 7 optimal weight: 0.0030 chunk 1 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 overall best weight: 5.9998 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.045281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.039173 restraints weight = 14846.230| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.83 r_work: 0.3063 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1646 Z= 0.135 Angle : 0.613 5.088 2268 Z= 0.298 Chirality : 0.050 0.287 270 Planarity : 0.005 0.066 284 Dihedral : 12.096 133.015 267 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.27 % Allowed : 23.78 % 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: -1.90 (0.60), residues: 197 helix: -1.00 (0.57), residues: 87 sheet: None (None), residues: 0 loop : -1.47 (0.60), 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 0.013 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 0.00326 / 0.13 ( 1646) covalent geometry : angle 0.61326 / 0.30 ( 2268) hydrogen bonds : bond 0.03546 / 2.07 ( 45) hydrogen bonds : angle 5.11732 / 3.71 ( 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 16 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.060 Fit side-chains REVERT: A 196 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8023 (p0) outliers start: 7 outliers final: 5 residues processed: 16 average time/residue: 0.0317 time to fit residues: 0.6526 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 : 0.043 ------------------------------------------------------------------------------- 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: 0.2980 chunk 18 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 overall best weight: 3.2584 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.045270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.039212 restraints weight = 15257.807| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.93 r_work: 0.3064 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3194 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= 0.111 Angle : 0.598 5.772 2268 Z= 0.293 Chirality : 0.048 0.251 270 Planarity : 0.005 0.063 284 Dihedral : 11.930 132.299 267 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.88 % Allowed : 22.56 % Favored : 72.56 % 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: -1.53 (0.61), residues: 197 helix: -0.72 (0.58), residues: 87 sheet: None (None), residues: 0 loop : -1.24 (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 0.012 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 0.00265 / 0.11 ( 1646) covalent geometry : angle 0.59826 / 0.29 ( 2268) hydrogen bonds : bond 0.03329 / 1.98 ( 45) hydrogen bonds : angle 4.84064 / 3.55 ( 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 18 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.059 Fit side-chains REVERT: A 196 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7983 (p0) outliers start: 8 outliers final: 5 residues processed: 18 average time/residue: 0.0320 time to fit residues: 0.7819 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 : 0.061 ------------------------------------------------------------------------------- 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 152 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: 6.9990 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.045384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.039274 restraints weight = 14820.654| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.83 r_work: 0.3055 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3270 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= 0.129 Angle : 0.612 6.464 2268 Z= 0.301 Chirality : 0.049 0.268 270 Planarity : 0.005 0.064 284 Dihedral : 12.003 132.864 267 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.66 % Allowed : 26.83 % Favored : 69.51 % 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: -1.21 (0.63), residues: 197 helix: -0.44 (0.60), residues: 86 sheet: None (None), residues: 0 loop : -1.07 (0.63), residues: 111 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 0.001 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 1646) covalent geometry : angle 0.61190 / 0.30 ( 2268) hydrogen bonds : bond 0.03179 / 1.84 ( 45) hydrogen bonds : angle 4.71324 / 3.47 ( 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 14 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 8 time to evaluate : 0.061 Fit side-chains REVERT: A 196 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7998 (p0) outliers start: 6 outliers final: 5 residues processed: 14 average time/residue: 0.0315 time to fit residues: 0.6178 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 : 0.058 ------------------------------------------------------------------------------- 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 111 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 152 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: 30.0000 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.045703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.039668 restraints weight = 14745.723| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.84 r_work: 0.3072 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3506 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= 0.110 Angle : 0.585 5.938 2268 Z= 0.288 Chirality : 0.047 0.228 270 Planarity : 0.005 0.062 284 Dihedral : 11.868 131.751 267 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.27 % Allowed : 27.44 % 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: -0.93 (0.63), residues: 197 helix: -0.22 (0.61), residues: 84 sheet: None (None), residues: 0 loop : -0.89 (0.62), residues: 113 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 0.012 0.001 PHE A 135 TRP 0.003 0.000 TRP A 119 HIS 0.001 0.001 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 1646) covalent geometry : angle 0.58535 / 0.29 ( 2268) hydrogen bonds : bond 0.02928 / 1.73 ( 45) hydrogen bonds : angle 4.56576 / 3.37 ( 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 16 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.061 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 16 average time/residue: 0.0324 time to fit residues: 0.7162 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 : 0.059 ------------------------------------------------------------------------------- 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 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 8 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 0.0970 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 overall best weight: 5.8186 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.044803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.038820 restraints weight = 15135.681| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.75 r_work: 0.3040 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3592 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= 0.138 Angle : 0.633 8.265 2268 Z= 0.310 Chirality : 0.050 0.263 270 Planarity : 0.005 0.062 284 Dihedral : 11.756 133.256 265 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.66 % Allowed : 28.66 % Favored : 67.68 % 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: -0.88 (0.63), residues: 197 helix: -0.23 (0.60), residues: 86 sheet: None (None), residues: 0 loop : -0.83 (0.63), residues: 111 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 0.00338 / 0.14 ( 1646) covalent geometry : angle 0.63281 / 0.31 ( 2268) hydrogen bonds : bond 0.03266 / 1.93 ( 45) hydrogen bonds : angle 4.56421 / 3.37 ( 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 15 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.062 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 15 average time/residue: 0.0470 time to fit residues: 0.8929 Evaluate side-chains 13 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 9 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 139 VAL Chi-restraints excluded: chain A residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 40.0000 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 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 = 0.3348 r_free = 0.3348 target = 0.044523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.038570 restraints weight = 15301.470| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.80 r_work: 0.3033 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3736 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= 0.139 Angle : 0.645 7.959 2268 Z= 0.318 Chirality : 0.049 0.246 270 Planarity : 0.005 0.062 284 Dihedral : 11.567 132.659 265 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.83 % Allowed : 30.49 % Favored : 67.68 % 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: -0.92 (0.62), residues: 197 helix: -0.32 (0.58), residues: 91 sheet: None (None), residues: 0 loop : -0.80 (0.64), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 160 TYR 0.008 0.001 TYR A 60 PHE 0.012 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 0.00343 / 0.14 ( 1646) covalent geometry : angle 0.64543 / 0.32 ( 2268) hydrogen bonds : bond 0.03204 / 1.88 ( 45) hydrogen bonds : angle 4.63146 / 3.46 ( 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 12 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.035 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 12 average time/residue: 0.0526 time to fit residues: 0.7773 Evaluate side-chains 12 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.061 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 3 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 0.2980 chunk 10 optimal weight: 20.0000 chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 overall best weight: 4.9786 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.044215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.038191 restraints weight = 15375.518| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.82 r_work: 0.3019 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1646 Z= 0.134 Angle : 0.639 8.114 2268 Z= 0.315 Chirality : 0.048 0.242 270 Planarity : 0.005 0.062 284 Dihedral : 11.276 132.454 265 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.44 % Allowed : 30.49 % Favored : 67.07 % 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: -0.39 (0.64), residues: 197 helix: 0.11 (0.62), residues: 83 sheet: None (None), residues: 0 loop : -0.46 (0.63), residues: 114 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 0.012 0.001 PHE A 135 TRP 0.004 0.001 TRP A 107 HIS 0.001 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.13 ( 1646) covalent geometry : angle 0.63879 / 0.32 ( 2268) hydrogen bonds : bond 0.03130 / 1.84 ( 45) hydrogen bonds : angle 4.54399 / 3.39 ( 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 12 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 8 time to evaluate : 0.060 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 12 average time/residue: 0.0352 time to fit residues: 0.5880 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 : 0.058 ------------------------------------------------------------------------------- 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 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 0.0010 chunk 9 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 overall best weight: 4.9994 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.044051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.037937 restraints weight = 15402.622| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.88 r_work: 0.3015 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3966 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 : 0.647 7.934 2268 Z= 0.320 Chirality : 0.049 0.248 270 Planarity : 0.005 0.062 284 Dihedral : 11.262 132.603 265 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.44 % Allowed : 30.49 % Favored : 67.07 % 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: -0.42 (0.63), residues: 197 helix: -0.04 (0.61), residues: 83 sheet: None (None), residues: 0 loop : -0.37 (0.63), residues: 114 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 0.001 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 1646) covalent geometry : angle 0.64688 / 0.32 ( 2268) hydrogen bonds : bond 0.03116 / 1.84 ( 45) hydrogen bonds : angle 4.51686 / 3.37 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 575.88 seconds wall clock time: 10 minutes 39.25 seconds (639.25 seconds total)