Starting phenix.real_space_refine on Thu Mar 6 03:57:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zsb_60410/03_2025/8zsb_60410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zsb_60410/03_2025/8zsb_60410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zsb_60410/03_2025/8zsb_60410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zsb_60410/03_2025/8zsb_60410.map" model { file = "/net/cci-nas-00/data/ceres_data/8zsb_60410/03_2025/8zsb_60410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zsb_60410/03_2025/8zsb_60410.cif" } resolution = 3.26 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= -0.003 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 42 5.16 5 C 3114 2.51 5 N 810 2.21 5 O 830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4798 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2398 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2390 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 307, 2390 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2431 Chain: "B" Number of atoms: 2398 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2390 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 307, 2390 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2431 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.40, per 1000 atoms: 1.13 Number of scatterers: 4798 At special positions: 0 Unit cell: (61.959, 66.307, 119.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 42 16.00 O 830 8.00 N 810 7.00 C 3114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 311 " 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 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 370 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 387 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 387 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 370 " 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1156 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 69.2% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 Processing helix chain 'A' and resid 35 through 61 Processing helix chain 'A' and resid 74 through 106 removed outlier: 3.594A pdb=" N GLU A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 134 Processing helix chain 'A' and resid 239 through 273 removed outlier: 3.645A pdb=" N VAL A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 removed outlier: 4.419A pdb=" N LEU A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A 315 " --> pdb=" O CYS A 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 315' Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.514A pdb=" N THR A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 3.821A pdb=" N ALA A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 342 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 363 removed outlier: 3.811A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 410 removed outlier: 4.389A pdb=" N MET A 397 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLU A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 33 Processing helix chain 'B' and resid 35 through 61 Processing helix chain 'B' and resid 74 through 106 removed outlier: 3.595A pdb=" N GLU B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 239 through 273 removed outlier: 3.689A pdb=" N VAL B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 removed outlier: 4.419A pdb=" N LEU B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR B 315 " --> pdb=" O CYS B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 315' Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.515A pdb=" N THR B 319 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Proline residue: B 334 - end of helix removed outlier: 3.821A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 363 removed outlier: 3.811A pdb=" N LEU B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 410 removed outlier: 4.389A pdb=" N MET B 397 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLU B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 378 removed outlier: 7.065A pdb=" N ARG A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 414 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 420 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 390 " --> pdb=" O GLU A 420 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 369 through 378 removed outlier: 3.890A pdb=" N GLU B 371 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 382 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR B 416 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA B 384 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLN B 418 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA B 386 " --> pdb=" O GLN B 418 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 1018 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: 1.15 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 767 1.27 - 1.41: 1220 1.41 - 1.54: 2841 1.54 - 1.68: 12 1.68 - 1.81: 62 Bond restraints: 4902 Sorted by residual: bond pdb=" CA LEU B 372 " pdb=" C LEU B 372 " ideal model delta sigma weight residual 1.520 1.417 0.104 1.21e-02 6.83e+03 7.37e+01 bond pdb=" CA ARG A 59 " pdb=" C ARG A 59 " ideal model delta sigma weight residual 1.524 1.419 0.105 1.24e-02 6.50e+03 7.15e+01 bond pdb=" CA ASN B 244 " pdb=" C ASN B 244 " ideal model delta sigma weight residual 1.524 1.417 0.107 1.29e-02 6.01e+03 6.87e+01 bond pdb=" C LEU B 243 " pdb=" O LEU B 243 " ideal model delta sigma weight residual 1.237 1.140 0.096 1.17e-02 7.31e+03 6.78e+01 bond pdb=" CA ALA B 95 " pdb=" CB ALA B 95 " ideal model delta sigma weight residual 1.528 1.399 0.130 1.59e-02 3.96e+03 6.65e+01 ... (remaining 4897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.74: 6581 4.74 - 9.47: 73 9.47 - 14.21: 11 14.21 - 18.95: 0 18.95 - 23.68: 1 Bond angle restraints: 6666 Sorted by residual: angle pdb=" N HIS A 65 " pdb=" CA HIS A 65 " pdb=" C HIS A 65 " ideal model delta sigma weight residual 112.24 135.92 -23.68 1.28e+00 6.10e-01 3.42e+02 angle pdb=" O PHE B 94 " pdb=" C PHE B 94 " pdb=" CA BPHE B 94 " ideal model delta sigma weight residual 120.55 130.78 -10.23 1.06e+00 8.90e-01 9.31e+01 angle pdb=" O PHE A 94 " pdb=" C PHE A 94 " pdb=" CA BPHE A 94 " ideal model delta sigma weight residual 120.55 130.49 -9.94 1.06e+00 8.90e-01 8.79e+01 angle pdb=" N GLY B 241 " pdb=" CA GLY B 241 " pdb=" C GLY B 241 " ideal model delta sigma weight residual 112.73 101.66 11.07 1.20e+00 6.94e-01 8.51e+01 angle pdb=" O PHE B 94 " pdb=" C PHE B 94 " pdb=" N ALA B 95 " ideal model delta sigma weight residual 122.12 112.72 9.40 1.06e+00 8.90e-01 7.87e+01 ... (remaining 6661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 2508 15.48 - 30.97: 291 30.97 - 46.45: 83 46.45 - 61.94: 19 61.94 - 77.42: 6 Dihedral angle restraints: 2907 sinusoidal: 1127 harmonic: 1780 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS B 291 " pdb=" CB CYS B 291 " ideal model delta sinusoidal sigma weight residual 93.00 170.42 -77.42 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" C HIS A 387 " pdb=" N HIS A 387 " pdb=" CA HIS A 387 " pdb=" CB HIS A 387 " ideal model delta harmonic sigma weight residual -122.60 -104.39 -18.21 0 2.50e+00 1.60e-01 5.31e+01 dihedral pdb=" C HIS B 387 " pdb=" N HIS B 387 " pdb=" CA HIS B 387 " pdb=" CB HIS B 387 " ideal model delta harmonic sigma weight residual -122.60 -104.80 -17.80 0 2.50e+00 1.60e-01 5.07e+01 ... (remaining 2904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 764 0.131 - 0.262: 24 0.262 - 0.392: 7 0.392 - 0.523: 1 0.523 - 0.654: 2 Chirality restraints: 798 Sorted by residual: chirality pdb=" CA HIS A 65 " pdb=" N HIS A 65 " pdb=" C HIS A 65 " pdb=" CB HIS A 65 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA HIS B 370 " pdb=" N HIS B 370 " pdb=" C HIS B 370 " pdb=" CB HIS B 370 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.50e+00 chirality pdb=" CA HIS A 370 " pdb=" N HIS A 370 " pdb=" C HIS A 370 " pdb=" CB HIS A 370 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.76e+00 ... (remaining 795 not shown) Planarity restraints: 832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 387 " -0.062 2.00e-02 2.50e+03 5.64e-02 4.78e+01 pdb=" CG HIS A 387 " 0.063 2.00e-02 2.50e+03 pdb=" ND1 HIS A 387 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS A 387 " 0.062 2.00e-02 2.50e+03 pdb=" CE1 HIS A 387 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS A 387 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 387 " -0.049 2.00e-02 2.50e+03 5.21e-02 4.07e+01 pdb=" CG HIS B 387 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS B 387 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 387 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 HIS B 387 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS B 387 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 67 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C THR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" O THR A 67 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 68 " -0.018 2.00e-02 2.50e+03 ... (remaining 829 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 26 2.50 - 3.10: 3658 3.10 - 3.70: 7314 3.70 - 4.30: 10445 4.30 - 4.90: 17076 Nonbonded interactions: 38519 Sorted by model distance: nonbonded pdb=" OE2 GLU B 420 " pdb="ZN ZN B 601 " model vdw 1.897 2.230 nonbonded pdb=" OE2 GLU A 420 " pdb="ZN ZN A 601 " model vdw 2.000 2.230 nonbonded pdb=" O HIS A 43 " pdb=" OG SER A 46 " model vdw 2.231 3.040 nonbonded pdb=" O HIS B 43 " pdb=" OG SER B 46 " model vdw 2.231 3.040 nonbonded pdb=" O ARG A 239 " pdb=" N GLN A 242 " model vdw 2.392 3.120 ... (remaining 38514 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 93 or resid 95 through 422 or resid 601)) selection = (chain 'B' and (resid 5 through 93 or resid 95 through 422 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.460 Find NCS groups from input model: 0.190 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 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 : 0.012 0.130 4902 Z= 0.800 Angle : 1.176 23.685 6666 Z= 0.825 Chirality : 0.072 0.654 798 Planarity : 0.007 0.062 832 Dihedral : 14.721 69.860 1736 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.28 % Allowed : 2.09 % Favored : 95.63 % Cbeta Deviations : 1.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.35), residues: 604 helix: 1.39 (0.25), residues: 404 sheet: 0.02 (0.81), residues: 38 loop : -0.66 (0.56), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 273 HIS 0.058 0.004 HIS B 387 PHE 0.019 0.002 PHE A 19 TYR 0.006 0.001 TYR B 396 ARG 0.005 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.520 Fit side-chains REVERT: A 37 MET cc_start: 0.6679 (mmm) cc_final: 0.5897 (mmt) REVERT: A 58 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 352 ASP cc_start: 0.8259 (p0) cc_final: 0.8058 (p0) REVERT: A 355 ASN cc_start: 0.8698 (m-40) cc_final: 0.8495 (m-40) REVERT: A 371 GLU cc_start: 0.8252 (tt0) cc_final: 0.7987 (tt0) REVERT: B 37 MET cc_start: 0.6569 (mmm) cc_final: 0.5797 (mmt) REVERT: B 238 ASP cc_start: 0.5770 (OUTLIER) cc_final: 0.5257 (m-30) outliers start: 10 outliers final: 5 residues processed: 134 average time/residue: 0.1774 time to fit residues: 29.8827 Evaluate side-chains 119 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 370 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 387 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.195152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147163 restraints weight = 9739.217| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 5.73 r_work: 0.3194 rms_B_bonded: 5.44 restraints_weight: 2.0000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4902 Z= 0.231 Angle : 0.552 6.601 6666 Z= 0.298 Chirality : 0.044 0.141 798 Planarity : 0.004 0.052 832 Dihedral : 5.735 56.577 664 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.52 % Allowed : 7.79 % Favored : 90.68 % 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: 2.14 (0.36), residues: 604 helix: 2.31 (0.25), residues: 410 sheet: -0.14 (0.76), residues: 52 loop : -0.66 (0.62), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.011 0.002 HIS A 370 PHE 0.007 0.001 PHE A 42 TYR 0.008 0.001 TYR A 396 ARG 0.006 0.001 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.547 Fit side-chains REVERT: A 37 MET cc_start: 0.6754 (mmm) cc_final: 0.5885 (mmt) REVERT: A 111 GLN cc_start: 0.8618 (mt0) cc_final: 0.8400 (mm-40) REVERT: A 350 GLN cc_start: 0.8650 (pm20) cc_final: 0.8440 (pm20) REVERT: B 21 PHE cc_start: 0.8151 (t80) cc_final: 0.7947 (t80) REVERT: B 37 MET cc_start: 0.6669 (mmm) cc_final: 0.5704 (mmt) REVERT: B 338 GLU cc_start: 0.8378 (tp30) cc_final: 0.7972 (tt0) REVERT: B 350 GLN cc_start: 0.8608 (pm20) cc_final: 0.8330 (pm20) REVERT: B 368 GLU cc_start: 0.7670 (pt0) cc_final: 0.7226 (pm20) REVERT: B 371 GLU cc_start: 0.8006 (tt0) cc_final: 0.7804 (tt0) outliers start: 6 outliers final: 4 residues processed: 129 average time/residue: 0.1720 time to fit residues: 28.3184 Evaluate side-chains 115 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 370 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.193770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131424 restraints weight = 12705.641| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 4.34 r_work: 0.3207 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4902 Z= 0.230 Angle : 0.548 8.991 6666 Z= 0.290 Chirality : 0.044 0.141 798 Planarity : 0.004 0.047 832 Dihedral : 5.180 51.470 658 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.52 % Allowed : 12.17 % Favored : 86.31 % 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: 2.23 (0.36), residues: 604 helix: 2.43 (0.25), residues: 408 sheet: -0.16 (0.79), residues: 52 loop : -0.73 (0.60), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 375 HIS 0.010 0.001 HIS B 370 PHE 0.007 0.001 PHE A 134 TYR 0.006 0.001 TYR B 396 ARG 0.005 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.539 Fit side-chains REVERT: A 37 MET cc_start: 0.6784 (mmm) cc_final: 0.5929 (mmt) REVERT: A 58 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8376 (tm-30) REVERT: A 359 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7734 (mt-10) REVERT: B 37 MET cc_start: 0.6930 (mmm) cc_final: 0.5991 (mmt) REVERT: B 359 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7577 (mt-10) outliers start: 6 outliers final: 2 residues processed: 122 average time/residue: 0.1470 time to fit residues: 23.4480 Evaluate side-chains 112 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain B residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.196217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147610 restraints weight = 8195.873| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 4.67 r_work: 0.3273 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4902 Z= 0.187 Angle : 0.517 6.155 6666 Z= 0.278 Chirality : 0.042 0.134 798 Planarity : 0.004 0.043 832 Dihedral : 4.336 42.794 654 Min Nonbonded Distance : 1.669 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.14 % Allowed : 13.69 % Favored : 85.17 % 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: 2.33 (0.36), residues: 604 helix: 2.46 (0.26), residues: 412 sheet: -0.14 (0.79), residues: 52 loop : -0.60 (0.60), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 375 HIS 0.007 0.001 HIS A 135 PHE 0.035 0.001 PHE B 21 TYR 0.012 0.001 TYR A 330 ARG 0.005 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.539 Fit side-chains REVERT: A 37 MET cc_start: 0.6750 (mmm) cc_final: 0.5795 (mmt) REVERT: A 58 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8260 (tm-30) REVERT: A 359 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 37 MET cc_start: 0.6789 (mmm) cc_final: 0.5812 (mmt) REVERT: B 75 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6463 (mt) REVERT: B 359 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7597 (mt-10) outliers start: 4 outliers final: 2 residues processed: 124 average time/residue: 0.1574 time to fit residues: 25.0819 Evaluate side-chains 116 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.196410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.136563 restraints weight = 17143.687| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 5.85 r_work: 0.3205 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4902 Z= 0.204 Angle : 0.501 5.370 6666 Z= 0.269 Chirality : 0.042 0.133 798 Planarity : 0.004 0.040 832 Dihedral : 3.921 15.373 652 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.95 % Allowed : 15.40 % Favored : 83.65 % 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: 2.23 (0.36), residues: 604 helix: 2.38 (0.26), residues: 412 sheet: -0.00 (0.79), residues: 50 loop : -0.70 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.008 0.001 HIS B 135 PHE 0.020 0.001 PHE B 21 TYR 0.006 0.001 TYR A 330 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.480 Fit side-chains REVERT: A 37 MET cc_start: 0.6764 (mmm) cc_final: 0.5763 (mmt) REVERT: A 58 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8328 (tm-30) REVERT: A 359 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 368 GLU cc_start: 0.8000 (pt0) cc_final: 0.7498 (pp20) REVERT: B 37 MET cc_start: 0.6781 (mmm) cc_final: 0.5739 (mmt) REVERT: B 58 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8350 (tm-30) outliers start: 3 outliers final: 3 residues processed: 118 average time/residue: 0.1338 time to fit residues: 20.9505 Evaluate side-chains 117 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 0.0370 chunk 58 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.193928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131777 restraints weight = 12850.085| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 4.06 r_work: 0.3287 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4902 Z= 0.182 Angle : 0.487 5.830 6666 Z= 0.262 Chirality : 0.042 0.134 798 Planarity : 0.004 0.039 832 Dihedral : 3.844 14.732 652 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.52 % Allowed : 16.16 % 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: 2.32 (0.36), residues: 604 helix: 2.45 (0.26), residues: 412 sheet: 0.15 (0.81), residues: 50 loop : -0.71 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.008 0.001 HIS B 135 PHE 0.016 0.001 PHE B 21 TYR 0.007 0.001 TYR A 330 ARG 0.004 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.6682 (mmm) cc_final: 0.5704 (mmt) REVERT: A 58 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 359 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7785 (mt-10) REVERT: A 368 GLU cc_start: 0.7910 (pt0) cc_final: 0.7527 (pp20) REVERT: A 369 VAL cc_start: 0.8345 (t) cc_final: 0.7995 (m) REVERT: B 37 MET cc_start: 0.6796 (mmm) cc_final: 0.5749 (mmt) REVERT: B 58 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8132 (tm-30) outliers start: 6 outliers final: 5 residues processed: 122 average time/residue: 0.1398 time to fit residues: 22.5383 Evaluate side-chains 120 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.196684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134845 restraints weight = 15042.587| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 4.71 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4902 Z= 0.195 Angle : 0.482 4.863 6666 Z= 0.261 Chirality : 0.042 0.134 798 Planarity : 0.004 0.038 832 Dihedral : 3.813 13.896 652 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.52 % Allowed : 17.68 % Favored : 80.80 % 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: 2.29 (0.36), residues: 604 helix: 2.40 (0.26), residues: 412 sheet: 0.21 (0.83), residues: 50 loop : -0.70 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.005 0.001 HIS B 135 PHE 0.015 0.001 PHE B 21 TYR 0.006 0.001 TYR A 396 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.6842 (mmm) cc_final: 0.5813 (mmt) REVERT: A 58 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 368 GLU cc_start: 0.7921 (pt0) cc_final: 0.7431 (pp20) REVERT: B 37 MET cc_start: 0.6886 (mmm) cc_final: 0.5863 (mmt) REVERT: B 58 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7587 (tm-30) outliers start: 6 outliers final: 5 residues processed: 122 average time/residue: 0.1443 time to fit residues: 23.0121 Evaluate side-chains 122 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 17 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.193670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.130172 restraints weight = 13229.865| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 4.16 r_work: 0.3289 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4902 Z= 0.190 Angle : 0.492 5.776 6666 Z= 0.265 Chirality : 0.042 0.134 798 Planarity : 0.004 0.036 832 Dihedral : 3.805 13.486 652 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.52 % Allowed : 19.01 % Favored : 79.47 % 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: 2.33 (0.36), residues: 604 helix: 2.40 (0.26), residues: 412 sheet: 0.26 (0.83), residues: 50 loop : -0.58 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.005 0.001 HIS B 135 PHE 0.021 0.001 PHE B 21 TYR 0.005 0.001 TYR A 330 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.6776 (mmm) cc_final: 0.5727 (mmt) REVERT: A 58 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8247 (tm-30) REVERT: A 359 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7957 (mt-10) REVERT: A 368 GLU cc_start: 0.7969 (pt0) cc_final: 0.7605 (pp20) REVERT: B 37 MET cc_start: 0.6768 (mmm) cc_final: 0.5746 (mmt) REVERT: B 58 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8082 (tm-30) outliers start: 6 outliers final: 6 residues processed: 126 average time/residue: 0.1400 time to fit residues: 23.1476 Evaluate side-chains 127 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 259 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 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 = 0.4170 r_free = 0.4170 target = 0.193446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125952 restraints weight = 12717.661| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 4.17 r_work: 0.3201 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4902 Z= 0.288 Angle : 0.549 5.642 6666 Z= 0.301 Chirality : 0.045 0.171 798 Planarity : 0.004 0.042 832 Dihedral : 3.960 15.726 652 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.71 % Allowed : 19.77 % Favored : 78.52 % 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: 2.10 (0.36), residues: 604 helix: 2.23 (0.26), residues: 410 sheet: 0.13 (0.82), residues: 50 loop : -0.61 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 375 HIS 0.005 0.001 HIS B 135 PHE 0.015 0.001 PHE B 21 TYR 0.008 0.001 TYR B 330 ARG 0.003 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8323 (tm-30) REVERT: A 359 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8024 (mt-10) REVERT: B 58 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8203 (tm-30) outliers start: 7 outliers final: 7 residues processed: 119 average time/residue: 0.1427 time to fit residues: 22.3024 Evaluate side-chains 117 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 259 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 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 = 0.4164 r_free = 0.4164 target = 0.192854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133860 restraints weight = 10939.822| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 4.17 r_work: 0.3260 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4902 Z= 0.218 Angle : 0.531 5.315 6666 Z= 0.293 Chirality : 0.044 0.190 798 Planarity : 0.004 0.040 832 Dihedral : 3.965 15.598 652 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.90 % Allowed : 20.15 % Favored : 77.95 % 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: 2.15 (0.36), residues: 604 helix: 2.27 (0.26), residues: 410 sheet: -0.05 (0.80), residues: 50 loop : -0.48 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.009 0.001 HIS A 387 PHE 0.024 0.001 PHE B 21 TYR 0.007 0.001 TYR A 330 ARG 0.003 0.000 ARG A 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8303 (tm-30) REVERT: A 359 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7998 (mt-10) REVERT: B 58 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8139 (tm-30) outliers start: 8 outliers final: 7 residues processed: 116 average time/residue: 0.1580 time to fit residues: 24.3869 Evaluate side-chains 119 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 259 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN ** B 410 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 = 0.4215 r_free = 0.4215 target = 0.197926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132095 restraints weight = 12954.132| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.22 r_work: 0.3275 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4902 Z= 0.201 Angle : 0.512 5.252 6666 Z= 0.282 Chirality : 0.043 0.206 798 Planarity : 0.004 0.049 832 Dihedral : 3.947 18.445 652 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.71 % Allowed : 20.53 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.36), residues: 604 helix: 2.33 (0.26), residues: 412 sheet: -0.21 (0.78), residues: 50 loop : -0.34 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.008 0.001 HIS A 370 PHE 0.020 0.001 PHE B 21 TYR 0.006 0.001 TYR A 330 ARG 0.003 0.000 ARG A 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3296.86 seconds wall clock time: 58 minutes 29.04 seconds (3509.04 seconds total)