Starting phenix.real_space_refine on Thu Nov 14 10:22:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exa_28656/11_2024/8exa_28656.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exa_28656/11_2024/8exa_28656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exa_28656/11_2024/8exa_28656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exa_28656/11_2024/8exa_28656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exa_28656/11_2024/8exa_28656.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exa_28656/11_2024/8exa_28656.cif" } resolution = 3.14 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 2 5.16 5 C 2984 2.51 5 N 1029 2.21 5 O 1385 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-5513/modules/chem_data/mon_lib" Total number of atoms: 5539 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2610 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2163 Classifications: {'RNA': 101} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 49, 'rna3p_pyr': 42} Link IDs: {'rna2p': 10, 'rna3p': 90} Chain breaks: 2 Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 252 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} 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: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Time building chain proxies: 4.31, per 1000 atoms: 0.78 Number of scatterers: 5539 At special positions: 0 Unit cell: (81.4, 86.9, 97.9, 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 2 16.00 P 139 15.00 O 1385 8.00 N 1029 7.00 C 2984 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: 1.62 Conformation dependent library (CDL) restraints added in 527.0 milliseconds 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 2 sheets defined 53.7% alpha, 15.2% beta 56 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 14 through 46 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 75 through 96 removed outlier: 3.714A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 236 through 271 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 288 through 299 removed outlier: 4.628A pdb=" N LEU A 293 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 360 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 121 removed outlier: 7.383A pdb=" N ILE A 154 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLU A 174 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 156 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 209 removed outlier: 4.215A pdb=" N VAL A 200 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE A 186 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU A 278 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL A 192 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL A 321 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR A 277 " --> pdb=" O VAL A 321 " (cutoff:3.500A) 169 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 923 1.33 - 1.45: 2154 1.45 - 1.57: 2579 1.57 - 1.69: 273 1.69 - 1.80: 3 Bond restraints: 5932 Sorted by residual: bond pdb=" N GLN A 80 " pdb=" CA GLN A 80 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.23e-02 6.61e+03 3.44e+00 bond pdb=" CB TRP A 313 " pdb=" CG TRP A 313 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 8.46e-01 bond pdb=" C3' DC C 3 " pdb=" O3' DC C 3 " ideal model delta sigma weight residual 1.422 1.448 -0.026 3.00e-02 1.11e+03 7.34e-01 bond pdb=" C4' DT C 0 " pdb=" O4' DT C 0 " ideal model delta sigma weight residual 1.450 1.433 0.017 2.00e-02 2.50e+03 6.97e-01 bond pdb=" CA GLN A 80 " pdb=" C GLN A 80 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.29e-02 6.01e+03 6.52e-01 ... (remaining 5927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 8117 0.99 - 1.97: 448 1.97 - 2.96: 87 2.96 - 3.94: 15 3.94 - 4.93: 6 Bond angle restraints: 8673 Sorted by residual: angle pdb=" CA TYR A 309 " pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 113.90 118.72 -4.82 1.80e+00 3.09e-01 7.18e+00 angle pdb=" C2' G B 3 " pdb=" C1' G B 3 " pdb=" N9 G B 3 " ideal model delta sigma weight residual 112.00 115.28 -3.28 1.50e+00 4.44e-01 4.79e+00 angle pdb=" N ILE A 275 " pdb=" CA ILE A 275 " pdb=" C ILE A 275 " ideal model delta sigma weight residual 106.53 109.29 -2.76 1.41e+00 5.03e-01 3.83e+00 angle pdb=" C2' U B 9 " pdb=" C1' U B 9 " pdb=" N1 U B 9 " ideal model delta sigma weight residual 114.00 111.36 2.64 1.50e+00 4.44e-01 3.10e+00 angle pdb=" C4' DG C -5 " pdb=" O4' DG C -5 " pdb=" C1' DG C -5 " ideal model delta sigma weight residual 109.70 107.08 2.62 1.50e+00 4.44e-01 3.05e+00 ... (remaining 8668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 3069 28.56 - 57.13: 370 57.13 - 85.69: 148 85.69 - 114.25: 1 114.25 - 142.82: 1 Dihedral angle restraints: 3589 sinusoidal: 2600 harmonic: 989 Sorted by residual: dihedral pdb=" C4' DC C 3 " pdb=" C3' DC C 3 " pdb=" O3' DC C 3 " pdb=" P DA C 4 " ideal model delta sinusoidal sigma weight residual 220.00 77.18 142.82 1 3.50e+01 8.16e-04 1.41e+01 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 -119.23 -40.77 1 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CA LEU A 136 " pdb=" C LEU A 136 " pdb=" N PRO A 137 " pdb=" CA PRO A 137 " ideal model delta harmonic sigma weight residual -180.00 -164.05 -15.95 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 3586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 769 0.030 - 0.060: 213 0.060 - 0.090: 47 0.090 - 0.119: 26 0.119 - 0.149: 7 Chirality restraints: 1062 Sorted by residual: 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 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" C1' A B 2 " pdb=" O4' A B 2 " pdb=" C2' A B 2 " pdb=" N9 A B 2 " both_signs ideal model delta sigma weight residual False 2.46 2.33 0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA PRO A 137 " pdb=" N PRO A 137 " pdb=" C PRO A 137 " pdb=" CB PRO A 137 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 1059 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 3 " -0.031 2.00e-02 2.50e+03 1.28e-02 4.95e+00 pdb=" N9 G B 3 " 0.028 2.00e-02 2.50e+03 pdb=" C8 G B 3 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G B 3 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 3 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 3 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G B 3 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G B 3 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G B 3 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G B 3 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 3 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 3 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 9 " 0.026 2.00e-02 2.50e+03 1.39e-02 4.35e+00 pdb=" N1 U B 9 " -0.031 2.00e-02 2.50e+03 pdb=" C2 U B 9 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U B 9 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U B 9 " 0.005 2.00e-02 2.50e+03 pdb=" C4 U B 9 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U B 9 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U B 9 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 9 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 2 " -0.023 2.00e-02 2.50e+03 1.03e-02 2.92e+00 pdb=" N9 A B 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 A B 2 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 2 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 2 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A B 2 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A B 2 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 2 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A B 2 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A B 2 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 2 " 0.003 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 899 2.76 - 3.29: 5072 3.29 - 3.83: 11101 3.83 - 4.36: 12729 4.36 - 4.90: 18341 Nonbonded interactions: 48142 Sorted by model distance: nonbonded pdb=" OG SER A 117 " pdb=" OP1 U B 4 " model vdw 2.223 3.040 nonbonded pdb=" O2 C B-107 " pdb=" N2 G B -6 " model vdw 2.251 3.120 nonbonded pdb=" NH1 ARG A 39 " pdb=" OE1 GLU A 87 " model vdw 2.275 3.120 nonbonded pdb=" N2 G B-114 " pdb=" O4 U B -89 " model vdw 2.301 3.120 nonbonded pdb=" NH1 ARG A 110 " pdb=" OP1 C B 5 " model vdw 2.319 3.120 ... (remaining 48137 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.950 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 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 : 0.004 0.029 5932 Z= 0.219 Angle : 0.538 4.927 8673 Z= 0.286 Chirality : 0.033 0.149 1062 Planarity : 0.003 0.023 596 Dihedral : 22.737 142.816 2953 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.40 % Allowed : 8.50 % Favored : 91.09 % 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: 0.27 (0.47), residues: 337 helix: 1.86 (0.40), residues: 175 sheet: -1.83 (0.63), residues: 65 loop : -1.41 (0.60), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 300 HIS 0.002 0.001 HIS A 166 PHE 0.018 0.002 PHE A 35 TYR 0.024 0.002 TYR A 309 ARG 0.002 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9058 (mt) cc_final: 0.8835 (mt) REVERT: A 95 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.7187 (mtm110) outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.2197 time to fit residues: 13.1089 Evaluate side-chains 39 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 227 GLN A 250 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5932 Z= 0.173 Angle : 0.499 5.111 8673 Z= 0.264 Chirality : 0.031 0.126 1062 Planarity : 0.003 0.020 596 Dihedral : 23.801 142.230 2371 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.24 % Allowed : 9.31 % Favored : 87.45 % 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 (0.48), residues: 337 helix: 2.63 (0.40), residues: 169 sheet: -1.68 (0.65), residues: 65 loop : -1.12 (0.60), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 300 HIS 0.002 0.001 HIS A 166 PHE 0.022 0.002 PHE A 35 TYR 0.021 0.002 TYR A 309 ARG 0.003 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.399 Fit side-chains REVERT: A 61 LEU cc_start: 0.8908 (mt) cc_final: 0.8677 (mt) REVERT: A 143 LYS cc_start: 0.7473 (tttt) cc_final: 0.6640 (mtmt) REVERT: A 255 ASN cc_start: 0.7488 (m110) cc_final: 0.7140 (m110) REVERT: A 264 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.7030 (tt) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 0.2064 time to fit residues: 12.7001 Evaluate side-chains 40 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5932 Z= 0.213 Angle : 0.522 5.712 8673 Z= 0.273 Chirality : 0.032 0.122 1062 Planarity : 0.003 0.021 596 Dihedral : 23.776 142.324 2371 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.83 % Allowed : 10.93 % Favored : 86.23 % 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 (0.48), residues: 337 helix: 2.61 (0.39), residues: 167 sheet: -1.65 (0.67), residues: 66 loop : -1.02 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 300 HIS 0.002 0.001 HIS A 166 PHE 0.021 0.002 PHE A 35 TYR 0.022 0.002 TYR A 309 ARG 0.005 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.382 Fit side-chains REVERT: A 61 LEU cc_start: 0.8910 (mt) cc_final: 0.8704 (mt) REVERT: A 143 LYS cc_start: 0.7379 (tttt) cc_final: 0.6583 (mtmt) REVERT: A 214 TYR cc_start: 0.7264 (m-80) cc_final: 0.6852 (m-80) REVERT: A 255 ASN cc_start: 0.7495 (m110) cc_final: 0.7109 (m110) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.2421 time to fit residues: 12.9966 Evaluate side-chains 42 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 12 optimal weight: 0.0570 chunk 37 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5932 Z= 0.255 Angle : 0.563 6.482 8673 Z= 0.292 Chirality : 0.034 0.123 1062 Planarity : 0.004 0.025 596 Dihedral : 23.775 143.129 2371 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.24 % Allowed : 10.93 % Favored : 85.83 % 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: 0.61 (0.48), residues: 337 helix: 2.07 (0.39), residues: 174 sheet: -1.70 (0.68), residues: 66 loop : -1.06 (0.62), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 300 HIS 0.004 0.001 HIS A 166 PHE 0.022 0.002 PHE A 35 TYR 0.024 0.002 TYR A 309 ARG 0.004 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8949 (mt) cc_final: 0.8742 (mt) REVERT: A 143 LYS cc_start: 0.7415 (tttt) cc_final: 0.6673 (mtmt) REVERT: A 302 GLU cc_start: 0.7562 (tt0) cc_final: 0.7322 (tt0) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 0.2837 time to fit residues: 15.3854 Evaluate side-chains 40 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5932 Z= 0.247 Angle : 0.550 6.005 8673 Z= 0.288 Chirality : 0.034 0.127 1062 Planarity : 0.004 0.027 596 Dihedral : 23.705 142.985 2371 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.64 % Allowed : 12.55 % Favored : 83.81 % 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: 0.59 (0.48), residues: 337 helix: 2.09 (0.39), residues: 174 sheet: -1.80 (0.67), residues: 67 loop : -1.05 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 300 HIS 0.003 0.001 HIS A 166 PHE 0.021 0.002 PHE A 35 TYR 0.023 0.002 TYR A 309 ARG 0.005 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 143 LYS cc_start: 0.7288 (tttt) cc_final: 0.6642 (mtmt) REVERT: A 255 ASN cc_start: 0.7387 (m110) cc_final: 0.7038 (m110) outliers start: 9 outliers final: 7 residues processed: 45 average time/residue: 0.2309 time to fit residues: 12.9772 Evaluate side-chains 42 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5932 Z= 0.215 Angle : 0.530 6.135 8673 Z= 0.277 Chirality : 0.033 0.129 1062 Planarity : 0.004 0.027 596 Dihedral : 23.681 143.033 2371 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.45 % Allowed : 12.96 % Favored : 82.59 % 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 (0.48), residues: 337 helix: 2.43 (0.39), residues: 167 sheet: -1.72 (0.68), residues: 66 loop : -1.12 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 300 HIS 0.003 0.001 HIS A 34 PHE 0.022 0.002 PHE A 35 TYR 0.022 0.002 TYR A 214 ARG 0.006 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 143 LYS cc_start: 0.7252 (tttt) cc_final: 0.6609 (mtmt) REVERT: A 255 ASN cc_start: 0.7277 (m110) cc_final: 0.6986 (m110) REVERT: A 289 ARG cc_start: 0.3856 (tmt170) cc_final: 0.3644 (tpt-90) outliers start: 11 outliers final: 7 residues processed: 44 average time/residue: 0.2327 time to fit residues: 12.8868 Evaluate side-chains 41 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5932 Z= 0.171 Angle : 0.493 5.061 8673 Z= 0.258 Chirality : 0.031 0.122 1062 Planarity : 0.003 0.029 596 Dihedral : 23.639 142.674 2371 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.05 % Allowed : 14.57 % Favored : 81.38 % 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 (0.48), residues: 337 helix: 2.61 (0.39), residues: 167 sheet: -1.65 (0.68), residues: 66 loop : -1.09 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 300 HIS 0.003 0.001 HIS A 34 PHE 0.016 0.002 PHE A 35 TYR 0.022 0.002 TYR A 214 ARG 0.005 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6575 (t80) REVERT: A 40 ILE cc_start: 0.5296 (OUTLIER) cc_final: 0.5070 (tp) REVERT: A 143 LYS cc_start: 0.7238 (tttt) cc_final: 0.6604 (mtmt) REVERT: A 250 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6786 (m90) outliers start: 10 outliers final: 5 residues processed: 44 average time/residue: 0.2449 time to fit residues: 13.4878 Evaluate side-chains 42 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.0870 chunk 38 optimal weight: 6.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5932 Z= 0.255 Angle : 0.559 6.083 8673 Z= 0.291 Chirality : 0.034 0.123 1062 Planarity : 0.004 0.031 596 Dihedral : 23.659 143.153 2371 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.45 % Allowed : 13.36 % Favored : 82.19 % 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: 0.51 (0.48), residues: 337 helix: 1.99 (0.39), residues: 174 sheet: -1.78 (0.67), residues: 67 loop : -1.08 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 300 HIS 0.003 0.001 HIS A 34 PHE 0.021 0.002 PHE A 35 TYR 0.023 0.002 TYR A 309 ARG 0.007 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6740 (t80) REVERT: A 40 ILE cc_start: 0.5294 (OUTLIER) cc_final: 0.5093 (tp) REVERT: A 143 LYS cc_start: 0.7271 (tttt) cc_final: 0.6638 (mtmt) REVERT: A 250 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.6716 (m90) REVERT: A 255 ASN cc_start: 0.7358 (m110) cc_final: 0.7064 (m110) outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 0.2423 time to fit residues: 14.0100 Evaluate side-chains 46 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5932 Z= 0.256 Angle : 0.567 6.086 8673 Z= 0.295 Chirality : 0.034 0.123 1062 Planarity : 0.004 0.042 596 Dihedral : 23.687 143.626 2371 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.64 % Allowed : 14.57 % Favored : 81.78 % 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: 0.38 (0.47), residues: 337 helix: 1.90 (0.39), residues: 174 sheet: -1.80 (0.67), residues: 66 loop : -1.20 (0.61), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 300 HIS 0.003 0.001 HIS A 262 PHE 0.019 0.002 PHE A 35 TYR 0.023 0.002 TYR A 309 ARG 0.007 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.356 Fit side-chains REVERT: A 35 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.6695 (t80) REVERT: A 143 LYS cc_start: 0.7283 (tttt) cc_final: 0.6654 (mtmt) REVERT: A 250 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6818 (m90) REVERT: A 255 ASN cc_start: 0.7438 (m110) cc_final: 0.7138 (m110) outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 0.2426 time to fit residues: 12.6253 Evaluate side-chains 42 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 11 optimal weight: 0.0980 chunk 34 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5932 Z= 0.240 Angle : 0.559 5.862 8673 Z= 0.292 Chirality : 0.034 0.126 1062 Planarity : 0.004 0.035 596 Dihedral : 23.681 143.406 2371 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.24 % Allowed : 14.98 % Favored : 81.78 % 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: 0.37 (0.47), residues: 337 helix: 1.90 (0.39), residues: 174 sheet: -1.83 (0.66), residues: 66 loop : -1.20 (0.62), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 300 HIS 0.003 0.001 HIS A 34 PHE 0.020 0.002 PHE A 35 TYR 0.023 0.002 TYR A 309 ARG 0.008 0.001 ARG A 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.391 Fit side-chains REVERT: A 35 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.6681 (t80) REVERT: A 143 LYS cc_start: 0.7266 (tttt) cc_final: 0.6633 (mtmt) REVERT: A 250 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6813 (m90) REVERT: A 255 ASN cc_start: 0.7475 (m110) cc_final: 0.7127 (m110) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.2462 time to fit residues: 12.8130 Evaluate side-chains 43 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.198239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.158850 restraints weight = 7331.865| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.65 r_work: 0.3842 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5932 Z= 0.149 Angle : 0.483 4.859 8673 Z= 0.254 Chirality : 0.030 0.122 1062 Planarity : 0.004 0.036 596 Dihedral : 23.629 142.294 2371 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.83 % Allowed : 14.98 % Favored : 82.19 % 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 (0.48), residues: 337 helix: 2.59 (0.38), residues: 169 sheet: -1.73 (0.67), residues: 67 loop : -1.23 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 300 HIS 0.003 0.001 HIS A 279 PHE 0.016 0.002 PHE A 35 TYR 0.019 0.002 TYR A 309 ARG 0.009 0.001 ARG A 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1219.33 seconds wall clock time: 23 minutes 0.95 seconds (1380.95 seconds total)