Starting phenix.real_space_refine on Fri Dec 8 00:43:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/12_2023/7p5j_13200.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/12_2023/7p5j_13200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/12_2023/7p5j_13200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/12_2023/7p5j_13200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/12_2023/7p5j_13200.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/12_2023/7p5j_13200.pdb" } resolution = 4.0 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= 0.004 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4034 2.51 5 N 1036 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6250 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3069 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 17, 'TRANS': 381} Chain breaks: 1 Chain: "B" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3069 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 17, 'TRANS': 381} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.70, per 1000 atoms: 0.59 Number of scatterers: 6250 At special positions: 0 Unit cell: (88.536, 71.61, 134.106, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1156 8.00 N 1036 7.00 C 4034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 385 " distance=2.03 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 370 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 501 " - " ASN A 284 " " NAG A 502 " - " ASN A 355 " " NAG B 501 " - " ASN B 284 " " NAG B 502 " - " ASN B 355 " " NAG C 1 " - " ASN A 130 " " NAG D 1 " - " ASN B 130 " Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.3 seconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 removed outlier: 3.604A pdb=" N HIS A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 70 removed outlier: 3.591A pdb=" N GLN A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 161 Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 198 through 238 removed outlier: 3.636A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 276 removed outlier: 4.116A pdb=" N VAL A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N MET A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 290 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.755A pdb=" N LEU A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 335 removed outlier: 3.759A pdb=" N ARG A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.805A pdb=" N GLN A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 368 removed outlier: 3.565A pdb=" N LYS A 345 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Proline residue: A 346 - end of helix removed outlier: 4.183A pdb=" N SER A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 386 removed outlier: 4.266A pdb=" N LEU A 373 " --> pdb=" O HIS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 418 Proline residue: A 414 - end of helix removed outlier: 4.580A pdb=" N ALA A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 18 Processing helix chain 'B' and resid 37 through 70 removed outlier: 3.620A pdb=" N ALA B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 161 Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.694A pdb=" N ALA B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 238 removed outlier: 3.757A pdb=" N VAL B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 205 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 275 removed outlier: 4.010A pdb=" N VAL B 248 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 290 Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 311 through 335 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.925A pdb=" N GLN B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 368 Processing helix chain 'B' and resid 369 through 385 removed outlier: 4.120A pdb=" N LEU B 373 " --> pdb=" O HIS B 369 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 418 Proline residue: B 414 - end of helix removed outlier: 4.576A pdb=" N ALA B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1656 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: 1.72 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1975 1.34 - 1.46: 1103 1.46 - 1.58: 3270 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 6378 Sorted by residual: bond pdb=" N ILE B 244 " pdb=" CA ILE B 244 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" CA PRO A 421 " pdb=" C PRO A 421 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 9.10e+00 bond pdb=" N VAL B 243 " pdb=" CA VAL B 243 " ideal model delta sigma weight residual 1.463 1.495 -0.032 1.14e-02 7.69e+03 8.03e+00 bond pdb=" N ASP B 137 " pdb=" CA ASP B 137 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.79e+00 bond pdb=" N LEU B 242 " pdb=" CA LEU B 242 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.16e-02 7.43e+03 6.65e+00 ... (remaining 6373 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.19: 165 106.19 - 113.20: 3599 113.20 - 120.22: 2339 120.22 - 127.23: 2526 127.23 - 134.25: 75 Bond angle restraints: 8704 Sorted by residual: angle pdb=" N PRO A 421 " pdb=" CA PRO A 421 " pdb=" C PRO A 421 " ideal model delta sigma weight residual 110.70 116.89 -6.19 1.22e+00 6.72e-01 2.57e+01 angle pdb=" CA PRO B 421 " pdb=" C PRO B 421 " pdb=" N PRO B 422 " ideal model delta sigma weight residual 117.93 123.81 -5.88 1.20e+00 6.94e-01 2.40e+01 angle pdb=" CA PRO A 421 " pdb=" C PRO A 421 " pdb=" N PRO A 422 " ideal model delta sigma weight residual 117.93 123.57 -5.64 1.20e+00 6.94e-01 2.21e+01 angle pdb=" O PRO B 421 " pdb=" C PRO B 421 " pdb=" N PRO B 422 " ideal model delta sigma weight residual 121.46 116.44 5.02 1.18e+00 7.18e-01 1.81e+01 angle pdb=" CA ASP B 137 " pdb=" CB ASP B 137 " pdb=" CG ASP B 137 " ideal model delta sigma weight residual 112.60 116.68 -4.08 1.00e+00 1.00e+00 1.67e+01 ... (remaining 8699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.06: 3516 21.06 - 42.12: 296 42.12 - 63.18: 58 63.18 - 84.24: 15 84.24 - 105.30: 15 Dihedral angle restraints: 3900 sinusoidal: 1590 harmonic: 2310 Sorted by residual: dihedral pdb=" CB CYS B 303 " pdb=" SG CYS B 303 " pdb=" SG CYS B 370 " pdb=" CB CYS B 370 " ideal model delta sinusoidal sigma weight residual 93.00 9.23 83.77 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CA ASP B 279 " pdb=" C ASP B 279 " pdb=" N PRO B 280 " pdb=" CA PRO B 280 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" C2 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" C4 NAG C 2 " pdb=" O4 NAG C 2 " ideal model delta sinusoidal sigma weight residual 175.11 69.81 105.30 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 3897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 930 0.061 - 0.122: 131 0.122 - 0.182: 8 0.182 - 0.243: 2 0.243 - 0.304: 1 Chirality restraints: 1072 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.39e+02 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 130 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 130 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1069 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.295 2.00e-02 2.50e+03 2.56e-01 8.19e+02 pdb=" C7 NAG D 2 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.454 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.266 2.00e-02 2.50e+03 2.21e-01 6.13e+02 pdb=" C7 NAG D 1 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.368 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 130 " -0.025 2.00e-02 2.50e+03 2.36e-02 6.95e+00 pdb=" CG ASN A 130 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 130 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 130 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.022 2.00e-02 2.50e+03 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1361 2.79 - 3.32: 6914 3.32 - 3.85: 10669 3.85 - 4.37: 11531 4.37 - 4.90: 19376 Nonbonded interactions: 49851 Sorted by model distance: nonbonded pdb=" O GLU B 154 " pdb=" OG1 THR B 157 " model vdw 2.264 2.440 nonbonded pdb=" O GLU A 154 " pdb=" OG1 THR A 157 " model vdw 2.274 2.440 nonbonded pdb=" O VAL A 90 " pdb=" OG SER A 93 " model vdw 2.286 2.440 nonbonded pdb=" O3 NAG C 1 " pdb=" O7 NAG C 2 " model vdw 2.330 2.440 nonbonded pdb=" OD1 ASN A 205 " pdb=" N VAL A 206 " model vdw 2.344 2.520 ... (remaining 49846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.610 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: 2.620 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.970 Find NCS groups from input model: 0.350 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 0.051 6378 Z= 0.262 Angle : 0.725 7.505 8704 Z= 0.405 Chirality : 0.043 0.304 1072 Planarity : 0.011 0.256 1086 Dihedral : 17.475 105.301 2392 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.60 % Allowed : 1.51 % Favored : 97.89 % 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: 2.65 (0.31), residues: 790 helix: 2.36 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.51 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 258 HIS 0.004 0.001 HIS B 128 PHE 0.029 0.002 PHE B 208 TYR 0.026 0.002 TYR A 299 ARG 0.004 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 239 time to evaluate : 0.703 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 241 average time/residue: 0.1458 time to fit residues: 48.1581 Evaluate side-chains 203 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1873 time to fit residues: 1.3342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6378 Z= 0.240 Angle : 0.712 9.691 8704 Z= 0.329 Chirality : 0.044 0.223 1072 Planarity : 0.005 0.067 1086 Dihedral : 9.818 70.095 1018 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.72 % Allowed : 16.01 % Favored : 81.27 % 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: 3.01 (0.30), residues: 790 helix: 2.59 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.51 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 258 HIS 0.005 0.001 HIS B 17 PHE 0.032 0.002 PHE A 208 TYR 0.019 0.002 TYR A 377 ARG 0.002 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 0.752 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 220 average time/residue: 0.1479 time to fit residues: 44.8469 Evaluate side-chains 214 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0632 time to fit residues: 2.4669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 HIS B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6378 Z= 0.219 Angle : 0.685 10.258 8704 Z= 0.313 Chirality : 0.040 0.182 1072 Planarity : 0.005 0.061 1086 Dihedral : 7.791 57.410 1018 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.06 % Allowed : 19.34 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.22 (0.30), residues: 790 helix: 2.74 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.51 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 258 HIS 0.006 0.001 HIS B 326 PHE 0.035 0.002 PHE B 208 TYR 0.026 0.002 TYR A 299 ARG 0.002 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 207 time to evaluate : 0.714 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 211 average time/residue: 0.1491 time to fit residues: 43.0536 Evaluate side-chains 199 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0592 time to fit residues: 1.2474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6378 Z= 0.247 Angle : 0.715 10.478 8704 Z= 0.327 Chirality : 0.041 0.202 1072 Planarity : 0.005 0.057 1086 Dihedral : 6.959 55.980 1018 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.02 % Allowed : 21.45 % Favored : 75.53 % 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: 3.17 (0.30), residues: 790 helix: 2.73 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.61 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 258 HIS 0.006 0.001 HIS B 326 PHE 0.028 0.002 PHE B 208 TYR 0.027 0.002 TYR A 299 ARG 0.002 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 0.639 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 216 average time/residue: 0.1512 time to fit residues: 44.4026 Evaluate side-chains 208 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 194 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0835 time to fit residues: 2.7845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6378 Z= 0.206 Angle : 0.708 12.230 8704 Z= 0.321 Chirality : 0.040 0.161 1072 Planarity : 0.005 0.051 1086 Dihedral : 6.572 55.606 1018 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.81 % Allowed : 22.96 % Favored : 75.23 % 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: 3.23 (0.30), residues: 790 helix: 2.79 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.67 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 258 HIS 0.010 0.001 HIS B 138 PHE 0.028 0.002 PHE B 208 TYR 0.027 0.002 TYR A 299 ARG 0.006 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 206 time to evaluate : 0.739 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 211 average time/residue: 0.1527 time to fit residues: 44.3620 Evaluate side-chains 205 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 197 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0611 time to fit residues: 1.8946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6378 Z= 0.217 Angle : 0.735 13.050 8704 Z= 0.335 Chirality : 0.041 0.212 1072 Planarity : 0.005 0.050 1086 Dihedral : 6.447 55.510 1018 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.21 % Allowed : 25.68 % Favored : 73.11 % 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: 3.15 (0.30), residues: 790 helix: 2.70 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.51 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 258 HIS 0.006 0.001 HIS B 326 PHE 0.016 0.001 PHE B 208 TYR 0.027 0.002 TYR A 299 ARG 0.005 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 200 time to evaluate : 0.704 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 202 average time/residue: 0.1475 time to fit residues: 41.1569 Evaluate side-chains 194 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1310 time to fit residues: 1.7060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6378 Z= 0.218 Angle : 0.736 13.456 8704 Z= 0.335 Chirality : 0.041 0.304 1072 Planarity : 0.004 0.049 1086 Dihedral : 6.374 55.193 1018 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.51 % Allowed : 26.89 % Favored : 71.60 % 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: 3.20 (0.30), residues: 790 helix: 2.71 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.39 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 258 HIS 0.005 0.001 HIS B 326 PHE 0.018 0.001 PHE B 208 TYR 0.025 0.002 TYR A 299 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 200 time to evaluate : 0.684 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 203 average time/residue: 0.1546 time to fit residues: 43.0395 Evaluate side-chains 201 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 194 time to evaluate : 0.747 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1053 time to fit residues: 2.0422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6378 Z= 0.250 Angle : 0.777 12.983 8704 Z= 0.356 Chirality : 0.043 0.256 1072 Planarity : 0.005 0.052 1086 Dihedral : 6.450 54.992 1018 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.21 % Allowed : 27.19 % Favored : 71.60 % 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: 3.11 (0.30), residues: 790 helix: 2.63 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.29 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 258 HIS 0.005 0.001 HIS B 326 PHE 0.019 0.002 PHE B 208 TYR 0.027 0.002 TYR A 299 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 200 time to evaluate : 0.731 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 204 average time/residue: 0.1519 time to fit residues: 42.5905 Evaluate side-chains 203 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 196 time to evaluate : 0.705 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0592 time to fit residues: 1.7138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 6378 Z= 0.235 Angle : 0.776 14.142 8704 Z= 0.355 Chirality : 0.043 0.273 1072 Planarity : 0.005 0.051 1086 Dihedral : 6.453 55.322 1018 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.76 % Allowed : 27.49 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.30), residues: 790 helix: 2.62 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.33 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 258 HIS 0.005 0.001 HIS B 326 PHE 0.018 0.001 PHE B 208 TYR 0.017 0.002 TYR A 299 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 198 time to evaluate : 0.736 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 199 average time/residue: 0.1463 time to fit residues: 40.1213 Evaluate side-chains 197 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 193 time to evaluate : 0.632 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1330 time to fit residues: 1.6365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 0.0570 chunk 6 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 6378 Z= 0.231 Angle : 0.791 14.202 8704 Z= 0.360 Chirality : 0.044 0.294 1072 Planarity : 0.005 0.055 1086 Dihedral : 6.428 56.156 1018 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 27.79 % Favored : 72.21 % 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: 3.02 (0.30), residues: 790 helix: 2.56 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.42 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 12 HIS 0.005 0.001 HIS B 326 PHE 0.017 0.001 PHE B 208 TYR 0.016 0.002 TYR A 377 ARG 0.003 0.000 ARG A 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 0.699 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1467 time to fit residues: 40.1841 Evaluate side-chains 196 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 54 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.0040 chunk 41 optimal weight: 0.0070 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.157968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137502 restraints weight = 9896.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140969 restraints weight = 5908.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143401 restraints weight = 4043.603| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6378 Z= 0.215 Angle : 0.771 14.284 8704 Z= 0.353 Chirality : 0.043 0.274 1072 Planarity : 0.004 0.055 1086 Dihedral : 6.338 59.415 1018 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.30 % Allowed : 28.40 % Favored : 71.30 % 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: 3.10 (0.30), residues: 790 helix: 2.62 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.41 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 258 HIS 0.005 0.001 HIS B 326 PHE 0.017 0.001 PHE B 24 TYR 0.015 0.001 TYR A 377 ARG 0.003 0.000 ARG A 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1519.35 seconds wall clock time: 28 minutes 13.14 seconds (1693.14 seconds total)