Starting phenix.real_space_refine on Thu Jul 18 20:54:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xct_38254/07_2024/8xct_38254_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xct_38254/07_2024/8xct_38254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xct_38254/07_2024/8xct_38254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xct_38254/07_2024/8xct_38254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xct_38254/07_2024/8xct_38254_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xct_38254/07_2024/8xct_38254_neut.cif" } resolution = 2.87 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= 0.002 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 3 5.49 5 S 14 5.16 5 C 2120 2.51 5 N 566 2.21 5 O 655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3358 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 417, 3271 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 396} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 417, 3271 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 396} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 3330 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 76 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 28} Link IDs: {None: 28} Time building chain proxies: 4.35, per 1000 atoms: 1.30 Number of scatterers: 3358 At special positions: 0 Unit cell: (68.432, 74.448, 73.696, 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 14 16.00 P 3 15.00 O 655 8.00 N 566 7.00 C 2120 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 - 3.50 Amino acid : False - 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: 1.50 Conformation dependent library (CDL) restraints added in 1.6 seconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 54.7% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.524A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.503A pdb=" N VAL A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.691A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.691A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.406A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1073 1.34 - 1.46: 560 1.46 - 1.57: 1747 1.57 - 1.69: 3 1.69 - 1.81: 27 Bond restraints: 3410 Sorted by residual: bond pdb=" C TRP A 89 " pdb=" CA BTRP A 89 " ideal model delta sigma weight residual 1.524 1.616 -0.093 1.29e-02 6.01e+03 5.19e+01 bond pdb=" O1N NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.477 1.548 -0.071 1.00e-02 1.00e+04 5.10e+01 bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.569 0.264 3.80e-02 6.93e+02 4.84e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.559 0.198 3.50e-02 8.16e+02 3.21e+01 bond pdb=" C6A NDP A 500 " pdb=" N1A NDP A 500 " ideal model delta sigma weight residual 1.368 1.251 0.117 2.90e-02 1.19e+03 1.62e+01 ... (remaining 3405 not shown) Histogram of bond angle deviations from ideal: 96.04 - 103.65: 58 103.65 - 111.26: 1418 111.26 - 118.86: 1358 118.86 - 126.47: 1719 126.47 - 134.07: 82 Bond angle restraints: 4635 Sorted by residual: angle pdb=" C1D NDP A 500 " pdb=" O4D NDP A 500 " pdb=" C4D NDP A 500 " ideal model delta sigma weight residual 105.41 127.48 -22.07 2.71e+00 1.37e-01 6.65e+01 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 119.21 -15.37 1.91e+00 2.73e-01 6.45e+01 angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 122.38 -14.64 1.95e+00 2.62e-01 5.61e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 109.48 7.98 1.17e+00 7.36e-01 4.68e+01 angle pdb=" O2X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.33 108.94 8.39 1.48e+00 4.57e-01 3.22e+01 ... (remaining 4630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 1872 23.85 - 47.69: 118 47.69 - 71.54: 24 71.54 - 95.38: 4 95.38 - 119.23: 1 Dihedral angle restraints: 2019 sinusoidal: 823 harmonic: 1196 Sorted by residual: dihedral pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " ideal model delta sinusoidal sigma weight residual 175.04 55.81 119.23 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" CA ASP A 256 " pdb=" CB ASP A 256 " pdb=" CG ASP A 256 " pdb=" OD1 ASP A 256 " ideal model delta sinusoidal sigma weight residual -30.00 -86.92 56.92 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA GLU A 366 " pdb=" CB GLU A 366 " pdb=" CG GLU A 366 " pdb=" CD GLU A 366 " ideal model delta sinusoidal sigma weight residual -180.00 -121.79 -58.21 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 441 0.079 - 0.158: 53 0.158 - 0.237: 3 0.237 - 0.316: 3 0.316 - 0.395: 3 Chirality restraints: 503 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.32 -0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" C2D NDP A 500 " pdb=" C1D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" O2D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.35 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 500 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 500 " -0.104 2.00e-02 2.50e+03 1.98e-01 3.93e+02 pdb=" C5N NDP A 500 " 0.256 2.00e-02 2.50e+03 pdb=" C6N NDP A 500 " -0.262 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.059 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" C3N NDP A 500 " 0.166 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " -0.038 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.106 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 143 " -0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO A 144 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.050 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 859 2.80 - 3.33: 3195 3.33 - 3.85: 5729 3.85 - 4.38: 6963 4.38 - 4.90: 11740 Nonbonded interactions: 28486 Sorted by model distance: nonbonded pdb=" OE2 GLU A 114 " pdb=" O HOH A 601 " model vdw 2.278 2.440 nonbonded pdb=" NE ARG A 73 " pdb=" OE2 GLU A 78 " model vdw 2.476 2.520 nonbonded pdb=" O VAL A 348 " pdb=" OG SER A 351 " model vdw 2.493 2.440 nonbonded pdb=" OD2 ASP A 47 " pdb=" OG SER A 116 " model vdw 2.517 2.440 nonbonded pdb=" OE1 GLN A 357 " pdb=" O HOH A 602 " model vdw 2.518 2.440 ... (remaining 28481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.750 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:14.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 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 : 0.009 0.264 3410 Z= 0.650 Angle : 1.090 22.067 4635 Z= 0.555 Chirality : 0.058 0.395 503 Planarity : 0.011 0.198 589 Dihedral : 16.215 119.230 1257 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.00 % Allowed : 0.88 % Favored : 94.12 % 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: 1.25 (0.42), residues: 416 helix: 2.05 (0.35), residues: 211 sheet: -0.28 (0.69), residues: 66 loop : -0.46 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.001 0.000 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.410 Fit side-chains REVERT: A 244 ASP cc_start: 0.6752 (OUTLIER) cc_final: 0.6327 (p0) REVERT: A 308 ASN cc_start: 0.7814 (m-40) cc_final: 0.7589 (m-40) outliers start: 17 outliers final: 3 residues processed: 80 average time/residue: 1.4230 time to fit residues: 116.8099 Evaluate side-chains 68 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 370 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3410 Z= 0.225 Angle : 0.508 4.653 4635 Z= 0.265 Chirality : 0.043 0.166 503 Planarity : 0.005 0.072 589 Dihedral : 8.359 122.615 477 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % Rotamer: Outliers : 2.06 % Allowed : 10.59 % Favored : 87.35 % 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: 1.67 (0.43), residues: 416 helix: 2.30 (0.35), residues: 213 sheet: -0.43 (0.68), residues: 68 loop : 0.08 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 263 HIS 0.005 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.375 Fit side-chains REVERT: A 277 THR cc_start: 0.8261 (m) cc_final: 0.7905 (p) REVERT: A 303 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8031 (pt0) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 1.2702 time to fit residues: 93.9822 Evaluate side-chains 66 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 379 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3410 Z= 0.205 Angle : 0.511 10.291 4635 Z= 0.260 Chirality : 0.043 0.152 503 Planarity : 0.005 0.060 589 Dihedral : 7.765 120.590 468 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 2.06 % Allowed : 14.71 % Favored : 83.24 % 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: 1.65 (0.43), residues: 416 helix: 2.29 (0.35), residues: 212 sheet: -0.29 (0.69), residues: 67 loop : -0.01 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.007 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.403 Fit side-chains REVERT: A 277 THR cc_start: 0.8282 (m) cc_final: 0.7889 (p) REVERT: A 303 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8023 (pt0) outliers start: 7 outliers final: 3 residues processed: 68 average time/residue: 1.3060 time to fit residues: 91.4206 Evaluate side-chains 66 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 379 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3410 Z= 0.235 Angle : 0.526 12.149 4635 Z= 0.268 Chirality : 0.044 0.152 503 Planarity : 0.005 0.054 589 Dihedral : 7.642 113.705 468 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 2.65 % Allowed : 14.71 % Favored : 82.65 % 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: 1.59 (0.43), residues: 416 helix: 2.26 (0.35), residues: 210 sheet: -0.07 (0.66), residues: 72 loop : -0.16 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.007 0.001 HIS A 388 PHE 0.011 0.002 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.383 Fit side-chains REVERT: A 204 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8369 (ttpp) REVERT: A 277 THR cc_start: 0.8283 (m) cc_final: 0.7825 (p) REVERT: A 303 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8005 (pt0) outliers start: 9 outliers final: 3 residues processed: 67 average time/residue: 1.2736 time to fit residues: 87.7541 Evaluate side-chains 68 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 379 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3410 Z= 0.157 Angle : 0.495 12.157 4635 Z= 0.250 Chirality : 0.042 0.127 503 Planarity : 0.005 0.048 589 Dihedral : 7.038 100.045 468 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 2.65 % Allowed : 14.12 % Favored : 83.24 % 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: 1.68 (0.43), residues: 416 helix: 2.31 (0.35), residues: 212 sheet: -0.27 (0.76), residues: 57 loop : -0.04 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.353 Fit side-chains REVERT: A 41 SER cc_start: 0.8864 (m) cc_final: 0.8565 (p) REVERT: A 303 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: A 366 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7101 (mt-10) outliers start: 9 outliers final: 1 residues processed: 68 average time/residue: 1.2504 time to fit residues: 87.4625 Evaluate side-chains 67 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 366 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 22 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 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3410 Z= 0.153 Angle : 0.495 11.341 4635 Z= 0.250 Chirality : 0.042 0.126 503 Planarity : 0.005 0.044 589 Dihedral : 6.248 76.953 468 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 2.35 % Allowed : 14.41 % Favored : 83.24 % 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: 1.73 (0.43), residues: 416 helix: 2.35 (0.35), residues: 212 sheet: -0.20 (0.76), residues: 57 loop : -0.02 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.006 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.367 Fit side-chains REVERT: A 13 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6995 (mt0) REVERT: A 41 SER cc_start: 0.8851 (m) cc_final: 0.8606 (p) REVERT: A 303 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7463 (pt0) outliers start: 8 outliers final: 0 residues processed: 68 average time/residue: 1.2020 time to fit residues: 84.1881 Evaluate side-chains 68 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3410 Z= 0.214 Angle : 0.498 8.352 4635 Z= 0.257 Chirality : 0.043 0.137 503 Planarity : 0.005 0.044 589 Dihedral : 5.721 67.692 465 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 1.47 % Allowed : 15.59 % Favored : 82.94 % 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: 1.70 (0.43), residues: 416 helix: 2.34 (0.35), residues: 211 sheet: -0.01 (0.72), residues: 62 loop : -0.15 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.006 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.378 Fit side-chains REVERT: A 13 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6989 (mt0) REVERT: A 41 SER cc_start: 0.8864 (m) cc_final: 0.8612 (p) REVERT: A 303 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7662 (pt0) outliers start: 5 outliers final: 0 residues processed: 64 average time/residue: 1.2811 time to fit residues: 84.3461 Evaluate side-chains 64 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3410 Z= 0.213 Angle : 0.499 8.176 4635 Z= 0.258 Chirality : 0.043 0.135 503 Planarity : 0.005 0.045 589 Dihedral : 5.286 55.521 465 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.41 % Favored : 97.35 % Rotamer: Outliers : 1.76 % Allowed : 15.59 % Favored : 82.65 % 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: 1.70 (0.43), residues: 416 helix: 2.33 (0.35), residues: 211 sheet: -0.04 (0.72), residues: 62 loop : -0.12 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.006 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.374 Fit side-chains REVERT: A 13 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6996 (mt0) REVERT: A 41 SER cc_start: 0.8861 (m) cc_final: 0.8599 (p) REVERT: A 303 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7966 (pt0) outliers start: 6 outliers final: 0 residues processed: 65 average time/residue: 1.2509 time to fit residues: 83.5871 Evaluate side-chains 64 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3410 Z= 0.175 Angle : 0.500 8.014 4635 Z= 0.256 Chirality : 0.042 0.124 503 Planarity : 0.004 0.045 589 Dihedral : 4.844 43.974 465 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 1.18 % Allowed : 17.06 % Favored : 81.76 % 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: 1.81 (0.43), residues: 416 helix: 2.36 (0.35), residues: 211 sheet: 0.10 (0.64), residues: 72 loop : 0.00 (0.58), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.006 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.386 Fit side-chains REVERT: A 13 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6979 (mt0) REVERT: A 41 SER cc_start: 0.8850 (m) cc_final: 0.8609 (p) REVERT: A 303 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7946 (pt0) outliers start: 4 outliers final: 0 residues processed: 66 average time/residue: 1.2550 time to fit residues: 85.3574 Evaluate side-chains 66 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3410 Z= 0.187 Angle : 0.498 8.255 4635 Z= 0.254 Chirality : 0.042 0.129 503 Planarity : 0.005 0.045 589 Dihedral : 4.757 42.824 465 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 1.18 % Allowed : 16.76 % Favored : 82.06 % 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: 1.72 (0.43), residues: 416 helix: 2.35 (0.35), residues: 211 sheet: -0.03 (0.72), residues: 62 loop : -0.10 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 HIS 0.005 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.353 Fit side-chains REVERT: A 13 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6993 (mt0) REVERT: A 41 SER cc_start: 0.8850 (m) cc_final: 0.8608 (p) REVERT: A 303 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7938 (pt0) outliers start: 4 outliers final: 0 residues processed: 64 average time/residue: 1.2617 time to fit residues: 83.1651 Evaluate side-chains 65 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.112792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.090661 restraints weight = 6381.794| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.00 r_work: 0.2682 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3410 Z= 0.252 Angle : 0.522 8.060 4635 Z= 0.270 Chirality : 0.043 0.140 503 Planarity : 0.005 0.045 589 Dihedral : 4.856 43.150 465 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 1.47 % Allowed : 16.76 % Favored : 81.76 % 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: 1.69 (0.43), residues: 416 helix: 2.31 (0.35), residues: 210 sheet: -0.06 (0.65), residues: 72 loop : -0.05 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.006 0.001 HIS A 388 PHE 0.013 0.002 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.002 0.000 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1927.57 seconds wall clock time: 34 minutes 8.43 seconds (2048.43 seconds total)