Starting phenix.real_space_refine on Thu Mar 6 01:50:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ex9_28655/03_2025/8ex9_28655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ex9_28655/03_2025/8ex9_28655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ex9_28655/03_2025/8ex9_28655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ex9_28655/03_2025/8ex9_28655.map" model { file = "/net/cci-nas-00/data/ceres_data/8ex9_28655/03_2025/8ex9_28655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ex9_28655/03_2025/8ex9_28655.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 139 5.49 5 S 1 5.16 5 C 2136 2.51 5 N 768 2.21 5 O 1155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4199 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1277 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 162} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2179 Classifications: {'RNA': 102} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 50, 'rna3p_pyr': 44} Link IDs: {'rna2p': 8, 'rna3p': 93} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {' C%rna3p_pyr:plan2': 1, ' C%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 273 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {' DC:plan2': 1, ' DC:plan': 1, ' DT:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Time building chain proxies: 3.62, per 1000 atoms: 0.86 Number of scatterers: 4199 At special positions: 0 Unit cell: (64.896, 83.2, 99.84, 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 1 16.00 P 139 15.00 O 1155 8.00 N 768 7.00 C 2136 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: 1.39 Conformation dependent library (CDL) restraints added in 278.6 milliseconds 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 308 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 45.2% alpha, 17.5% beta 50 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 14 through 46 removed outlier: 3.701A pdb=" N TYR A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 75 through 97 removed outlier: 3.542A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 121 removed outlier: 4.335A pdb=" N ASN A 156 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 158 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 171 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS A 143 " --> pdb=" O TYR A 12 " (cutoff:3.500A) 78 hydrogen bonds defined for protein. 222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 127 hydrogen bonds 222 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 710 1.33 - 1.45: 1878 1.45 - 1.57: 1705 1.57 - 1.69: 273 1.69 - 1.81: 1 Bond restraints: 4567 Sorted by residual: bond pdb=" N GLY A 130 " pdb=" CA GLY A 130 " ideal model delta sigma weight residual 1.442 1.449 -0.007 7.70e-03 1.69e+04 9.04e-01 bond pdb=" O4' DT C 0 " pdb=" C1' DT C 0 " ideal model delta sigma weight residual 1.414 1.398 0.016 2.00e-02 2.50e+03 6.78e-01 bond pdb=" C3' DT C 0 " pdb=" C2' DT C 0 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.00e-02 2.50e+03 6.65e-01 bond pdb=" O4' DA D 4 " pdb=" C1' DA D 4 " ideal model delta sigma weight residual 1.414 1.398 0.016 2.00e-02 2.50e+03 6.28e-01 bond pdb=" C2' DC C 1 " pdb=" C1' DC C 1 " ideal model delta sigma weight residual 1.525 1.540 -0.015 2.00e-02 2.50e+03 5.57e-01 ... (remaining 4562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.79: 6268 0.79 - 1.59: 433 1.59 - 2.38: 96 2.38 - 3.17: 27 3.17 - 3.96: 6 Bond angle restraints: 6830 Sorted by residual: angle pdb=" C2' U B -34 " pdb=" C1' U B -34 " pdb=" N1 U B -34 " ideal model delta sigma weight residual 112.00 115.67 -3.67 1.50e+00 4.44e-01 5.98e+00 angle pdb=" CA GLY A 130 " pdb=" C GLY A 130 " pdb=" N GLU A 131 " ideal model delta sigma weight residual 114.65 116.66 -2.01 9.20e-01 1.18e+00 4.78e+00 angle pdb=" C4' DA D -8 " pdb=" C3' DA D -8 " pdb=" C2' DA D -8 " ideal model delta sigma weight residual 102.40 105.07 -2.67 1.50e+00 4.44e-01 3.17e+00 angle pdb=" C2' G B 3 " pdb=" C1' G B 3 " pdb=" N9 G B 3 " ideal model delta sigma weight residual 112.00 114.58 -2.58 1.50e+00 4.44e-01 2.97e+00 angle pdb=" C4' DT C 0 " pdb=" O4' DT C 0 " pdb=" C1' DT C 0 " ideal model delta sigma weight residual 109.70 107.21 2.49 1.50e+00 4.44e-01 2.75e+00 ... (remaining 6825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.38: 2128 20.38 - 40.75: 300 40.75 - 61.13: 238 61.13 - 81.50: 95 81.50 - 101.88: 3 Dihedral angle restraints: 2764 sinusoidal: 2285 harmonic: 479 Sorted by residual: dihedral pdb=" O4' U B -89 " pdb=" C1' U B -89 " pdb=" N1 U B -89 " pdb=" C2 U B -89 " ideal model delta sinusoidal sigma weight residual -160.00 -65.40 -94.60 1 1.50e+01 4.44e-03 4.61e+01 dihedral pdb=" O5' A B -95 " pdb=" C5' A B -95 " pdb=" C4' A B -95 " pdb=" C3' A B -95 " ideal model delta sinusoidal sigma weight residual -65.00 -123.14 58.14 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" O5' A B 2 " pdb=" C5' A B 2 " pdb=" C4' A B 2 " pdb=" C3' A B 2 " ideal model delta sinusoidal sigma weight residual 175.00 117.25 57.75 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 2761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 727 0.036 - 0.071: 99 0.071 - 0.107: 28 0.107 - 0.143: 5 0.143 - 0.178: 1 Chirality restraints: 860 Sorted by residual: chirality pdb=" C1' U B -34 " pdb=" O4' U B -34 " pdb=" C2' U B -34 " pdb=" N1 U B -34 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA PHE A 35 " pdb=" N PHE A 35 " pdb=" C PHE A 35 " pdb=" CB PHE A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" C1' G B 3 " pdb=" O4' G B 3 " pdb=" C2' G B 3 " pdb=" N9 G B 3 " both_signs ideal model delta sigma weight residual False 2.46 2.34 0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 857 not shown) Planarity restraints: 359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 3 " -0.027 2.00e-02 2.50e+03 1.11e-02 3.68e+00 pdb=" N9 G B 3 " 0.023 2.00e-02 2.50e+03 pdb=" C8 G B 3 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G B 3 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G B 3 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 3 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G B 3 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B 3 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G B 3 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 3 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B 3 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 3 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B -34 " 0.023 2.00e-02 2.50e+03 1.25e-02 3.52e+00 pdb=" N1 U B -34 " -0.028 2.00e-02 2.50e+03 pdb=" C2 U B -34 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U B -34 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U B -34 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U B -34 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U B -34 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U B -34 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B -34 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B-114 " -0.020 2.00e-02 2.50e+03 9.23e-03 2.56e+00 pdb=" N9 G B-114 " 0.021 2.00e-02 2.50e+03 pdb=" C8 G B-114 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B-114 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G B-114 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B-114 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G B-114 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G B-114 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G B-114 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G B-114 " 0.008 2.00e-02 2.50e+03 pdb=" N3 G B-114 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G B-114 " 0.001 2.00e-02 2.50e+03 ... (remaining 356 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 464 2.74 - 3.28: 3804 3.28 - 3.82: 8592 3.82 - 4.36: 10535 4.36 - 4.90: 13713 Nonbonded interactions: 37108 Sorted by model distance: nonbonded pdb=" N2 G B-106 " pdb=" O6 G B -5 " model vdw 2.200 3.120 nonbonded pdb=" OH TYR A 12 " pdb=" OP1 G B-106 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 170 " pdb=" O2' A B 2 " model vdw 2.246 3.040 nonbonded pdb=" OG SER A 117 " pdb=" OP1 U B 4 " model vdw 2.266 3.040 nonbonded pdb=" O2' C B -92 " pdb=" N1 A B -88 " model vdw 2.282 3.120 ... (remaining 37103 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: 0.010 Normalize map: mean=0, sd=1: 0.790 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.930 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 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 : 0.003 0.024 4567 Z= 0.171 Angle : 0.491 3.964 6830 Z= 0.270 Chirality : 0.029 0.178 860 Planarity : 0.004 0.038 359 Dihedral : 24.066 101.879 2456 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.79 % Allowed : 3.97 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.62), residues: 162 helix: 0.89 (0.60), residues: 73 sheet: -5.10 (0.72), residues: 19 loop : -1.83 (0.61), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 70 HIS 0.003 0.001 HIS A 34 PHE 0.015 0.001 PHE A 35 TYR 0.011 0.001 TYR A 118 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.238 Fit side-chains REVERT: A 52 TYR cc_start: 0.7894 (t80) cc_final: 0.7558 (t80) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 1.5350 time to fit residues: 31.7363 Evaluate side-chains 17 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.236348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.186734 restraints weight = 4667.133| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 1.16 r_work: 0.4099 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4567 Z= 0.230 Angle : 0.546 11.161 6830 Z= 0.287 Chirality : 0.031 0.162 860 Planarity : 0.004 0.041 359 Dihedral : 24.788 101.395 2182 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.38 % Allowed : 12.70 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.67), residues: 162 helix: 1.45 (0.62), residues: 67 sheet: -3.00 (0.81), residues: 33 loop : -0.75 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 70 HIS 0.003 0.001 HIS A 34 PHE 0.017 0.001 PHE A 35 TYR 0.011 0.002 TYR A 118 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.242 Fit side-chains REVERT: A 52 TYR cc_start: 0.8122 (t80) cc_final: 0.7798 (t80) outliers start: 3 outliers final: 1 residues processed: 13 average time/residue: 1.5474 time to fit residues: 20.9553 Evaluate side-chains 11 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.233916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.183782 restraints weight = 4662.057| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 1.17 r_work: 0.4071 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4567 Z= 0.272 Angle : 0.580 10.590 6830 Z= 0.303 Chirality : 0.033 0.168 860 Planarity : 0.005 0.043 359 Dihedral : 24.732 101.128 2182 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.97 % Allowed : 14.29 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.64), residues: 162 helix: 1.23 (0.60), residues: 67 sheet: -2.74 (0.83), residues: 33 loop : -1.03 (0.74), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 70 HIS 0.004 0.002 HIS A 34 PHE 0.019 0.002 PHE A 35 TYR 0.010 0.002 TYR A 118 ARG 0.004 0.001 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.225 Fit side-chains REVERT: A 52 TYR cc_start: 0.8194 (t80) cc_final: 0.7920 (t80) outliers start: 5 outliers final: 3 residues processed: 14 average time/residue: 1.0975 time to fit residues: 16.1833 Evaluate side-chains 12 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.235360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.187109 restraints weight = 4724.485| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 1.16 r_work: 0.4105 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4567 Z= 0.302 Angle : 0.598 10.961 6830 Z= 0.312 Chirality : 0.034 0.166 860 Planarity : 0.005 0.046 359 Dihedral : 24.719 98.271 2182 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.56 % Allowed : 13.49 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.63), residues: 162 helix: 0.96 (0.59), residues: 67 sheet: -2.73 (0.82), residues: 33 loop : -1.04 (0.75), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 141 HIS 0.005 0.002 HIS A 34 PHE 0.021 0.002 PHE A 35 TYR 0.012 0.002 TYR A 118 ARG 0.002 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 10 time to evaluate : 0.234 Fit side-chains REVERT: A 52 TYR cc_start: 0.8104 (t80) cc_final: 0.7851 (t80) outliers start: 7 outliers final: 5 residues processed: 16 average time/residue: 0.9672 time to fit residues: 16.3487 Evaluate side-chains 13 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 8 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.233850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.183998 restraints weight = 4781.810| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 1.17 r_work: 0.4071 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3922 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4567 Z= 0.241 Angle : 0.564 10.883 6830 Z= 0.296 Chirality : 0.032 0.155 860 Planarity : 0.004 0.046 359 Dihedral : 24.715 98.097 2182 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.56 % Allowed : 15.87 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.64), residues: 162 helix: 1.15 (0.59), residues: 67 sheet: -2.68 (0.83), residues: 33 loop : -0.96 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 70 HIS 0.004 0.002 HIS A 34 PHE 0.019 0.002 PHE A 35 TYR 0.010 0.002 TYR A 118 ARG 0.002 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.235 Fit side-chains REVERT: A 52 TYR cc_start: 0.8192 (t80) cc_final: 0.7912 (t80) outliers start: 7 outliers final: 5 residues processed: 15 average time/residue: 1.0654 time to fit residues: 16.8349 Evaluate side-chains 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 9 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.236253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.188578 restraints weight = 4744.609| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 1.16 r_work: 0.4117 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4567 Z= 0.269 Angle : 0.576 11.089 6830 Z= 0.301 Chirality : 0.032 0.160 860 Planarity : 0.004 0.046 359 Dihedral : 24.702 98.236 2182 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.76 % Allowed : 17.46 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.64), residues: 162 helix: 1.12 (0.59), residues: 67 sheet: -2.67 (0.83), residues: 33 loop : -0.98 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 70 HIS 0.004 0.001 HIS A 34 PHE 0.020 0.002 PHE A 35 TYR 0.013 0.002 TYR A 118 ARG 0.002 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.239 Fit side-chains REVERT: A 52 TYR cc_start: 0.8078 (t80) cc_final: 0.7817 (t80) outliers start: 6 outliers final: 5 residues processed: 14 average time/residue: 1.0483 time to fit residues: 15.4996 Evaluate side-chains 13 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 8 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.236262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.188591 restraints weight = 4731.460| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 1.16 r_work: 0.4117 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4567 Z= 0.269 Angle : 0.574 11.100 6830 Z= 0.300 Chirality : 0.032 0.160 860 Planarity : 0.004 0.046 359 Dihedral : 24.699 98.240 2182 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 7.14 % Allowed : 15.08 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.64), residues: 162 helix: 1.12 (0.59), residues: 67 sheet: -2.68 (0.83), residues: 33 loop : -0.99 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 70 HIS 0.004 0.001 HIS A 34 PHE 0.020 0.002 PHE A 35 TYR 0.013 0.002 TYR A 118 ARG 0.002 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 9 time to evaluate : 0.247 Fit side-chains REVERT: A 52 TYR cc_start: 0.8076 (t80) cc_final: 0.7815 (t80) outliers start: 9 outliers final: 6 residues processed: 16 average time/residue: 1.0176 time to fit residues: 17.2500 Evaluate side-chains 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 8 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.236728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.189235 restraints weight = 4660.530| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 1.13 r_work: 0.4131 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4567 Z= 0.241 Angle : 0.563 11.090 6830 Z= 0.295 Chirality : 0.032 0.158 860 Planarity : 0.004 0.046 359 Dihedral : 24.696 98.291 2182 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.56 % Allowed : 16.67 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.64), residues: 162 helix: 1.20 (0.59), residues: 67 sheet: -2.66 (0.83), residues: 33 loop : -0.96 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 70 HIS 0.003 0.001 HIS A 34 PHE 0.019 0.002 PHE A 35 TYR 0.010 0.002 TYR A 118 ARG 0.002 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.212 Fit side-chains REVERT: A 52 TYR cc_start: 0.8086 (t80) cc_final: 0.7826 (t80) outliers start: 7 outliers final: 5 residues processed: 15 average time/residue: 1.9558 time to fit residues: 30.7978 Evaluate side-chains 13 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 8 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.236213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.188489 restraints weight = 4739.153| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 1.16 r_work: 0.4118 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4567 Z= 0.276 Angle : 0.580 11.106 6830 Z= 0.303 Chirality : 0.033 0.161 860 Planarity : 0.004 0.046 359 Dihedral : 24.681 98.300 2182 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.76 % Allowed : 16.67 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.64), residues: 162 helix: 1.10 (0.59), residues: 67 sheet: -2.67 (0.83), residues: 33 loop : -1.00 (0.75), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 70 HIS 0.004 0.002 HIS A 34 PHE 0.020 0.002 PHE A 35 TYR 0.011 0.002 TYR A 118 ARG 0.002 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 8 time to evaluate : 0.317 Fit side-chains REVERT: A 52 TYR cc_start: 0.8096 (t80) cc_final: 0.7836 (t80) outliers start: 6 outliers final: 5 residues processed: 13 average time/residue: 2.2395 time to fit residues: 30.1361 Evaluate side-chains 13 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 8 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.237732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.190387 restraints weight = 4677.786| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 1.13 r_work: 0.4135 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4567 Z= 0.215 Angle : 0.552 11.105 6830 Z= 0.289 Chirality : 0.031 0.150 860 Planarity : 0.004 0.046 359 Dihedral : 24.674 98.344 2182 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.76 % Allowed : 16.67 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.65), residues: 162 helix: 1.37 (0.60), residues: 67 sheet: -2.63 (0.83), residues: 33 loop : -0.90 (0.77), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 70 HIS 0.003 0.001 HIS A 34 PHE 0.018 0.001 PHE A 35 TYR 0.010 0.002 TYR A 118 ARG 0.002 0.000 ARG A 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.232 Fit side-chains REVERT: A 52 TYR cc_start: 0.8084 (t80) cc_final: 0.7826 (t80) outliers start: 6 outliers final: 5 residues processed: 14 average time/residue: 1.0902 time to fit residues: 16.0812 Evaluate side-chains 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 9 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.233499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.185487 restraints weight = 4733.244| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 1.18 r_work: 0.4064 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4567 Z= 0.357 Angle : 0.644 10.411 6830 Z= 0.335 Chirality : 0.037 0.173 860 Planarity : 0.005 0.045 359 Dihedral : 24.698 97.821 2182 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.76 % Allowed : 16.67 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.63), residues: 162 helix: 0.67 (0.58), residues: 67 sheet: -2.75 (0.83), residues: 33 loop : -1.06 (0.75), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 70 HIS 0.006 0.002 HIS A 34 PHE 0.022 0.002 PHE A 35 TYR 0.012 0.002 TYR A 118 ARG 0.003 0.001 ARG A 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2884.84 seconds wall clock time: 52 minutes 35.30 seconds (3155.30 seconds total)