Starting phenix.real_space_refine on Thu Feb 15 08:18:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8j_15914/02_2024/8b8j_15914.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8j_15914/02_2024/8b8j_15914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8j_15914/02_2024/8b8j_15914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8j_15914/02_2024/8b8j_15914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8j_15914/02_2024/8b8j_15914.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8j_15914/02_2024/8b8j_15914.pdb" } resolution = 2.96 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= 0.001 sd= 0.019 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 Ca 6 9.91 5 S 76 5.16 5 C 7686 2.51 5 N 1884 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11686 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5840 Classifications: {'peptide': 709} Link IDs: {'PTRANS': 32, 'TRANS': 676} Chain breaks: 8 Chain: "B" Number of atoms: 5840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5840 Classifications: {'peptide': 709} Link IDs: {'PTRANS': 32, 'TRANS': 676} Chain breaks: 8 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.67, per 1000 atoms: 0.57 Number of scatterers: 11686 At special positions: 0 Unit cell: (126.294, 83.328, 113.274, 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) Ca 6 19.99 S 76 16.00 O 2034 8.00 N 1884 7.00 C 7686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 2.1 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 64.7% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 90 through 108 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 293 through 327 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.513A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 Processing helix chain 'A' and resid 447 through 473 Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.568A pdb=" N ALA A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 5.505A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 638 removed outlier: 3.880A pdb=" N LYS A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A 617 " --> pdb=" O MET A 613 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) Proline residue: A 628 - end of helix removed outlier: 3.525A pdb=" N GLY A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 662 through 681 removed outlier: 3.796A pdb=" N TYR A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.953A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.599A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 759 Processing helix chain 'A' and resid 762 through 766 Processing helix chain 'A' and resid 797 through 802 removed outlier: 3.769A pdb=" N LEU A 801 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 802 " --> pdb=" O TYR A 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 797 through 802' Processing helix chain 'A' and resid 825 through 856 Processing helix chain 'A' and resid 861 through 875 removed outlier: 3.601A pdb=" N SER A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 108 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 364 through 375 removed outlier: 3.512A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 Processing helix chain 'B' and resid 447 through 473 Processing helix chain 'B' and resid 474 through 488 Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.568A pdb=" N ALA B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.504A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 638 removed outlier: 3.879A pdb=" N LYS B 616 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B 617 " --> pdb=" O MET B 613 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) Proline residue: B 628 - end of helix removed outlier: 3.525A pdb=" N GLY B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 662 through 681 removed outlier: 3.797A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.953A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.599A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 759 Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'B' and resid 797 through 802 removed outlier: 3.770A pdb=" N LEU B 801 " --> pdb=" O PRO B 797 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 802 " --> pdb=" O TYR B 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 797 through 802' Processing helix chain 'B' and resid 825 through 856 Processing helix chain 'B' and resid 861 through 875 removed outlier: 3.601A pdb=" N SER B 866 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348 removed outlier: 3.627A pdb=" N TRP A 359 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 657 through 658 removed outlier: 6.940A pdb=" N GLN A 657 " --> pdb=" O ARG A 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 785 Processing sheet with id=AA5, first strand: chain 'B' and resid 111 through 116 Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 348 removed outlier: 3.628A pdb=" N TRP B 359 " --> pdb=" O MET B 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 657 through 658 removed outlier: 6.942A pdb=" N GLN B 657 " --> pdb=" O ARG B 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 782 through 785 720 hydrogen bonds defined for protein. 2106 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: 3.95 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3544 1.34 - 1.46: 2910 1.46 - 1.58: 5430 1.58 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 11998 Sorted by residual: bond pdb=" C PRO A 763 " pdb=" N PRO A 764 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.60e-01 bond pdb=" C PRO B 763 " pdb=" N PRO B 764 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.32e-01 bond pdb=" C GLY B 387 " pdb=" O GLY B 387 " ideal model delta sigma weight residual 1.234 1.243 -0.010 1.21e-02 6.83e+03 6.18e-01 bond pdb=" C VAL B 384 " pdb=" O VAL B 384 " ideal model delta sigma weight residual 1.237 1.245 -0.009 1.13e-02 7.83e+03 5.83e-01 bond pdb=" C PHE A 382 " pdb=" O PHE A 382 " ideal model delta sigma weight residual 1.236 1.227 0.010 1.26e-02 6.30e+03 5.78e-01 ... (remaining 11993 not shown) Histogram of bond angle deviations from ideal: 100.22 - 106.97: 352 106.97 - 113.72: 6528 113.72 - 120.47: 4817 120.47 - 127.22: 4429 127.22 - 133.97: 140 Bond angle restraints: 16266 Sorted by residual: angle pdb=" CA LEU A 662 " pdb=" CB LEU A 662 " pdb=" CG LEU A 662 " ideal model delta sigma weight residual 116.30 126.23 -9.93 3.50e+00 8.16e-02 8.04e+00 angle pdb=" CA LEU B 662 " pdb=" CB LEU B 662 " pdb=" CG LEU B 662 " ideal model delta sigma weight residual 116.30 126.20 -9.90 3.50e+00 8.16e-02 7.99e+00 angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 114.03 -3.33 1.22e+00 6.72e-01 7.47e+00 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 114.02 -3.32 1.22e+00 6.72e-01 7.42e+00 angle pdb=" C PRO B 541 " pdb=" N ARG B 542 " pdb=" CA ARG B 542 " ideal model delta sigma weight residual 125.02 129.32 -4.30 1.76e+00 3.23e-01 5.98e+00 ... (remaining 16261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 6739 17.49 - 34.97: 290 34.97 - 52.45: 29 52.45 - 69.94: 8 69.94 - 87.42: 2 Dihedral angle restraints: 7068 sinusoidal: 2882 harmonic: 4186 Sorted by residual: dihedral pdb=" CA LYS A 590 " pdb=" C LYS A 590 " pdb=" N TYR A 591 " pdb=" CA TYR A 591 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA LYS B 590 " pdb=" C LYS B 590 " pdb=" N TYR B 591 " pdb=" CA TYR B 591 " ideal model delta harmonic sigma weight residual -180.00 -163.23 -16.77 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA GLU B 539 " pdb=" CB GLU B 539 " pdb=" CG GLU B 539 " pdb=" CD GLU B 539 " ideal model delta sinusoidal sigma weight residual 60.00 117.32 -57.32 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 7065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1077 0.028 - 0.055: 429 0.055 - 0.083: 210 0.083 - 0.110: 54 0.110 - 0.138: 16 Chirality restraints: 1786 Sorted by residual: chirality pdb=" CB ILE A 474 " pdb=" CA ILE A 474 " pdb=" CG1 ILE A 474 " pdb=" CG2 ILE A 474 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CB ILE B 474 " pdb=" CA ILE B 474 " pdb=" CG1 ILE B 474 " pdb=" CG2 ILE B 474 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ARG B 542 " pdb=" N ARG B 542 " pdb=" C ARG B 542 " pdb=" CB ARG B 542 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1783 not shown) Planarity restraints: 2010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 762 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO B 763 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 763 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 763 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 762 " -0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 763 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 763 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 763 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 818 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO A 819 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 819 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 819 " 0.020 5.00e-02 4.00e+02 ... (remaining 2007 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1522 2.75 - 3.29: 12048 3.29 - 3.82: 20078 3.82 - 4.36: 22392 4.36 - 4.90: 39120 Nonbonded interactions: 95160 Sorted by model distance: nonbonded pdb=" O CYS B 365 " pdb=" OG SER B 368 " model vdw 2.211 2.440 nonbonded pdb=" O CYS A 365 " pdb=" OG SER A 368 " model vdw 2.212 2.440 nonbonded pdb=" OD1 ASP A 375 " pdb=" OG SER A 748 " model vdw 2.214 2.440 nonbonded pdb=" OD1 ASP B 375 " pdb=" OG SER B 748 " model vdw 2.214 2.440 nonbonded pdb=" OD1 ASN A 778 " pdb=" NH1 ARG A 808 " model vdw 2.258 2.520 ... (remaining 95155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.320 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 33.240 Find NCS groups from input model: 0.660 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: 0.010 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 : 0.003 0.030 11998 Z= 0.187 Angle : 0.464 9.926 16266 Z= 0.249 Chirality : 0.038 0.138 1786 Planarity : 0.004 0.043 2010 Dihedral : 9.830 87.425 4348 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.25 % Allowed : 5.25 % Favored : 93.50 % 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: 2.21 (0.23), residues: 1382 helix: 2.62 (0.17), residues: 848 sheet: 1.10 (0.58), residues: 64 loop : -0.73 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 397 HIS 0.002 0.000 HIS A 249 PHE 0.014 0.001 PHE B 560 TYR 0.013 0.001 TYR A 580 ARG 0.002 0.000 ARG B 813 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.8677 (m-40) cc_final: 0.8347 (p0) REVERT: A 326 LEU cc_start: 0.8975 (mt) cc_final: 0.8741 (mt) REVERT: A 385 PHE cc_start: 0.8610 (t80) cc_final: 0.8405 (t80) REVERT: A 406 TYR cc_start: 0.8568 (t80) cc_final: 0.8228 (t80) REVERT: A 409 ASP cc_start: 0.8854 (m-30) cc_final: 0.8369 (t0) REVERT: A 461 PHE cc_start: 0.8306 (t80) cc_final: 0.7785 (m-10) REVERT: A 524 LEU cc_start: 0.9711 (mm) cc_final: 0.9280 (tp) REVERT: A 527 ILE cc_start: 0.9626 (mm) cc_final: 0.9386 (mt) REVERT: A 544 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7156 (tp40) REVERT: A 548 GLU cc_start: 0.8978 (tp30) cc_final: 0.8711 (mm-30) REVERT: A 553 MET cc_start: 0.8156 (tpp) cc_final: 0.7720 (tpp) REVERT: A 597 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8407 (t70) REVERT: B 296 ILE cc_start: 0.7948 (mp) cc_final: 0.7609 (mm) REVERT: B 327 ASP cc_start: 0.7904 (t0) cc_final: 0.7663 (t0) REVERT: B 409 ASP cc_start: 0.8527 (m-30) cc_final: 0.8112 (t0) REVERT: B 548 GLU cc_start: 0.9093 (tp30) cc_final: 0.8529 (tp30) REVERT: B 749 ASP cc_start: 0.7937 (t70) cc_final: 0.7211 (t0) REVERT: B 855 TYR cc_start: 0.7994 (t80) cc_final: 0.7739 (t80) outliers start: 16 outliers final: 3 residues processed: 204 average time/residue: 1.0183 time to fit residues: 228.3065 Evaluate side-chains 121 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 685 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN A 351 GLN A 401 GLN A 559 GLN A 726 GLN A 730 GLN A 779 ASN B 308 GLN B 401 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN B 695 ASN B 726 GLN B 730 GLN B 830 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 11998 Z= 0.268 Angle : 0.620 13.390 16266 Z= 0.319 Chirality : 0.042 0.221 1786 Planarity : 0.005 0.044 2010 Dihedral : 4.844 55.259 1570 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.82 % Allowed : 11.52 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.22), residues: 1382 helix: 2.25 (0.17), residues: 868 sheet: 1.67 (0.65), residues: 44 loop : -0.83 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 333 HIS 0.004 0.001 HIS B 249 PHE 0.027 0.002 PHE B 462 TYR 0.015 0.001 TYR B 580 ARG 0.012 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 1.468 Fit side-chains REVERT: A 68 GLN cc_start: 0.8033 (mp10) cc_final: 0.7820 (mp10) REVERT: A 108 HIS cc_start: 0.8435 (OUTLIER) cc_final: 0.8074 (t-90) REVERT: A 234 ASN cc_start: 0.8753 (m-40) cc_final: 0.8460 (p0) REVERT: A 282 LYS cc_start: 0.6338 (OUTLIER) cc_final: 0.5996 (tptt) REVERT: A 409 ASP cc_start: 0.8717 (m-30) cc_final: 0.8201 (t0) REVERT: A 524 LEU cc_start: 0.9698 (mm) cc_final: 0.8929 (tp) REVERT: A 527 ILE cc_start: 0.9666 (mm) cc_final: 0.9420 (mt) REVERT: A 528 TYR cc_start: 0.9026 (m-10) cc_final: 0.8436 (m-80) REVERT: A 548 GLU cc_start: 0.8991 (tp30) cc_final: 0.8243 (tp30) REVERT: A 553 MET cc_start: 0.8201 (tpp) cc_final: 0.7783 (tpp) REVERT: A 597 ASP cc_start: 0.8708 (m-30) cc_final: 0.8467 (t70) REVERT: A 602 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.9008 (tm) REVERT: A 750 MET cc_start: 0.9184 (ttp) cc_final: 0.8972 (ttm) REVERT: B 99 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7604 (mp10) REVERT: B 242 TYR cc_start: 0.8515 (m-80) cc_final: 0.8100 (m-80) REVERT: B 375 ASP cc_start: 0.7882 (t70) cc_final: 0.7552 (t70) REVERT: B 409 ASP cc_start: 0.8509 (m-30) cc_final: 0.8087 (t0) REVERT: B 538 PHE cc_start: 0.8289 (t80) cc_final: 0.7828 (t80) REVERT: B 548 GLU cc_start: 0.9130 (tp30) cc_final: 0.8547 (mp0) REVERT: B 612 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8677 (mp) REVERT: B 842 MET cc_start: 0.8547 (ttt) cc_final: 0.8322 (ttt) REVERT: B 855 TYR cc_start: 0.8028 (t80) cc_final: 0.7814 (t80) outliers start: 36 outliers final: 17 residues processed: 153 average time/residue: 1.0531 time to fit residues: 177.5767 Evaluate side-chains 129 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 859 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 113 optimal weight: 0.0170 chunk 126 optimal weight: 0.7980 chunk 43 optimal weight: 0.0570 chunk 102 optimal weight: 4.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN A 695 ASN A 820 GLN B 525 ASN B 730 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11998 Z= 0.205 Angle : 0.553 11.079 16266 Z= 0.284 Chirality : 0.040 0.197 1786 Planarity : 0.004 0.048 2010 Dihedral : 4.354 55.381 1565 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.29 % Allowed : 13.24 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.22), residues: 1382 helix: 2.26 (0.17), residues: 876 sheet: 1.58 (0.63), residues: 44 loop : -0.88 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.003 0.001 HIS A 249 PHE 0.023 0.002 PHE B 462 TYR 0.015 0.001 TYR B 580 ARG 0.007 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8137 (mp10) cc_final: 0.7879 (mp10) REVERT: A 76 VAL cc_start: 0.9030 (t) cc_final: 0.8591 (p) REVERT: A 108 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.8382 (t-90) REVERT: A 234 ASN cc_start: 0.8769 (m-40) cc_final: 0.8493 (p0) REVERT: A 409 ASP cc_start: 0.8862 (m-30) cc_final: 0.8334 (t0) REVERT: A 507 MET cc_start: 0.6427 (pmm) cc_final: 0.6096 (pmt) REVERT: A 524 LEU cc_start: 0.9709 (mm) cc_final: 0.9475 (mt) REVERT: A 553 MET cc_start: 0.8211 (tpp) cc_final: 0.7733 (tpp) REVERT: A 597 ASP cc_start: 0.8717 (m-30) cc_final: 0.8497 (t70) REVERT: B 99 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7638 (mp10) REVERT: B 242 TYR cc_start: 0.8463 (m-80) cc_final: 0.8145 (m-80) REVERT: B 409 ASP cc_start: 0.8468 (m-30) cc_final: 0.8048 (t0) REVERT: B 526 THR cc_start: 0.9546 (OUTLIER) cc_final: 0.8965 (t) REVERT: B 529 GLU cc_start: 0.8751 (tt0) cc_final: 0.8068 (pt0) REVERT: B 536 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7130 (p) REVERT: B 538 PHE cc_start: 0.8422 (t80) cc_final: 0.8126 (t80) REVERT: B 548 GLU cc_start: 0.9116 (tp30) cc_final: 0.8338 (tp30) REVERT: B 855 TYR cc_start: 0.8012 (t80) cc_final: 0.7781 (t80) outliers start: 42 outliers final: 14 residues processed: 149 average time/residue: 1.1551 time to fit residues: 188.3954 Evaluate side-chains 124 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 859 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 0.0980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11998 Z= 0.218 Angle : 0.557 10.646 16266 Z= 0.286 Chirality : 0.040 0.198 1786 Planarity : 0.004 0.048 2010 Dihedral : 4.328 55.673 1565 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.39 % Allowed : 13.17 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.22), residues: 1382 helix: 2.31 (0.17), residues: 866 sheet: 1.54 (0.62), residues: 44 loop : -0.94 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 829 HIS 0.003 0.001 HIS A 249 PHE 0.025 0.002 PHE B 462 TYR 0.014 0.001 TYR A 827 ARG 0.019 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 116 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8200 (mp10) cc_final: 0.7967 (mp10) REVERT: A 94 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8129 (tp40) REVERT: A 108 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8383 (t-90) REVERT: A 234 ASN cc_start: 0.8834 (m-40) cc_final: 0.8614 (p0) REVERT: A 409 ASP cc_start: 0.8716 (m-30) cc_final: 0.8163 (t0) REVERT: A 507 MET cc_start: 0.6503 (pmm) cc_final: 0.6068 (pmt) REVERT: A 536 THR cc_start: 0.7531 (OUTLIER) cc_final: 0.7326 (p) REVERT: A 553 MET cc_start: 0.8253 (tpp) cc_final: 0.7769 (tpp) REVERT: B 99 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: B 296 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7647 (mt) REVERT: B 409 ASP cc_start: 0.8580 (m-30) cc_final: 0.8195 (t0) REVERT: B 458 SER cc_start: 0.8748 (m) cc_final: 0.8433 (p) REVERT: B 526 THR cc_start: 0.9585 (OUTLIER) cc_final: 0.9228 (t) REVERT: B 529 GLU cc_start: 0.8776 (tt0) cc_final: 0.8133 (pt0) REVERT: B 536 THR cc_start: 0.7367 (OUTLIER) cc_final: 0.7120 (p) REVERT: B 538 PHE cc_start: 0.8387 (t80) cc_final: 0.8093 (t80) REVERT: B 548 GLU cc_start: 0.9111 (tp30) cc_final: 0.8350 (tp30) REVERT: B 855 TYR cc_start: 0.8008 (t80) cc_final: 0.7780 (t80) outliers start: 56 outliers final: 20 residues processed: 163 average time/residue: 1.0141 time to fit residues: 182.5758 Evaluate side-chains 133 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 859 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 30.0000 chunk 45 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS A 559 GLN A 710 GLN A 730 GLN A 830 HIS B 275 HIS B 351 GLN B 730 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 11998 Z= 0.458 Angle : 0.681 15.345 16266 Z= 0.352 Chirality : 0.045 0.216 1786 Planarity : 0.005 0.048 2010 Dihedral : 4.677 56.621 1565 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.08 % Allowed : 14.18 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.22), residues: 1382 helix: 2.02 (0.17), residues: 864 sheet: 1.12 (0.62), residues: 44 loop : -0.95 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 829 HIS 0.006 0.001 HIS B 830 PHE 0.026 0.002 PHE B 462 TYR 0.013 0.002 TYR A 138 ARG 0.018 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 108 time to evaluate : 1.339 Fit side-chains REVERT: A 51 GLU cc_start: 0.7577 (mp0) cc_final: 0.7112 (mp0) REVERT: A 94 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8138 (tp40) REVERT: A 108 HIS cc_start: 0.8499 (OUTLIER) cc_final: 0.8183 (t-90) REVERT: A 242 TYR cc_start: 0.8669 (m-80) cc_final: 0.8361 (m-80) REVERT: A 282 LYS cc_start: 0.6613 (tptm) cc_final: 0.6228 (tptt) REVERT: A 409 ASP cc_start: 0.8663 (m-30) cc_final: 0.8173 (t0) REVERT: A 507 MET cc_start: 0.6459 (pmm) cc_final: 0.5963 (pmt) REVERT: A 548 GLU cc_start: 0.9030 (tp30) cc_final: 0.8332 (tp30) REVERT: A 553 MET cc_start: 0.8309 (tpp) cc_final: 0.7858 (tpp) REVERT: B 322 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8744 (mp) REVERT: B 409 ASP cc_start: 0.8533 (m-30) cc_final: 0.8150 (t0) REVERT: B 526 THR cc_start: 0.9591 (OUTLIER) cc_final: 0.9260 (p) REVERT: B 529 GLU cc_start: 0.8773 (tt0) cc_final: 0.8264 (pt0) REVERT: B 536 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7383 (p) REVERT: B 538 PHE cc_start: 0.8302 (t80) cc_final: 0.7992 (t80) REVERT: B 548 GLU cc_start: 0.9144 (tp30) cc_final: 0.8415 (tp30) REVERT: B 687 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8172 (mp) REVERT: B 742 MET cc_start: 0.8428 (mpt) cc_final: 0.8183 (mtp) REVERT: B 749 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.7432 (t0) REVERT: B 855 TYR cc_start: 0.8002 (t80) cc_final: 0.7787 (t80) outliers start: 52 outliers final: 27 residues processed: 149 average time/residue: 1.0289 time to fit residues: 169.1104 Evaluate side-chains 133 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 859 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 135 optimal weight: 0.0000 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.0170 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN A 779 ASN B 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 11998 Z= 0.178 Angle : 0.579 13.168 16266 Z= 0.293 Chirality : 0.040 0.150 1786 Planarity : 0.004 0.051 2010 Dihedral : 4.266 23.680 1562 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.21 % Allowed : 15.05 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1382 helix: 2.18 (0.17), residues: 864 sheet: 1.37 (0.65), residues: 44 loop : -1.04 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 397 HIS 0.003 0.001 HIS A 143 PHE 0.027 0.001 PHE B 462 TYR 0.013 0.001 TYR B 580 ARG 0.015 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 115 time to evaluate : 1.298 Fit side-chains REVERT: A 51 GLU cc_start: 0.7463 (mp0) cc_final: 0.7003 (mp0) REVERT: A 68 GLN cc_start: 0.8218 (mp10) cc_final: 0.7887 (pm20) REVERT: A 94 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8058 (tp40) REVERT: A 108 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.8144 (t-90) REVERT: A 242 TYR cc_start: 0.8654 (m-80) cc_final: 0.8235 (m-80) REVERT: A 409 ASP cc_start: 0.8742 (m-30) cc_final: 0.8222 (t0) REVERT: A 507 MET cc_start: 0.6400 (pmm) cc_final: 0.5885 (pmt) REVERT: A 524 LEU cc_start: 0.9735 (mt) cc_final: 0.9451 (pp) REVERT: A 526 THR cc_start: 0.9518 (OUTLIER) cc_final: 0.9039 (p) REVERT: A 529 GLU cc_start: 0.8776 (tt0) cc_final: 0.8268 (pt0) REVERT: A 548 GLU cc_start: 0.9026 (tp30) cc_final: 0.8674 (mp0) REVERT: A 553 MET cc_start: 0.8277 (tpp) cc_final: 0.7797 (tpp) REVERT: A 668 TYR cc_start: 0.9086 (m-80) cc_final: 0.8814 (m-80) REVERT: A 687 LEU cc_start: 0.8519 (mt) cc_final: 0.8189 (mp) REVERT: A 742 MET cc_start: 0.8690 (mtt) cc_final: 0.8300 (mtm) REVERT: B 48 ARG cc_start: 0.8475 (ppp80) cc_final: 0.8163 (ppp80) REVERT: B 386 MET cc_start: 0.8156 (tpp) cc_final: 0.7775 (mmm) REVERT: B 409 ASP cc_start: 0.8573 (m-30) cc_final: 0.8174 (t0) REVERT: B 458 SER cc_start: 0.8704 (m) cc_final: 0.8395 (p) REVERT: B 526 THR cc_start: 0.9635 (OUTLIER) cc_final: 0.9302 (p) REVERT: B 529 GLU cc_start: 0.8752 (tt0) cc_final: 0.8215 (pt0) REVERT: B 538 PHE cc_start: 0.8290 (t80) cc_final: 0.7917 (t80) REVERT: B 548 GLU cc_start: 0.9085 (tp30) cc_final: 0.8553 (mp0) REVERT: B 668 TYR cc_start: 0.9108 (m-80) cc_final: 0.8844 (m-80) REVERT: B 742 MET cc_start: 0.8570 (mpt) cc_final: 0.8138 (mtp) REVERT: B 749 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.7249 (t0) REVERT: B 855 TYR cc_start: 0.8027 (t80) cc_final: 0.7796 (t80) outliers start: 41 outliers final: 16 residues processed: 146 average time/residue: 1.0203 time to fit residues: 164.9765 Evaluate side-chains 128 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 0.0070 chunk 83 optimal weight: 3.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11998 Z= 0.295 Angle : 0.607 12.323 16266 Z= 0.312 Chirality : 0.041 0.182 1786 Planarity : 0.005 0.055 2010 Dihedral : 4.240 20.959 1562 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.66 % Allowed : 16.38 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.22), residues: 1382 helix: 2.16 (0.17), residues: 864 sheet: 0.54 (0.62), residues: 62 loop : -0.93 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 397 HIS 0.003 0.001 HIS B 830 PHE 0.027 0.002 PHE B 462 TYR 0.014 0.001 TYR A 827 ARG 0.016 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 107 time to evaluate : 1.268 Fit side-chains REVERT: A 51 GLU cc_start: 0.7541 (mp0) cc_final: 0.7198 (mp0) REVERT: A 68 GLN cc_start: 0.8256 (mp10) cc_final: 0.8004 (pm20) REVERT: A 94 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8084 (tp40) REVERT: A 108 HIS cc_start: 0.8461 (OUTLIER) cc_final: 0.8151 (t-90) REVERT: A 242 TYR cc_start: 0.8641 (m-80) cc_final: 0.8303 (m-80) REVERT: A 409 ASP cc_start: 0.8753 (m-30) cc_final: 0.8245 (t0) REVERT: A 507 MET cc_start: 0.6367 (pmm) cc_final: 0.6095 (pmt) REVERT: A 524 LEU cc_start: 0.9724 (mt) cc_final: 0.9362 (pp) REVERT: A 526 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9268 (p) REVERT: A 529 GLU cc_start: 0.8766 (tt0) cc_final: 0.8303 (pt0) REVERT: A 548 GLU cc_start: 0.9029 (tp30) cc_final: 0.8340 (tp30) REVERT: A 553 MET cc_start: 0.8319 (tpp) cc_final: 0.7828 (tpp) REVERT: A 742 MET cc_start: 0.8667 (mtt) cc_final: 0.8291 (mtm) REVERT: B 142 MET cc_start: 0.7242 (mtp) cc_final: 0.7004 (mtm) REVERT: B 409 ASP cc_start: 0.8595 (m-30) cc_final: 0.8197 (t0) REVERT: B 458 SER cc_start: 0.8712 (m) cc_final: 0.8399 (p) REVERT: B 524 LEU cc_start: 0.9716 (mt) cc_final: 0.9399 (pp) REVERT: B 526 THR cc_start: 0.9623 (OUTLIER) cc_final: 0.9293 (p) REVERT: B 529 GLU cc_start: 0.8756 (tt0) cc_final: 0.8250 (pt0) REVERT: B 538 PHE cc_start: 0.8243 (t80) cc_final: 0.7849 (t80) REVERT: B 548 GLU cc_start: 0.9102 (tp30) cc_final: 0.8352 (tp30) REVERT: B 687 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8243 (mp) REVERT: B 742 MET cc_start: 0.8513 (mpt) cc_final: 0.8265 (mtp) REVERT: B 749 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.7339 (t0) outliers start: 34 outliers final: 20 residues processed: 135 average time/residue: 1.0892 time to fit residues: 161.3183 Evaluate side-chains 129 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 122 optimal weight: 0.0980 chunk 129 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11998 Z= 0.199 Angle : 0.595 11.985 16266 Z= 0.296 Chirality : 0.040 0.157 1786 Planarity : 0.004 0.053 2010 Dihedral : 4.177 21.889 1562 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.59 % Allowed : 16.46 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.22), residues: 1382 helix: 2.18 (0.17), residues: 870 sheet: 0.67 (0.62), residues: 62 loop : -1.02 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 397 HIS 0.002 0.001 HIS A 249 PHE 0.028 0.001 PHE B 462 TYR 0.013 0.001 TYR A 406 ARG 0.013 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 1.250 Fit side-chains REVERT: A 51 GLU cc_start: 0.7549 (mp0) cc_final: 0.7209 (mp0) REVERT: A 94 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8082 (tp40) REVERT: A 108 HIS cc_start: 0.8441 (OUTLIER) cc_final: 0.8160 (t-90) REVERT: A 386 MET cc_start: 0.8090 (tpp) cc_final: 0.7814 (mmm) REVERT: A 409 ASP cc_start: 0.8739 (m-30) cc_final: 0.8214 (t0) REVERT: A 507 MET cc_start: 0.6390 (pmm) cc_final: 0.5949 (pmt) REVERT: A 524 LEU cc_start: 0.9706 (mt) cc_final: 0.9403 (pp) REVERT: A 526 THR cc_start: 0.9583 (OUTLIER) cc_final: 0.9149 (p) REVERT: A 529 GLU cc_start: 0.8734 (tt0) cc_final: 0.8291 (pt0) REVERT: A 548 GLU cc_start: 0.9034 (tp30) cc_final: 0.8674 (mp0) REVERT: A 553 MET cc_start: 0.8300 (tpp) cc_final: 0.7849 (tpp) REVERT: A 668 TYR cc_start: 0.9100 (m-80) cc_final: 0.8819 (m-80) REVERT: A 742 MET cc_start: 0.8632 (mtt) cc_final: 0.8249 (mtm) REVERT: B 386 MET cc_start: 0.8169 (tpp) cc_final: 0.7811 (mmm) REVERT: B 409 ASP cc_start: 0.8577 (m-30) cc_final: 0.8175 (t0) REVERT: B 458 SER cc_start: 0.8776 (m) cc_final: 0.8485 (p) REVERT: B 524 LEU cc_start: 0.9675 (mt) cc_final: 0.9432 (pp) REVERT: B 526 THR cc_start: 0.9606 (OUTLIER) cc_final: 0.9282 (p) REVERT: B 529 GLU cc_start: 0.8750 (tt0) cc_final: 0.8211 (pt0) REVERT: B 538 PHE cc_start: 0.8284 (t80) cc_final: 0.7904 (t80) REVERT: B 548 GLU cc_start: 0.9081 (tp30) cc_final: 0.8526 (mp0) REVERT: B 742 MET cc_start: 0.8579 (mpt) cc_final: 0.8260 (mtp) REVERT: B 749 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.7293 (t0) outliers start: 33 outliers final: 21 residues processed: 134 average time/residue: 1.0242 time to fit residues: 151.4560 Evaluate side-chains 129 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11998 Z= 0.210 Angle : 0.593 12.224 16266 Z= 0.298 Chirality : 0.040 0.175 1786 Planarity : 0.005 0.067 2010 Dihedral : 4.178 21.592 1562 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.35 % Allowed : 17.16 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.22), residues: 1382 helix: 2.22 (0.17), residues: 868 sheet: 0.63 (0.62), residues: 62 loop : -0.96 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 397 HIS 0.002 0.001 HIS A 249 PHE 0.029 0.001 PHE B 462 TYR 0.014 0.001 TYR A 827 ARG 0.018 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.235 Fit side-chains REVERT: A 51 GLU cc_start: 0.7541 (mp0) cc_final: 0.7113 (mp0) REVERT: A 94 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8079 (tp40) REVERT: A 108 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.8209 (t-90) REVERT: A 386 MET cc_start: 0.8066 (tpp) cc_final: 0.7835 (mmm) REVERT: A 409 ASP cc_start: 0.8738 (m-30) cc_final: 0.8212 (t0) REVERT: A 507 MET cc_start: 0.6254 (pmm) cc_final: 0.5799 (pmt) REVERT: A 524 LEU cc_start: 0.9702 (mt) cc_final: 0.9447 (pp) REVERT: A 526 THR cc_start: 0.9580 (OUTLIER) cc_final: 0.9163 (p) REVERT: A 529 GLU cc_start: 0.8732 (tt0) cc_final: 0.8298 (pt0) REVERT: A 548 GLU cc_start: 0.9040 (tp30) cc_final: 0.8675 (mp0) REVERT: A 553 MET cc_start: 0.8311 (tpp) cc_final: 0.7840 (tpp) REVERT: A 742 MET cc_start: 0.8634 (mtt) cc_final: 0.8236 (mtm) REVERT: B 386 MET cc_start: 0.8248 (tpp) cc_final: 0.7877 (mmm) REVERT: B 409 ASP cc_start: 0.8579 (m-30) cc_final: 0.8173 (t0) REVERT: B 458 SER cc_start: 0.8729 (m) cc_final: 0.8475 (p) REVERT: B 524 LEU cc_start: 0.9655 (mt) cc_final: 0.9340 (pp) REVERT: B 526 THR cc_start: 0.9626 (OUTLIER) cc_final: 0.9189 (p) REVERT: B 529 GLU cc_start: 0.8761 (tt0) cc_final: 0.8265 (pt0) REVERT: B 538 PHE cc_start: 0.8300 (t80) cc_final: 0.7912 (t80) REVERT: B 548 GLU cc_start: 0.9078 (tp30) cc_final: 0.8331 (tp30) REVERT: B 742 MET cc_start: 0.8585 (mpt) cc_final: 0.8261 (mtp) outliers start: 30 outliers final: 23 residues processed: 133 average time/residue: 1.0180 time to fit residues: 149.4720 Evaluate side-chains 131 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 863 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 139 optimal weight: 0.0770 chunk 128 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 118 optimal weight: 0.0470 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11998 Z= 0.179 Angle : 0.599 12.385 16266 Z= 0.300 Chirality : 0.040 0.160 1786 Planarity : 0.005 0.060 2010 Dihedral : 4.163 23.009 1562 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.35 % Allowed : 17.24 % Favored : 80.41 % 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: 1.81 (0.22), residues: 1382 helix: 2.26 (0.17), residues: 876 sheet: 0.68 (0.61), residues: 62 loop : -0.95 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 397 HIS 0.006 0.001 HIS A 108 PHE 0.028 0.001 PHE B 462 TYR 0.026 0.001 TYR B 637 ARG 0.016 0.000 ARG A 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 1.274 Fit side-chains REVERT: A 94 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8071 (tp40) REVERT: A 108 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.8319 (t-90) REVERT: A 113 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6640 (pm20) REVERT: A 386 MET cc_start: 0.8038 (tpp) cc_final: 0.7813 (mmm) REVERT: A 409 ASP cc_start: 0.8726 (m-30) cc_final: 0.8190 (t0) REVERT: A 507 MET cc_start: 0.6117 (pmm) cc_final: 0.5638 (pmt) REVERT: A 524 LEU cc_start: 0.9680 (mt) cc_final: 0.9358 (pp) REVERT: A 526 THR cc_start: 0.9609 (OUTLIER) cc_final: 0.9293 (p) REVERT: A 529 GLU cc_start: 0.8740 (tt0) cc_final: 0.8306 (pt0) REVERT: A 548 GLU cc_start: 0.9032 (tp30) cc_final: 0.8675 (mp0) REVERT: A 553 MET cc_start: 0.8296 (tpp) cc_final: 0.7859 (tpp) REVERT: A 668 TYR cc_start: 0.9089 (m-80) cc_final: 0.8830 (m-80) REVERT: A 742 MET cc_start: 0.8649 (mtt) cc_final: 0.8250 (mtm) REVERT: A 750 MET cc_start: 0.9338 (ttp) cc_final: 0.9053 (ttm) REVERT: B 386 MET cc_start: 0.8211 (tpp) cc_final: 0.7847 (mmm) REVERT: B 409 ASP cc_start: 0.8696 (m-30) cc_final: 0.8270 (t0) REVERT: B 458 SER cc_start: 0.8696 (m) cc_final: 0.8432 (p) REVERT: B 503 LEU cc_start: 0.1647 (OUTLIER) cc_final: 0.0678 (tt) REVERT: B 524 LEU cc_start: 0.9653 (mt) cc_final: 0.9333 (pp) REVERT: B 526 THR cc_start: 0.9624 (OUTLIER) cc_final: 0.9164 (p) REVERT: B 529 GLU cc_start: 0.8755 (tt0) cc_final: 0.8247 (pt0) REVERT: B 538 PHE cc_start: 0.8333 (t80) cc_final: 0.7825 (t80) REVERT: B 548 GLU cc_start: 0.9067 (tp30) cc_final: 0.8319 (tp30) REVERT: B 668 TYR cc_start: 0.9098 (m-80) cc_final: 0.8817 (m-80) outliers start: 30 outliers final: 20 residues processed: 133 average time/residue: 1.0230 time to fit residues: 150.2874 Evaluate side-chains 132 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 685 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 863 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN B 779 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.120070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084915 restraints weight = 21688.314| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.95 r_work: 0.3049 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11998 Z= 0.293 Angle : 0.642 12.324 16266 Z= 0.322 Chirality : 0.041 0.176 1786 Planarity : 0.005 0.059 2010 Dihedral : 4.180 20.806 1562 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.19 % Allowed : 17.24 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.22), residues: 1382 helix: 2.17 (0.17), residues: 870 sheet: 0.53 (0.62), residues: 62 loop : -0.93 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 273 HIS 0.005 0.001 HIS A 108 PHE 0.028 0.002 PHE B 462 TYR 0.014 0.001 TYR B 827 ARG 0.016 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3540.44 seconds wall clock time: 64 minutes 21.58 seconds (3861.58 seconds total)