Starting phenix.real_space_refine on Mon Sep 23 18:19:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex9_28655/09_2024/8ex9_28655.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex9_28655/09_2024/8ex9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex9_28655/09_2024/8ex9_28655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex9_28655/09_2024/8ex9_28655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex9_28655/09_2024/8ex9_28655.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex9_28655/09_2024/8ex9_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-5461/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: 3.69, per 1000 atoms: 0.88 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: 1.29 Conformation dependent library (CDL) restraints added in 175.3 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: 2.27 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: 1.75 Time building geometry restraints manager: 1.50 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: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.510 Find NCS groups from input model: 0.030 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.980 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.226 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: 1.6801 time to fit residues: 34.6541 Evaluate side-chains 17 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 fitting. rotamer outliers: 3 poor density : 11 time to evaluate : 0.236 Fit side-chains REVERT: A 52 TYR cc_start: 0.8086 (t80) cc_final: 0.7796 (t80) outliers start: 3 outliers final: 1 residues processed: 13 average time/residue: 1.5873 time to fit residues: 21.4815 Evaluate side-chains 11 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4567 Z= 0.234 Angle : 0.548 11.035 6830 Z= 0.288 Chirality : 0.031 0.155 860 Planarity : 0.004 0.042 359 Dihedral : 24.707 100.779 2182 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.78 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: -0.55 (0.65), residues: 162 helix: 1.44 (0.61), residues: 67 sheet: -2.69 (0.82), residues: 33 loop : -0.90 (0.75), 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 0.018 0.002 PHE A 35 TYR 0.011 0.002 TYR A 118 ARG 0.002 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 16 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 11 time to evaluate : 0.232 Fit side-chains REVERT: A 52 TYR cc_start: 0.8109 (t80) cc_final: 0.7784 (t80) REVERT: A 138 LYS cc_start: 0.7292 (tppp) cc_final: 0.7087 (tppt) outliers start: 5 outliers final: 3 residues processed: 15 average time/residue: 1.2964 time to fit residues: 20.2877 Evaluate side-chains 13 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 10 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 12 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4567 Z= 0.300 Angle : 0.602 10.498 6830 Z= 0.314 Chirality : 0.034 0.172 860 Planarity : 0.005 0.044 359 Dihedral : 24.705 98.362 2182 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.76 % Allowed : 15.08 % Favored : 80.16 % 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: -0.89 (0.64), residues: 162 helix: 1.04 (0.59), residues: 67 sheet: -2.71 (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 70 HIS 0.005 0.002 HIS A 34 PHE 0.021 0.002 PHE A 35 TYR 0.011 0.002 TYR A 118 ARG 0.003 0.001 ARG A 160 *********************** 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 fitting. rotamer outliers: 6 poor density : 11 time to evaluate : 0.292 Fit side-chains REVERT: A 52 TYR cc_start: 0.8166 (t80) cc_final: 0.7921 (t80) REVERT: A 148 GLN cc_start: 0.6976 (tt0) cc_final: 0.6505 (mt0) REVERT: A 172 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8147 (tp) outliers start: 6 outliers final: 4 residues processed: 16 average time/residue: 1.1408 time to fit residues: 19.2374 Evaluate side-chains 14 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 9 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 158 THR Chi-restraints excluded: chain A residue 172 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.1142 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= 0.243 Angle : 0.563 11.025 6830 Z= 0.296 Chirality : 0.032 0.156 860 Planarity : 0.004 0.046 359 Dihedral : 24.698 97.945 2182 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.92 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: -0.78 (0.64), residues: 162 helix: 1.15 (0.59), residues: 67 sheet: -2.71 (0.83), residues: 33 loop : -0.95 (0.76), 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 0.018 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 15 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 9 time to evaluate : 0.279 Fit side-chains REVERT: A 52 TYR cc_start: 0.8150 (t80) cc_final: 0.7903 (t80) REVERT: A 138 LYS cc_start: 0.7397 (tppp) cc_final: 0.7180 (tppt) outliers start: 6 outliers final: 4 residues processed: 14 average time/residue: 1.1106 time to fit residues: 16.4047 Evaluate side-chains 13 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 9 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4567 Z= 0.304 Angle : 0.599 10.799 6830 Z= 0.312 Chirality : 0.034 0.166 860 Planarity : 0.005 0.046 359 Dihedral : 24.672 98.267 2182 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % 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: -0.98 (0.63), residues: 162 helix: 0.94 (0.59), residues: 67 sheet: -2.77 (0.82), residues: 33 loop : -1.05 (0.75), 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 0.012 0.002 TYR A 118 ARG 0.003 0.001 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 18 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 11 time to evaluate : 0.246 Fit side-chains REVERT: A 52 TYR cc_start: 0.8161 (t80) cc_final: 0.7907 (t80) REVERT: A 148 GLN cc_start: 0.6957 (tt0) cc_final: 0.6558 (mt0) outliers start: 7 outliers final: 5 residues processed: 17 average time/residue: 1.0383 time to fit residues: 18.6024 Evaluate side-chains 14 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 9 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4567 Z= 0.244 Angle : 0.567 10.900 6830 Z= 0.298 Chirality : 0.032 0.157 860 Planarity : 0.004 0.047 359 Dihedral : 24.663 98.126 2182 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.06 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: -0.78 (0.64), residues: 162 helix: 1.17 (0.60), residues: 67 sheet: -2.73 (0.82), residues: 33 loop : -0.97 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 70 HIS 0.004 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 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 15 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 9 time to evaluate : 0.239 Fit side-chains REVERT: A 52 TYR cc_start: 0.8161 (t80) cc_final: 0.7900 (t80) REVERT: A 138 LYS cc_start: 0.7553 (tppp) cc_final: 0.7316 (tppt) REVERT: A 148 GLN cc_start: 0.6926 (tt0) cc_final: 0.6530 (mt0) outliers start: 6 outliers final: 4 residues processed: 14 average time/residue: 1.2435 time to fit residues: 18.2659 Evaluate side-chains 13 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 9 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 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 26 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 20 optimal weight: 9.9990 chunk 7 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1249 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= 0.283 Angle : 0.586 11.021 6830 Z= 0.306 Chirality : 0.033 0.163 860 Planarity : 0.004 0.047 359 Dihedral : 24.641 98.211 2182 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.06 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: -0.90 (0.64), residues: 162 helix: 1.03 (0.59), residues: 67 sheet: -2.75 (0.82), residues: 33 loop : -1.01 (0.75), 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 0.012 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 15 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 9 time to evaluate : 0.263 Fit side-chains REVERT: A 52 TYR cc_start: 0.8150 (t80) cc_final: 0.7886 (t80) outliers start: 6 outliers final: 5 residues processed: 14 average time/residue: 1.2187 time to fit residues: 17.9226 Evaluate side-chains 14 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 9 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1253 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= 0.274 Angle : 0.581 10.996 6830 Z= 0.303 Chirality : 0.033 0.162 860 Planarity : 0.004 0.047 359 Dihedral : 24.640 98.238 2182 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.06 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: -0.87 (0.64), residues: 162 helix: 1.05 (0.59), residues: 67 sheet: -2.75 (0.82), residues: 33 loop : -0.99 (0.75), 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 0.012 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 16 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 10 time to evaluate : 0.229 Fit side-chains REVERT: A 52 TYR cc_start: 0.8147 (t80) cc_final: 0.7884 (t80) outliers start: 6 outliers final: 5 residues processed: 15 average time/residue: 1.3911 time to fit residues: 21.7715 Evaluate side-chains 14 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 9 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 21 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 0.0770 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4567 Z= 0.211 Angle : 0.549 11.023 6830 Z= 0.289 Chirality : 0.031 0.149 860 Planarity : 0.004 0.048 359 Dihedral : 24.623 98.228 2182 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.97 % Allowed : 17.46 % 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: -0.56 (0.65), residues: 162 helix: 1.40 (0.60), residues: 67 sheet: -2.71 (0.82), residues: 33 loop : -0.86 (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 0.009 0.002 TYR A 52 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 14 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 9 time to evaluate : 0.220 Fit side-chains REVERT: A 52 TYR cc_start: 0.8149 (t80) cc_final: 0.7894 (t80) REVERT: A 138 LYS cc_start: 0.7435 (tppp) cc_final: 0.7230 (tppt) outliers start: 5 outliers final: 4 residues processed: 13 average time/residue: 1.1837 time to fit residues: 16.1739 Evaluate side-chains 13 residues out of total 143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 9 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.4720 r_free = 0.4720 target = 0.232550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.184423 restraints weight = 4744.584| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 1.24 r_work: 0.4049 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4567 Z= 0.388 Angle : 0.672 10.335 6830 Z= 0.348 Chirality : 0.038 0.177 860 Planarity : 0.005 0.045 359 Dihedral : 24.708 97.368 2182 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.07 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: -1.32 (0.62), residues: 162 helix: 0.49 (0.58), residues: 67 sheet: -2.81 (0.82), residues: 33 loop : -1.09 (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 0.021 0.002 PHE A 35 TYR 0.011 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: 1187.86 seconds wall clock time: 22 minutes 5.68 seconds (1325.68 seconds total)