Starting phenix.real_space_refine on Tue Mar 11 15:34:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p5c_13198/03_2025/7p5c_13198.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p5c_13198/03_2025/7p5c_13198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p5c_13198/03_2025/7p5c_13198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p5c_13198/03_2025/7p5c_13198.map" model { file = "/net/cci-nas-00/data/ceres_data/7p5c_13198/03_2025/7p5c_13198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p5c_13198/03_2025/7p5c_13198.cif" } resolution = 3.2 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= 0.006 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 26 5.16 5 C 4038 2.51 5 N 1012 2.21 5 O 1146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6222 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3055 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 14, 'TRANS': 377} Chain breaks: 1 Chain: "B" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3055 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 14, 'TRANS': 377} 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: 4.63, per 1000 atoms: 0.74 Number of scatterers: 6222 At special positions: 0 Unit cell: (79.422, 71.61, 127.596, 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 26 16.00 O 1146 8.00 N 1012 7.00 C 4038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 366 " distance=2.04 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 366 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 601 " - " ASN A 144 " " NAG A 602 " - " ASN A 351 " " NAG B 601 " - " ASN B 144 " " NAG B 602 " - " ASN B 351 " " NAG C 1 " - " ASN A 126 " " NAG D 1 " - " ASN B 126 " Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 820.0 milliseconds 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 87.8% 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 9 through 17 removed outlier: 3.579A pdb=" N ARG A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 66 removed outlier: 3.608A pdb=" N ALA A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 158 removed outlier: 4.456A pdb=" N GLU A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 161 through 185 removed outlier: 3.595A pdb=" N ILE A 185 " --> pdb=" O TYR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 234 Processing helix chain 'A' and resid 235 through 273 removed outlier: 4.042A pdb=" N ASP A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.784A pdb=" N TYR A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 307 through 336 removed outlier: 3.521A pdb=" N THR A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 339 through 364 removed outlier: 4.286A pdb=" N GLY A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 409 removed outlier: 4.283A pdb=" N LEU A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'B' and resid 9 through 17 removed outlier: 3.572A pdb=" N ARG B 17 " --> pdb=" O SER B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 66 removed outlier: 3.583A pdb=" N ALA B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 145 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 161 through 184 Processing helix chain 'B' and resid 194 through 233 Processing helix chain 'B' and resid 235 through 273 removed outlier: 3.547A pdb=" N PHE B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.879A pdb=" N TYR B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 283 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 307 through 330 Processing helix chain 'B' and resid 331 through 336 removed outlier: 4.284A pdb=" N GLU B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 364 Processing helix chain 'B' and resid 365 through 383 removed outlier: 4.179A pdb=" N LEU B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 407 removed outlier: 3.677A pdb=" N ALA B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 removed outlier: 3.684A pdb=" N TRP B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1638 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: 1.83 Time building geometry restraints manager: 1.96 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: 1950 1.34 - 1.46: 1139 1.46 - 1.58: 3249 1.58 - 1.70: 0 1.70 - 1.81: 32 Bond restraints: 6370 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.72e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 6365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 8572 1.99 - 3.98: 111 3.98 - 5.96: 26 5.96 - 7.95: 5 7.95 - 9.94: 2 Bond angle restraints: 8716 Sorted by residual: angle pdb=" C PHE B 21 " pdb=" N ASP B 22 " pdb=" CA ASP B 22 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" CA LEU A 250 " pdb=" CB LEU A 250 " pdb=" CG LEU A 250 " ideal model delta sigma weight residual 116.30 126.24 -9.94 3.50e+00 8.16e-02 8.06e+00 angle pdb=" N VAL A 332 " pdb=" CA VAL A 332 " pdb=" C VAL A 332 " ideal model delta sigma weight residual 108.88 114.50 -5.62 2.16e+00 2.14e-01 6.78e+00 angle pdb=" N ASP B 22 " pdb=" CA ASP B 22 " pdb=" CB ASP B 22 " ideal model delta sigma weight residual 110.49 114.74 -4.25 1.69e+00 3.50e-01 6.33e+00 angle pdb=" N VAL B 332 " pdb=" CA VAL B 332 " pdb=" C VAL B 332 " ideal model delta sigma weight residual 108.88 114.25 -5.37 2.16e+00 2.14e-01 6.18e+00 ... (remaining 8711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3364 17.69 - 35.37: 358 35.37 - 53.06: 58 53.06 - 70.75: 19 70.75 - 88.44: 3 Dihedral angle restraints: 3802 sinusoidal: 1526 harmonic: 2276 Sorted by residual: dihedral pdb=" CA GLY A 352 " pdb=" C GLY A 352 " pdb=" N THR A 353 " pdb=" CA THR A 353 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA HIS B 145 " pdb=" C HIS B 145 " pdb=" N THR B 146 " pdb=" CA THR B 146 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CB GLU A 335 " pdb=" CG GLU A 335 " pdb=" CD GLU A 335 " pdb=" OE1 GLU A 335 " ideal model delta sinusoidal sigma weight residual 0.00 88.44 -88.44 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 976 0.070 - 0.140: 76 0.140 - 0.209: 0 0.209 - 0.279: 1 0.279 - 0.349: 1 Chirality restraints: 1054 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 126 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 126 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CG LEU A 293 " pdb=" CB LEU A 293 " pdb=" CD1 LEU A 293 " pdb=" CD2 LEU A 293 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1051 not shown) Planarity restraints: 1078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 381 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C CYS A 381 " 0.028 2.00e-02 2.50e+03 pdb=" O CYS A 381 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR A 382 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 352 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C GLY A 352 " 0.028 2.00e-02 2.50e+03 pdb=" O GLY A 352 " -0.010 2.00e-02 2.50e+03 pdb=" N THR A 353 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 380 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C PHE A 380 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE A 380 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS A 381 " -0.008 2.00e-02 2.50e+03 ... (remaining 1075 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1033 2.76 - 3.29: 6302 3.29 - 3.83: 10690 3.83 - 4.36: 12122 4.36 - 4.90: 21329 Nonbonded interactions: 51476 Sorted by model distance: nonbonded pdb=" O VAL A 12 " pdb=" OG SER A 268 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASN A 126 " pdb=" N2 NAG C 1 " model vdw 2.228 3.120 nonbonded pdb=" OD1 ASP B 275 " pdb=" OH TYR B 373 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP A 275 " pdb=" OH TYR A 373 " model vdw 2.261 3.040 nonbonded pdb=" O VAL B 12 " pdb=" OG SER B 268 " model vdw 2.291 3.040 ... (remaining 51471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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 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: 0.490 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.800 Find NCS groups from input model: 0.210 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 0.038 6370 Z= 0.280 Angle : 0.604 9.939 8716 Z= 0.285 Chirality : 0.041 0.349 1054 Planarity : 0.003 0.026 1072 Dihedral : 14.521 88.436 2326 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.41 (0.29), residues: 776 helix: 1.91 (0.20), residues: 646 sheet: None (None), residues: 0 loop : 0.16 (0.56), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 10 HIS 0.003 0.001 HIS A 20 PHE 0.007 0.001 PHE A 394 TYR 0.010 0.001 TYR A 390 ARG 0.006 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 106 TYR cc_start: 0.8214 (t80) cc_final: 0.7807 (t80) REVERT: B 229 VAL cc_start: 0.8989 (t) cc_final: 0.8759 (t) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1861 time to fit residues: 25.2806 Evaluate side-chains 90 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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: 0.9980 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.127200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.105198 restraints weight = 6903.976| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.51 r_work: 0.2960 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6370 Z= 0.254 Angle : 0.597 9.119 8716 Z= 0.292 Chirality : 0.039 0.221 1054 Planarity : 0.004 0.036 1072 Dihedral : 5.486 51.135 1014 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.07 % Allowed : 6.10 % Favored : 92.84 % 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: 3.27 (0.29), residues: 776 helix: 2.57 (0.19), residues: 650 sheet: None (None), residues: 0 loop : -0.04 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 10 HIS 0.002 0.001 HIS A 116 PHE 0.007 0.001 PHE A 394 TYR 0.008 0.001 TYR A 120 ARG 0.005 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 106 TYR cc_start: 0.8276 (t80) cc_final: 0.8040 (t80) outliers start: 7 outliers final: 4 residues processed: 107 average time/residue: 0.1825 time to fit residues: 25.9353 Evaluate side-chains 103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 0.0570 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.130876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.108603 restraints weight = 6895.385| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.53 r_work: 0.3004 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6370 Z= 0.151 Angle : 0.514 8.637 8716 Z= 0.252 Chirality : 0.036 0.264 1054 Planarity : 0.003 0.034 1072 Dihedral : 4.636 44.454 1014 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.22 % Allowed : 9.45 % Favored : 89.33 % 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: 3.86 (0.28), residues: 776 helix: 2.98 (0.19), residues: 652 sheet: None (None), residues: 0 loop : 0.03 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 11 HIS 0.002 0.000 HIS B 145 PHE 0.004 0.001 PHE A 394 TYR 0.025 0.001 TYR B 120 ARG 0.003 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.670 Fit side-chains REVERT: A 56 LEU cc_start: 0.7769 (tt) cc_final: 0.7460 (tp) REVERT: B 22 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7831 (p0) REVERT: B 127 ARG cc_start: 0.6694 (mmt180) cc_final: 0.6387 (mmt-90) REVERT: B 344 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8459 (mm) outliers start: 8 outliers final: 3 residues processed: 110 average time/residue: 0.1901 time to fit residues: 27.4049 Evaluate side-chains 108 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.130165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.107878 restraints weight = 6898.970| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.52 r_work: 0.2994 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6370 Z= 0.190 Angle : 0.521 9.119 8716 Z= 0.254 Chirality : 0.036 0.248 1054 Planarity : 0.003 0.034 1072 Dihedral : 4.399 39.057 1014 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.52 % Allowed : 10.82 % Favored : 87.65 % 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: 3.99 (0.28), residues: 776 helix: 3.08 (0.18), residues: 650 sheet: None (None), residues: 0 loop : 0.08 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 10 HIS 0.003 0.001 HIS A 370 PHE 0.006 0.001 PHE B 394 TYR 0.018 0.001 TYR B 120 ARG 0.004 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.668 Fit side-chains REVERT: A 35 GLU cc_start: 0.7797 (pm20) cc_final: 0.7576 (pm20) REVERT: A 56 LEU cc_start: 0.8093 (tt) cc_final: 0.7830 (tp) REVERT: B 22 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7908 (p0) REVERT: B 35 GLU cc_start: 0.7690 (tt0) cc_final: 0.7367 (tt0) REVERT: B 127 ARG cc_start: 0.6772 (mmt180) cc_final: 0.6428 (mmt-90) REVERT: B 344 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8543 (mm) outliers start: 10 outliers final: 6 residues processed: 106 average time/residue: 0.2132 time to fit residues: 28.9700 Evaluate side-chains 109 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.127748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.105502 restraints weight = 6978.841| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.52 r_work: 0.2959 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6370 Z= 0.251 Angle : 0.544 8.253 8716 Z= 0.264 Chirality : 0.037 0.222 1054 Planarity : 0.003 0.037 1072 Dihedral : 4.318 33.868 1014 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.29 % Allowed : 11.74 % Favored : 85.98 % 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: 3.90 (0.28), residues: 776 helix: 2.95 (0.18), residues: 660 sheet: None (None), residues: 0 loop : 0.21 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 10 HIS 0.002 0.001 HIS A 116 PHE 0.009 0.001 PHE B 394 TYR 0.017 0.001 TYR B 120 ARG 0.004 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.669 Fit side-chains REVERT: A 35 GLU cc_start: 0.7822 (pm20) cc_final: 0.7578 (pm20) REVERT: A 56 LEU cc_start: 0.8092 (tt) cc_final: 0.7829 (tp) REVERT: A 95 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6343 (mp) REVERT: B 22 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7996 (p0) REVERT: B 35 GLU cc_start: 0.7849 (tt0) cc_final: 0.7602 (tt0) REVERT: B 344 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8576 (mm) outliers start: 15 outliers final: 11 residues processed: 105 average time/residue: 0.2023 time to fit residues: 27.4434 Evaluate side-chains 109 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.128156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.105821 restraints weight = 6859.421| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.51 r_work: 0.2966 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6370 Z= 0.228 Angle : 0.537 7.982 8716 Z= 0.262 Chirality : 0.037 0.215 1054 Planarity : 0.003 0.036 1072 Dihedral : 4.179 27.851 1014 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.13 % Allowed : 12.50 % Favored : 85.37 % 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: 3.95 (0.28), residues: 776 helix: 2.99 (0.18), residues: 660 sheet: None (None), residues: 0 loop : 0.20 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 10 HIS 0.003 0.001 HIS B 370 PHE 0.007 0.001 PHE B 394 TYR 0.016 0.001 TYR B 120 ARG 0.006 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.616 Fit side-chains REVERT: A 35 GLU cc_start: 0.7867 (pm20) cc_final: 0.7596 (pm20) REVERT: A 56 LEU cc_start: 0.8094 (tt) cc_final: 0.7832 (tp) REVERT: A 95 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6339 (mp) REVERT: B 22 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7983 (p0) REVERT: B 127 ARG cc_start: 0.6820 (mmt180) cc_final: 0.6492 (mmt-90) REVERT: B 344 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8575 (mm) outliers start: 14 outliers final: 9 residues processed: 100 average time/residue: 0.2273 time to fit residues: 28.8794 Evaluate side-chains 103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 55 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.128415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.106011 restraints weight = 6852.225| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.52 r_work: 0.2967 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6370 Z= 0.216 Angle : 0.525 7.689 8716 Z= 0.256 Chirality : 0.036 0.204 1054 Planarity : 0.003 0.037 1072 Dihedral : 4.033 22.807 1014 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.29 % Allowed : 13.87 % Favored : 83.84 % 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: 4.01 (0.28), residues: 776 helix: 3.01 (0.18), residues: 662 sheet: None (None), residues: 0 loop : 0.24 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 10 HIS 0.002 0.001 HIS B 20 PHE 0.007 0.001 PHE B 394 TYR 0.016 0.001 TYR B 120 ARG 0.007 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.644 Fit side-chains REVERT: A 35 GLU cc_start: 0.7849 (pm20) cc_final: 0.7381 (pm20) REVERT: A 56 LEU cc_start: 0.8143 (tt) cc_final: 0.7842 (tp) REVERT: A 95 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6291 (mp) REVERT: B 22 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7986 (p0) REVERT: B 127 ARG cc_start: 0.6860 (mmt180) cc_final: 0.6515 (mmt-90) REVERT: B 152 GLN cc_start: 0.7540 (mt0) cc_final: 0.7222 (mm-40) REVERT: B 344 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8560 (mm) REVERT: B 372 ASP cc_start: 0.7935 (m-30) cc_final: 0.7534 (m-30) outliers start: 15 outliers final: 9 residues processed: 104 average time/residue: 0.2180 time to fit residues: 29.0337 Evaluate side-chains 104 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.127035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.104667 restraints weight = 6848.833| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.52 r_work: 0.2952 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6370 Z= 0.268 Angle : 0.551 7.585 8716 Z= 0.268 Chirality : 0.037 0.184 1054 Planarity : 0.003 0.037 1072 Dihedral : 4.111 23.411 1014 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.29 % Allowed : 14.48 % Favored : 83.23 % 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: 3.87 (0.28), residues: 776 helix: 2.91 (0.18), residues: 662 sheet: None (None), residues: 0 loop : 0.28 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 10 HIS 0.002 0.001 HIS B 20 PHE 0.010 0.001 PHE B 394 TYR 0.015 0.001 TYR B 120 ARG 0.005 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.635 Fit side-chains REVERT: A 35 GLU cc_start: 0.7849 (pm20) cc_final: 0.7383 (pm20) REVERT: A 56 LEU cc_start: 0.8141 (tt) cc_final: 0.7839 (tp) REVERT: A 95 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6333 (mp) REVERT: B 127 ARG cc_start: 0.6787 (mmt180) cc_final: 0.6462 (mmt-90) REVERT: B 152 GLN cc_start: 0.7591 (mt0) cc_final: 0.7230 (mm-40) REVERT: B 344 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8569 (mm) outliers start: 15 outliers final: 10 residues processed: 101 average time/residue: 0.2102 time to fit residues: 27.4023 Evaluate side-chains 103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 12 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.128730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.106261 restraints weight = 6933.219| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.54 r_work: 0.2972 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6370 Z= 0.179 Angle : 0.534 10.412 8716 Z= 0.259 Chirality : 0.036 0.201 1054 Planarity : 0.003 0.037 1072 Dihedral : 3.939 22.968 1014 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.13 % Allowed : 14.94 % Favored : 82.93 % 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: 4.05 (0.28), residues: 776 helix: 3.05 (0.18), residues: 662 sheet: None (None), residues: 0 loop : 0.22 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 10 HIS 0.002 0.001 HIS B 20 PHE 0.005 0.001 PHE A 307 TYR 0.016 0.001 TYR B 120 ARG 0.005 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.712 Fit side-chains REVERT: A 35 GLU cc_start: 0.7804 (pm20) cc_final: 0.7339 (pm20) REVERT: A 56 LEU cc_start: 0.8107 (tt) cc_final: 0.7800 (tp) REVERT: A 95 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6224 (mp) REVERT: A 372 ASP cc_start: 0.7553 (m-30) cc_final: 0.7341 (m-30) REVERT: B 127 ARG cc_start: 0.6775 (mmt180) cc_final: 0.6437 (mmt-90) REVERT: B 152 GLN cc_start: 0.7557 (mt0) cc_final: 0.7204 (mm-40) REVERT: B 330 ARG cc_start: 0.7759 (ptm-80) cc_final: 0.7385 (ptp90) REVERT: B 344 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8526 (mm) REVERT: B 372 ASP cc_start: 0.7855 (m-30) cc_final: 0.7460 (m-30) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.2340 time to fit residues: 30.2729 Evaluate side-chains 107 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 0.0170 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.129041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.106689 restraints weight = 6963.929| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.53 r_work: 0.2991 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6370 Z= 0.182 Angle : 0.528 10.366 8716 Z= 0.256 Chirality : 0.036 0.198 1054 Planarity : 0.003 0.037 1072 Dihedral : 3.884 22.704 1014 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.98 % Allowed : 15.70 % Favored : 82.32 % 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: 4.11 (0.28), residues: 776 helix: 3.10 (0.18), residues: 660 sheet: None (None), residues: 0 loop : 0.21 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 67 HIS 0.002 0.001 HIS B 370 PHE 0.005 0.001 PHE B 394 TYR 0.015 0.001 TYR B 120 ARG 0.006 0.000 ARG A 330 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.602 Fit side-chains REVERT: A 35 GLU cc_start: 0.7777 (pm20) cc_final: 0.7342 (pm20) REVERT: A 56 LEU cc_start: 0.8150 (tt) cc_final: 0.7848 (tp) REVERT: A 95 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6291 (mp) REVERT: B 127 ARG cc_start: 0.6858 (mmt180) cc_final: 0.6513 (mmt-90) REVERT: B 330 ARG cc_start: 0.7770 (ptm-80) cc_final: 0.7413 (ptp90) REVERT: B 344 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8541 (mm) outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.2326 time to fit residues: 29.6880 Evaluate side-chains 103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.129429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.106580 restraints weight = 7009.707| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.58 r_work: 0.2971 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6370 Z= 0.194 Angle : 0.528 10.296 8716 Z= 0.255 Chirality : 0.036 0.193 1054 Planarity : 0.003 0.037 1072 Dihedral : 3.869 22.707 1014 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.83 % Allowed : 15.85 % Favored : 82.32 % 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: 4.11 (0.28), residues: 776 helix: 3.10 (0.18), residues: 660 sheet: None (None), residues: 0 loop : 0.20 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 67 HIS 0.002 0.001 HIS B 20 PHE 0.006 0.001 PHE B 394 TYR 0.015 0.001 TYR B 120 ARG 0.006 0.000 ARG A 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3153.57 seconds wall clock time: 54 minutes 44.65 seconds (3284.65 seconds total)