Starting phenix.real_space_refine on Thu Nov 14 07:22:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsb_60410/11_2024/8zsb_60410.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsb_60410/11_2024/8zsb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsb_60410/11_2024/8zsb_60410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsb_60410/11_2024/8zsb_60410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsb_60410/11_2024/8zsb_60410.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsb_60410/11_2024/8zsb_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-5513/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: 5.91, per 1000 atoms: 1.23 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: 1.41 Conformation dependent library (CDL) restraints added in 1.3 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: 0.62 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: 1.45 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 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: 0.00 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: 0.480 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.090 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.290 ------------------------------------------------------------------------------- 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 : 0.529 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: 0.1758 time to fit residues: 29.5975 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 : 0.517 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 : 0.606 Fit side-chains REVERT: A 37 MET cc_start: 0.6896 (mmm) cc_final: 0.6135 (mmt) REVERT: B 37 MET cc_start: 0.6782 (mmm) cc_final: 0.5879 (mmt) REVERT: B 337 LYS cc_start: 0.8910 (ttpp) cc_final: 0.8667 (ttpp) REVERT: B 338 GLU cc_start: 0.7532 (tp30) cc_final: 0.7200 (tt0) REVERT: B 368 GLU cc_start: 0.7652 (pt0) cc_final: 0.7260 (pm20) outliers start: 6 outliers final: 4 residues processed: 129 average time/residue: 0.1692 time to fit residues: 27.9831 Evaluate side-chains 114 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 30 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2126 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= 0.231 Angle : 0.551 8.733 6666 Z= 0.293 Chirality : 0.043 0.137 798 Planarity : 0.004 0.047 832 Dihedral : 5.173 51.248 658 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.14 % Allowed : 13.31 % Favored : 85.55 % 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: 2.22 (0.36), residues: 604 helix: 2.44 (0.25), residues: 408 sheet: -0.18 (0.79), residues: 52 loop : -0.77 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 375 HIS 0.010 0.002 HIS B 370 PHE 0.034 0.001 PHE B 21 TYR 0.006 0.001 TYR A 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 123 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.547 Fit side-chains REVERT: A 37 MET cc_start: 0.6891 (mmm) cc_final: 0.6125 (mmt) REVERT: A 58 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 359 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7667 (mt-10) REVERT: B 37 MET cc_start: 0.6949 (mmm) cc_final: 0.6096 (mmt) REVERT: B 359 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7472 (mt-10) outliers start: 4 outliers final: 2 residues processed: 120 average time/residue: 0.1520 time to fit residues: 23.7790 Evaluate side-chains 115 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 41 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2377 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= 0.206 Angle : 0.520 7.506 6666 Z= 0.277 Chirality : 0.043 0.133 798 Planarity : 0.004 0.043 832 Dihedral : 4.370 42.090 654 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.14 % Allowed : 14.45 % Favored : 84.41 % 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: 2.30 (0.36), residues: 604 helix: 2.51 (0.26), residues: 408 sheet: -0.01 (0.79), residues: 50 loop : -0.82 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.007 0.001 HIS A 135 PHE 0.019 0.001 PHE B 21 TYR 0.012 0.001 TYR A 330 ARG 0.004 0.000 ARG A 381 *********************** 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 124 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.579 Fit side-chains REVERT: A 37 MET cc_start: 0.6921 (mmm) cc_final: 0.6056 (mmt) REVERT: A 58 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7573 (tm-30) REVERT: A 359 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7739 (mt-10) REVERT: B 37 MET cc_start: 0.6908 (mmm) cc_final: 0.6022 (mmt) REVERT: B 359 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7481 (mt-10) outliers start: 4 outliers final: 3 residues processed: 123 average time/residue: 0.1536 time to fit residues: 24.4194 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 : 0.526 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 0.0060 chunk 40 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2625 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= 0.167 Angle : 0.494 7.412 6666 Z= 0.263 Chirality : 0.042 0.133 798 Planarity : 0.004 0.040 832 Dihedral : 3.867 14.447 652 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.76 % Allowed : 16.54 % Favored : 82.70 % 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: 2.39 (0.36), residues: 604 helix: 2.49 (0.26), residues: 412 sheet: 0.05 (0.80), residues: 50 loop : -0.61 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 375 HIS 0.008 0.001 HIS B 135 PHE 0.014 0.001 PHE B 21 TYR 0.016 0.001 TYR B 330 ARG 0.004 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 122 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.550 Fit side-chains REVERT: A 37 MET cc_start: 0.6741 (mmm) cc_final: 0.5806 (mmt) REVERT: A 58 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 359 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7734 (mt-10) REVERT: B 37 MET cc_start: 0.6740 (mmm) cc_final: 0.5810 (mmt) REVERT: B 58 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7587 (tm-30) REVERT: B 359 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7567 (mt-10) outliers start: 2 outliers final: 2 residues processed: 122 average time/residue: 0.1464 time to fit residues: 23.5708 Evaluate side-chains 117 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE 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 14 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.0470 chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2788 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= 0.179 Angle : 0.485 6.872 6666 Z= 0.259 Chirality : 0.042 0.133 798 Planarity : 0.004 0.038 832 Dihedral : 3.816 14.149 652 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.14 % Allowed : 16.92 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.36), residues: 604 helix: 2.49 (0.26), residues: 412 sheet: 0.22 (0.83), residues: 50 loop : -0.54 (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 0.012 0.001 PHE B 21 TYR 0.006 0.001 TYR A 396 ARG 0.003 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 121 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.539 Fit side-chains REVERT: A 37 MET cc_start: 0.6780 (mmm) cc_final: 0.5837 (mmt) REVERT: A 58 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7660 (tm-30) REVERT: B 37 MET cc_start: 0.6833 (mmm) cc_final: 0.5890 (mmt) REVERT: B 58 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7524 (tm-30) outliers start: 4 outliers final: 3 residues processed: 119 average time/residue: 0.1475 time to fit residues: 23.1650 Evaluate side-chains 118 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE 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 32 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2839 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= 0.211 Angle : 0.513 10.230 6666 Z= 0.271 Chirality : 0.042 0.165 798 Planarity : 0.004 0.037 832 Dihedral : 3.823 13.740 652 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.95 % Allowed : 19.01 % Favored : 80.04 % 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: 2.39 (0.36), residues: 604 helix: 2.45 (0.26), residues: 412 sheet: 0.26 (0.84), residues: 50 loop : -0.57 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.005 0.001 HIS B 135 PHE 0.010 0.001 PHE B 134 TYR 0.006 0.001 TYR B 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 120 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.524 Fit side-chains REVERT: A 37 MET cc_start: 0.6941 (mmm) cc_final: 0.6029 (mmt) REVERT: A 58 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 37 MET cc_start: 0.6905 (mmm) cc_final: 0.5965 (mmt) REVERT: B 58 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7557 (tm-30) outliers start: 3 outliers final: 2 residues processed: 119 average time/residue: 0.1655 time to fit residues: 25.7273 Evaluate side-chains 117 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE 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 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 0.0870 chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4902 Z= 0.194 Angle : 0.494 7.605 6666 Z= 0.264 Chirality : 0.042 0.156 798 Planarity : 0.004 0.036 832 Dihedral : 3.802 13.684 652 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.76 % Allowed : 19.77 % 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: 2.38 (0.36), residues: 604 helix: 2.43 (0.26), residues: 412 sheet: 0.25 (0.83), residues: 50 loop : -0.49 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.005 0.001 HIS B 135 PHE 0.010 0.001 PHE B 134 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 121 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.561 Fit side-chains REVERT: A 37 MET cc_start: 0.6896 (mmm) cc_final: 0.5966 (mmt) REVERT: A 58 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7685 (tm-30) REVERT: B 37 MET cc_start: 0.6902 (mmm) cc_final: 0.5968 (mmt) REVERT: B 58 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7587 (tm-30) outliers start: 2 outliers final: 2 residues processed: 121 average time/residue: 0.1571 time to fit residues: 24.7444 Evaluate side-chains 118 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.0170 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 0.0370 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4902 Z= 0.159 Angle : 0.483 7.016 6666 Z= 0.257 Chirality : 0.042 0.133 798 Planarity : 0.004 0.036 832 Dihedral : 3.716 11.991 652 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.76 % Allowed : 20.34 % Favored : 78.90 % 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: 2.52 (0.36), residues: 604 helix: 2.51 (0.26), residues: 412 sheet: 0.20 (0.83), residues: 50 loop : -0.32 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 375 HIS 0.005 0.001 HIS B 135 PHE 0.009 0.001 PHE B 134 TYR 0.005 0.001 TYR A 396 ARG 0.003 0.000 ARG A 381 *********************** 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 127 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.565 Fit side-chains REVERT: A 37 MET cc_start: 0.6752 (mmm) cc_final: 0.5805 (mmt) REVERT: A 58 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 37 MET cc_start: 0.6781 (mmm) cc_final: 0.5815 (mmt) REVERT: B 58 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7584 (tm-30) outliers start: 2 outliers final: 2 residues processed: 127 average time/residue: 0.1519 time to fit residues: 25.3338 Evaluate side-chains 122 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.0870 chunk 47 optimal weight: 0.7980 chunk 19 optimal weight: 0.0170 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4902 Z= 0.159 Angle : 0.489 8.719 6666 Z= 0.259 Chirality : 0.042 0.133 798 Planarity : 0.004 0.035 832 Dihedral : 3.678 11.178 652 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.95 % Allowed : 20.53 % 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: 2.61 (0.36), residues: 604 helix: 2.57 (0.26), residues: 412 sheet: 0.18 (0.82), residues: 50 loop : -0.24 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 375 HIS 0.004 0.001 HIS B 135 PHE 0.010 0.001 PHE B 21 TYR 0.004 0.001 TYR B 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 127 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.578 Fit side-chains REVERT: A 37 MET cc_start: 0.6716 (mmm) cc_final: 0.5748 (mmt) REVERT: A 44 MET cc_start: 0.6652 (mmt) cc_final: 0.6364 (mmt) REVERT: A 58 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7702 (tm-30) REVERT: A 337 LYS cc_start: 0.8756 (ttpp) cc_final: 0.8382 (ttpp) REVERT: B 58 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7604 (tm-30) REVERT: B 337 LYS cc_start: 0.8730 (ttpp) cc_final: 0.8371 (ttpp) REVERT: B 352 ASP cc_start: 0.8150 (p0) cc_final: 0.7910 (p0) outliers start: 3 outliers final: 3 residues processed: 126 average time/residue: 0.1409 time to fit residues: 23.5624 Evaluate side-chains 122 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE 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 48 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** 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 = 0.4225 r_free = 0.4225 target = 0.198463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137797 restraints weight = 10033.925| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.94 r_work: 0.3302 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4902 Z= 0.202 Angle : 0.519 7.137 6666 Z= 0.283 Chirality : 0.043 0.181 798 Planarity : 0.004 0.047 832 Dihedral : 3.718 12.478 652 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.95 % Allowed : 20.72 % Favored : 78.33 % 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: 2.63 (0.36), residues: 604 helix: 2.63 (0.26), residues: 402 sheet: 0.18 (0.81), residues: 50 loop : -0.16 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.006 0.001 HIS B 135 PHE 0.013 0.001 PHE B 134 TYR 0.005 0.001 TYR B 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: 1408.85 seconds wall clock time: 26 minutes 7.44 seconds (1567.44 seconds total)