Starting phenix.real_space_refine on Fri Mar 15 07:30:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/03_2024/6of4_20042.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/03_2024/6of4_20042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/03_2024/6of4_20042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/03_2024/6of4_20042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/03_2024/6of4_20042.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/03_2024/6of4_20042.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 0.673 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7028 2.51 5 N 1920 2.21 5 O 1996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10998 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4048 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 52, 'TRANS': 475} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4048 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 52, 'TRANS': 475} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 6.47, per 1000 atoms: 0.59 Number of scatterers: 10998 At special positions: 0 Unit cell: (146.88, 89.64, 89.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1996 8.00 N 1920 7.00 C 7028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.32 Conformation dependent library (CDL) restraints added in 2.2 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: 2652 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 40.4% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 4.271A pdb=" N LEU A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 67 through 84 removed outlier: 3.500A pdb=" N GLU A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 115 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 134 through 147 removed outlier: 4.261A pdb=" N VAL A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.935A pdb=" N LEU B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 242 through 258 removed outlier: 3.501A pdb=" N ASN B 246 " --> pdb=" O HIS B 242 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 292 through 296 removed outlier: 4.522A pdb=" N SER B 296 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.870A pdb=" N CYS B 333 " --> pdb=" O PRO B 330 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS B 334 " --> pdb=" O PRO B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 334' Processing helix chain 'B' and resid 367 through 387 Processing helix chain 'B' and resid 403 through 417 Processing helix chain 'B' and resid 429 through 443 removed outlier: 3.633A pdb=" N SER B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 Processing helix chain 'B' and resid 535 through 544 removed outlier: 4.239A pdb=" N SER B 540 " --> pdb=" O PRO B 536 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.591A pdb=" N LEU B 658 " --> pdb=" O PRO B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 691 removed outlier: 4.045A pdb=" N VAL B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS B 691 " --> pdb=" O LYS B 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 4.271A pdb=" N LEU D 15 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 41 through 64 Processing helix chain 'D' and resid 67 through 84 removed outlier: 3.500A pdb=" N GLU D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 115 Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 134 through 147 removed outlier: 4.261A pdb=" N VAL D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 170 Processing helix chain 'D' and resid 171 through 174 Processing helix chain 'E' and resid 196 through 202 removed outlier: 3.935A pdb=" N LEU E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU E 202 " --> pdb=" O GLN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 211 Proline residue: E 208 - end of helix Processing helix chain 'E' and resid 242 through 258 removed outlier: 3.502A pdb=" N ASN E 246 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG E 258 " --> pdb=" O THR E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 292 through 296 removed outlier: 4.522A pdb=" N SER E 296 " --> pdb=" O LYS E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 334 removed outlier: 3.870A pdb=" N CYS E 333 " --> pdb=" O PRO E 330 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS E 334 " --> pdb=" O PRO E 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 330 through 334' Processing helix chain 'E' and resid 367 through 387 Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 429 through 443 removed outlier: 3.632A pdb=" N SER E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 484 Processing helix chain 'E' and resid 535 through 544 removed outlier: 4.238A pdb=" N SER E 540 " --> pdb=" O PRO E 536 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP E 541 " --> pdb=" O GLU E 537 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN E 544 " --> pdb=" O SER E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 660 removed outlier: 3.591A pdb=" N LEU E 658 " --> pdb=" O PRO E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 677 through 691 removed outlier: 4.045A pdb=" N VAL E 681 " --> pdb=" O THR E 677 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU E 684 " --> pdb=" O TYR E 680 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS E 691 " --> pdb=" O LYS E 687 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349 removed outlier: 3.672A pdb=" N GLU B 646 " --> pdb=" O SER B 639 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 637 " --> pdb=" O HIS B 648 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 650 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE B 635 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU B 550 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU B 632 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET B 548 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 122 through 125 removed outlier: 3.963A pdb=" N ARG B 123 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 130 " --> pdb=" O ARG B 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 358 removed outlier: 7.026A pdb=" N LEU B 320 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N MET B 356 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 318 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 420 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 349 removed outlier: 3.672A pdb=" N GLU E 646 " --> pdb=" O SER E 639 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY E 637 " --> pdb=" O HIS E 648 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU E 650 " --> pdb=" O ILE E 635 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE E 635 " --> pdb=" O LEU E 650 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU E 550 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU E 632 " --> pdb=" O MET E 548 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET E 548 " --> pdb=" O LEU E 632 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.963A pdb=" N ARG E 123 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL E 130 " --> pdb=" O ARG E 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 159 through 161 Processing sheet with id=AB1, first strand: chain 'E' and resid 351 through 358 removed outlier: 7.027A pdb=" N LEU E 320 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N MET E 356 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL E 318 " --> pdb=" O MET E 356 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU E 420 " --> pdb=" O ILE E 263 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1392 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: 3.16 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3528 1.34 - 1.45: 1629 1.45 - 1.57: 6051 1.57 - 1.69: 0 1.69 - 1.80: 88 Bond restraints: 11296 Sorted by residual: bond pdb=" C ALA E 535 " pdb=" N PRO E 536 " ideal model delta sigma weight residual 1.335 1.309 0.026 1.38e-02 5.25e+03 3.49e+00 bond pdb=" C ALA B 535 " pdb=" N PRO B 536 " ideal model delta sigma weight residual 1.335 1.310 0.025 1.38e-02 5.25e+03 3.38e+00 bond pdb=" CB TRP A 355 " pdb=" CG TRP A 355 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.04e+00 bond pdb=" CB TRP D 355 " pdb=" CG TRP D 355 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.01e+00 bond pdb=" CB TRP D 60 " pdb=" CG TRP D 60 " ideal model delta sigma weight residual 1.498 1.447 0.051 3.10e-02 1.04e+03 2.74e+00 ... (remaining 11291 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.68: 506 105.68 - 112.79: 6024 112.79 - 119.89: 3619 119.89 - 127.00: 5025 127.00 - 134.11: 238 Bond angle restraints: 15412 Sorted by residual: angle pdb=" N PRO E 455 " pdb=" CA PRO E 455 " pdb=" CB PRO E 455 " ideal model delta sigma weight residual 103.00 110.52 -7.52 1.10e+00 8.26e-01 4.67e+01 angle pdb=" N PRO B 455 " pdb=" CA PRO B 455 " pdb=" CB PRO B 455 " ideal model delta sigma weight residual 103.00 110.48 -7.48 1.10e+00 8.26e-01 4.62e+01 angle pdb=" N ALA B 290 " pdb=" CA ALA B 290 " pdb=" C ALA B 290 " ideal model delta sigma weight residual 110.80 124.04 -13.24 2.13e+00 2.20e-01 3.86e+01 angle pdb=" N ALA E 290 " pdb=" CA ALA E 290 " pdb=" C ALA E 290 " ideal model delta sigma weight residual 110.80 124.02 -13.22 2.13e+00 2.20e-01 3.85e+01 angle pdb=" C HIS A 146 " pdb=" N GLU A 147 " pdb=" CA GLU A 147 " ideal model delta sigma weight residual 122.15 106.53 15.62 2.83e+00 1.25e-01 3.05e+01 ... (remaining 15407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 6128 17.44 - 34.87: 436 34.87 - 52.31: 86 52.31 - 69.75: 78 69.75 - 87.18: 14 Dihedral angle restraints: 6742 sinusoidal: 2650 harmonic: 4092 Sorted by residual: dihedral pdb=" CA ARG B 295 " pdb=" C ARG B 295 " pdb=" N SER B 296 " pdb=" CA SER B 296 " ideal model delta harmonic sigma weight residual -180.00 -132.61 -47.39 0 5.00e+00 4.00e-02 8.98e+01 dihedral pdb=" CA ARG E 295 " pdb=" C ARG E 295 " pdb=" N SER E 296 " pdb=" CA SER E 296 " ideal model delta harmonic sigma weight residual -180.00 -132.61 -47.39 0 5.00e+00 4.00e-02 8.98e+01 dihedral pdb=" CA ALA D 91 " pdb=" C ALA D 91 " pdb=" N GLY D 92 " pdb=" CA GLY D 92 " ideal model delta harmonic sigma weight residual -180.00 -148.19 -31.81 0 5.00e+00 4.00e-02 4.05e+01 ... (remaining 6739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1012 0.048 - 0.096: 511 0.096 - 0.143: 149 0.143 - 0.191: 48 0.191 - 0.239: 6 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA ALA B 290 " pdb=" N ALA B 290 " pdb=" C ALA B 290 " pdb=" CB ALA B 290 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ALA E 290 " pdb=" N ALA E 290 " pdb=" C ALA E 290 " pdb=" CB ALA E 290 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PRO E 455 " pdb=" N PRO E 455 " pdb=" C PRO E 455 " pdb=" CB PRO E 455 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1723 not shown) Planarity restraints: 1978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 330 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.56e+00 pdb=" N PRO E 331 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 331 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 331 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 330 " 0.049 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO B 331 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 509 " 0.042 5.00e-02 4.00e+02 6.20e-02 6.14e+00 pdb=" N PRO E 510 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 510 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 510 " 0.034 5.00e-02 4.00e+02 ... (remaining 1975 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 187 2.65 - 3.21: 10602 3.21 - 3.78: 15009 3.78 - 4.34: 19213 4.34 - 4.90: 33309 Nonbonded interactions: 78320 Sorted by model distance: nonbonded pdb=" OG SER E 272 " pdb=" O MET E 424 " model vdw 2.091 2.440 nonbonded pdb=" OG SER B 272 " pdb=" O MET B 424 " model vdw 2.091 2.440 nonbonded pdb=" O SER B 444 " pdb=" OG1 THR B 445 " model vdw 2.170 2.440 nonbonded pdb=" O SER E 444 " pdb=" OG1 THR E 445 " model vdw 2.170 2.440 nonbonded pdb=" NH2 ARG E 201 " pdb=" OD1 ASN E 215 " model vdw 2.229 2.520 ... (remaining 78315 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } 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=0.20 max=1.00 mean=0.96 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: 0.670 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: 3.100 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 32.590 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.010 0.064 11296 Z= 0.692 Angle : 1.187 15.624 15412 Z= 0.643 Chirality : 0.062 0.239 1726 Planarity : 0.009 0.073 1978 Dihedral : 15.119 87.184 4090 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 3.55 % Allowed : 19.61 % Favored : 76.85 % Rotamer: Outliers : 2.54 % Allowed : 6.44 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.17), residues: 1382 helix: -2.88 (0.15), residues: 456 sheet: -1.37 (0.33), residues: 202 loop : -4.37 (0.18), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 297 HIS 0.008 0.002 HIS D 68 PHE 0.026 0.003 PHE A 107 TYR 0.034 0.004 TYR E 530 ARG 0.005 0.001 ARG A 56 *********************** 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 331 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 301 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 120 ASN cc_start: 0.7377 (t0) cc_final: 0.7076 (t0) REVERT: B 128 ARG cc_start: 0.6520 (ptt180) cc_final: 0.6009 (ptp-170) REVERT: B 139 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6937 (m-10) REVERT: B 156 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8584 (tp) REVERT: B 164 ILE cc_start: 0.8876 (mt) cc_final: 0.8546 (pt) REVERT: B 183 THR cc_start: 0.7986 (m) cc_final: 0.7723 (t) REVERT: B 275 SER cc_start: 0.8651 (m) cc_final: 0.8430 (t) REVERT: B 557 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8849 (tp30) REVERT: B 723 VAL cc_start: 0.9126 (t) cc_final: 0.8848 (p) REVERT: E 109 MET cc_start: 0.3795 (mtm) cc_final: 0.3156 (tmm) REVERT: E 156 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8813 (tt) REVERT: E 183 THR cc_start: 0.8287 (m) cc_final: 0.7934 (t) REVERT: E 239 LEU cc_start: 0.7453 (tp) cc_final: 0.7247 (tt) REVERT: E 298 LYS cc_start: 0.8540 (mptt) cc_final: 0.8219 (mmtt) REVERT: E 349 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6570 (mp0) REVERT: E 376 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8018 (tpp80) REVERT: E 557 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8901 (tp30) REVERT: E 665 GLU cc_start: 0.7645 (pt0) cc_final: 0.7202 (pt0) outliers start: 30 outliers final: 5 residues processed: 324 average time/residue: 0.2603 time to fit residues: 114.1546 Evaluate side-chains 197 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 188 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 376 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 0.0270 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.0030 chunk 81 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 overall best weight: 0.4848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS B 115 GLN B 144 ASN B 151 GLN B 174 HIS B 533 GLN D 62 GLN D 146 HIS E 115 GLN E 533 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11296 Z= 0.202 Angle : 0.803 11.117 15412 Z= 0.399 Chirality : 0.045 0.268 1726 Planarity : 0.007 0.057 1978 Dihedral : 6.665 80.653 1548 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.51 % Allowed : 10.06 % Favored : 89.44 % Rotamer: Outliers : 3.14 % Allowed : 13.90 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.70 % 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: -1.15 (0.23), residues: 1382 helix: 1.97 (0.22), residues: 478 sheet: -0.38 (0.33), residues: 256 loop : -3.27 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 297 HIS 0.013 0.001 HIS B 174 PHE 0.015 0.002 PHE B 379 TYR 0.016 0.002 TYR E 423 ARG 0.006 0.001 ARG B 376 *********************** 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 273 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 HIS cc_start: 0.7703 (t70) cc_final: 0.6781 (t70) REVERT: B 198 GLN cc_start: 0.8880 (tp40) cc_final: 0.8648 (tp40) REVERT: B 309 GLN cc_start: 0.8689 (pm20) cc_final: 0.8410 (pm20) REVERT: B 395 VAL cc_start: 0.8354 (p) cc_final: 0.8134 (p) REVERT: B 557 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8692 (tp30) REVERT: D 62 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8248 (tp40) REVERT: E 109 MET cc_start: 0.4523 (mtm) cc_final: 0.3436 (tmm) REVERT: E 128 ARG cc_start: 0.6338 (ptt180) cc_final: 0.5955 (ptp-170) REVERT: E 129 LEU cc_start: 0.7593 (mp) cc_final: 0.7331 (tt) REVERT: E 156 ILE cc_start: 0.8981 (mt) cc_final: 0.8776 (tt) REVERT: E 239 LEU cc_start: 0.7454 (tp) cc_final: 0.7218 (tt) REVERT: E 396 ASN cc_start: 0.6969 (p0) cc_final: 0.6758 (p0) REVERT: E 557 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8710 (tp30) outliers start: 37 outliers final: 19 residues processed: 259 average time/residue: 0.1975 time to fit residues: 75.3476 Evaluate side-chains 209 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 189 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 ASN Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 666 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 0.0050 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 242 HIS B 327 ASN E 327 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11296 Z= 0.191 Angle : 0.703 9.273 15412 Z= 0.343 Chirality : 0.043 0.182 1726 Planarity : 0.006 0.055 1978 Dihedral : 5.693 71.960 1528 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.91 % Favored : 89.65 % Rotamer: Outliers : 3.81 % Allowed : 15.51 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.01 (0.24), residues: 1382 helix: 3.03 (0.23), residues: 480 sheet: 0.48 (0.37), residues: 208 loop : -2.57 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.010 0.001 HIS E 532 PHE 0.030 0.002 PHE B 332 TYR 0.011 0.001 TYR E 423 ARG 0.006 0.001 ARG A 160 *********************** 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 240 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 195 time to evaluate : 1.291 Fit side-chains REVERT: B 174 HIS cc_start: 0.7358 (t70) cc_final: 0.6790 (t70) REVERT: B 309 GLN cc_start: 0.8668 (pm20) cc_final: 0.8345 (pm20) REVERT: B 512 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7382 (ttt90) REVERT: B 557 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8758 (tp30) REVERT: E 109 MET cc_start: 0.4295 (mtm) cc_final: 0.3264 (tmm) REVERT: E 239 LEU cc_start: 0.7584 (tp) cc_final: 0.7325 (tt) REVERT: E 557 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8737 (tp30) outliers start: 45 outliers final: 24 residues processed: 219 average time/residue: 0.1882 time to fit residues: 61.8792 Evaluate side-chains 211 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain D residue 66 CYS Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 351 MET Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 666 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 0.3980 chunk 135 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11296 Z= 0.252 Angle : 0.688 9.094 15412 Z= 0.340 Chirality : 0.043 0.218 1726 Planarity : 0.006 0.049 1978 Dihedral : 5.499 65.451 1528 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.70 % Favored : 90.01 % Rotamer: Outliers : 3.39 % Allowed : 17.12 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.05 (0.24), residues: 1382 helix: 2.87 (0.23), residues: 488 sheet: -0.24 (0.32), residues: 262 loop : -2.48 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 400 HIS 0.004 0.001 HIS E 370 PHE 0.015 0.002 PHE B 332 TYR 0.019 0.002 TYR E 423 ARG 0.005 0.001 ARG B 417 *********************** 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 245 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 205 time to evaluate : 1.238 Fit side-chains REVERT: A 66 CYS cc_start: 0.8537 (t) cc_final: 0.8334 (t) REVERT: B 165 ASP cc_start: 0.8567 (m-30) cc_final: 0.8360 (m-30) REVERT: B 174 HIS cc_start: 0.7467 (t70) cc_final: 0.6917 (t70) REVERT: B 198 GLN cc_start: 0.8997 (tp40) cc_final: 0.8796 (tp-100) REVERT: B 309 GLN cc_start: 0.8684 (pm20) cc_final: 0.8339 (pm20) REVERT: B 512 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7268 (ttt90) REVERT: B 557 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8801 (tp30) REVERT: D 66 CYS cc_start: 0.8511 (t) cc_final: 0.8306 (t) REVERT: E 109 MET cc_start: 0.4430 (mtm) cc_final: 0.3337 (tmm) REVERT: E 239 LEU cc_start: 0.7716 (tp) cc_final: 0.7441 (tt) REVERT: E 309 GLN cc_start: 0.8566 (pm20) cc_final: 0.8317 (pm20) REVERT: E 557 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8772 (tp30) outliers start: 40 outliers final: 26 residues processed: 227 average time/residue: 0.1844 time to fit residues: 63.8663 Evaluate side-chains 223 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 196 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 351 MET Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 666 LEU Chi-restraints excluded: chain E residue 674 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11296 Z= 0.393 Angle : 0.736 10.154 15412 Z= 0.367 Chirality : 0.045 0.153 1726 Planarity : 0.006 0.052 1978 Dihedral : 5.548 62.681 1528 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.22 % Favored : 88.49 % Rotamer: Outliers : 4.15 % Allowed : 17.54 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.23 (0.24), residues: 1382 helix: 2.64 (0.23), residues: 488 sheet: -0.38 (0.31), residues: 260 loop : -2.48 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 171 HIS 0.006 0.001 HIS E 648 PHE 0.018 0.002 PHE A 107 TYR 0.016 0.002 TYR E 626 ARG 0.005 0.001 ARG B 417 *********************** 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 243 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 1.216 Fit side-chains REVERT: B 165 ASP cc_start: 0.8654 (m-30) cc_final: 0.8449 (m-30) REVERT: B 174 HIS cc_start: 0.7638 (t70) cc_final: 0.7044 (t70) REVERT: B 185 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7703 (t0) REVERT: B 309 GLN cc_start: 0.8662 (pm20) cc_final: 0.8321 (pm20) REVERT: B 512 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7176 (ttt90) REVERT: B 557 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8806 (tp30) REVERT: D 66 CYS cc_start: 0.8550 (t) cc_final: 0.8337 (t) REVERT: E 109 MET cc_start: 0.4376 (mtm) cc_final: 0.3527 (tmm) REVERT: E 165 ASP cc_start: 0.8586 (m-30) cc_final: 0.8386 (m-30) REVERT: E 239 LEU cc_start: 0.7757 (tp) cc_final: 0.7473 (tt) REVERT: E 309 GLN cc_start: 0.8667 (pm20) cc_final: 0.8419 (pm20) REVERT: E 512 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7035 (ttt90) REVERT: E 557 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8831 (tp30) outliers start: 49 outliers final: 36 residues processed: 222 average time/residue: 0.1874 time to fit residues: 62.6190 Evaluate side-chains 226 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 187 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 400 TRP Chi-restraints excluded: chain E residue 512 ARG Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 666 LEU Chi-restraints excluded: chain E residue 674 ASP Chi-restraints excluded: chain E residue 723 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 0.0010 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11296 Z= 0.201 Angle : 0.646 8.532 15412 Z= 0.317 Chirality : 0.042 0.150 1726 Planarity : 0.006 0.048 1978 Dihedral : 5.089 34.144 1528 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.68 % Favored : 91.17 % Rotamer: Outliers : 3.90 % Allowed : 18.31 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.04 (0.24), residues: 1382 helix: 2.91 (0.23), residues: 488 sheet: -0.29 (0.31), residues: 262 loop : -2.33 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 400 HIS 0.003 0.001 HIS E 648 PHE 0.012 0.001 PHE B 332 TYR 0.010 0.001 TYR B 382 ARG 0.005 0.000 ARG A 160 *********************** 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 242 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 196 time to evaluate : 1.329 Fit side-chains REVERT: B 165 ASP cc_start: 0.8580 (m-30) cc_final: 0.8358 (m-30) REVERT: B 185 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7400 (t0) REVERT: B 557 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8733 (tp30) REVERT: B 649 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7675 (pp) REVERT: D 362 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8726 (tt) REVERT: E 109 MET cc_start: 0.4143 (mtm) cc_final: 0.3303 (tmm) REVERT: E 165 ASP cc_start: 0.8554 (m-30) cc_final: 0.8342 (m-30) REVERT: E 512 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7010 (ttt90) REVERT: E 543 ILE cc_start: 0.8333 (tp) cc_final: 0.8090 (tp) REVERT: E 557 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8793 (tp30) REVERT: E 649 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7697 (pp) outliers start: 46 outliers final: 28 residues processed: 222 average time/residue: 0.1774 time to fit residues: 60.2147 Evaluate side-chains 224 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 400 TRP Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 512 ARG Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 723 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.0030 chunk 83 optimal weight: 0.8980 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 454 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11296 Z= 0.264 Angle : 0.660 8.314 15412 Z= 0.325 Chirality : 0.043 0.154 1726 Planarity : 0.006 0.046 1978 Dihedral : 4.994 31.390 1528 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.99 % Favored : 89.87 % Rotamer: Outliers : 4.15 % Allowed : 18.39 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.02 (0.24), residues: 1382 helix: 2.81 (0.24), residues: 488 sheet: -0.30 (0.31), residues: 262 loop : -2.27 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 400 HIS 0.004 0.001 HIS E 648 PHE 0.011 0.001 PHE B 312 TYR 0.025 0.002 TYR E 423 ARG 0.004 0.000 ARG A 160 *********************** 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 253 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 204 time to evaluate : 1.193 Fit side-chains REVERT: A 362 ILE cc_start: 0.9143 (mt) cc_final: 0.8762 (tt) REVERT: B 165 ASP cc_start: 0.8604 (m-30) cc_final: 0.8381 (m-30) REVERT: B 185 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7343 (t0) REVERT: B 512 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7079 (ttt90) REVERT: B 557 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8779 (tp30) REVERT: B 649 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7691 (pp) REVERT: D 362 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8763 (tt) REVERT: E 109 MET cc_start: 0.4324 (mtm) cc_final: 0.3488 (tmm) REVERT: E 131 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7721 (pp) REVERT: E 165 ASP cc_start: 0.8575 (m-30) cc_final: 0.8353 (m-30) REVERT: E 512 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7022 (ttt90) REVERT: E 543 ILE cc_start: 0.8407 (tp) cc_final: 0.8163 (tp) REVERT: E 557 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8808 (tp30) REVERT: E 649 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7699 (pp) outliers start: 49 outliers final: 33 residues processed: 232 average time/residue: 0.1910 time to fit residues: 66.7368 Evaluate side-chains 239 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 400 TRP Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 512 ARG Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 674 ASP Chi-restraints excluded: chain E residue 723 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11296 Z= 0.210 Angle : 0.639 7.968 15412 Z= 0.313 Chirality : 0.042 0.168 1726 Planarity : 0.005 0.045 1978 Dihedral : 4.899 29.607 1528 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.83 % Favored : 91.03 % Rotamer: Outliers : 3.47 % Allowed : 19.41 % Favored : 77.12 % 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: 0.15 (0.24), residues: 1382 helix: 2.95 (0.24), residues: 486 sheet: -0.22 (0.31), residues: 262 loop : -2.21 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 400 HIS 0.003 0.001 HIS B 648 PHE 0.012 0.001 PHE B 312 TYR 0.024 0.001 TYR E 423 ARG 0.004 0.000 ARG B 417 *********************** 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 244 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 203 time to evaluate : 1.328 Fit side-chains REVERT: A 362 ILE cc_start: 0.9129 (mt) cc_final: 0.8764 (tt) REVERT: B 109 MET cc_start: 0.2224 (OUTLIER) cc_final: 0.1646 (tmm) REVERT: B 165 ASP cc_start: 0.8559 (m-30) cc_final: 0.8330 (m-30) REVERT: B 185 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7281 (t0) REVERT: B 512 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7048 (ttt90) REVERT: B 557 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8767 (tp30) REVERT: B 649 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7673 (pp) REVERT: D 362 ILE cc_start: 0.9121 (mt) cc_final: 0.8780 (tt) REVERT: E 109 MET cc_start: 0.4224 (mtm) cc_final: 0.3394 (tmm) REVERT: E 131 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7659 (pp) REVERT: E 165 ASP cc_start: 0.8559 (m-30) cc_final: 0.8335 (m-30) REVERT: E 512 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6989 (ttt90) REVERT: E 543 ILE cc_start: 0.8355 (tp) cc_final: 0.8107 (tp) REVERT: E 557 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8797 (tp30) REVERT: E 649 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7684 (pp) outliers start: 41 outliers final: 30 residues processed: 227 average time/residue: 0.1886 time to fit residues: 64.5742 Evaluate side-chains 237 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 200 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 400 TRP Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 512 ARG Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 674 ASP Chi-restraints excluded: chain E residue 723 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.8980 chunk 125 optimal weight: 0.0770 chunk 129 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 0.0470 chunk 118 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 132 optimal weight: 0.0270 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11296 Z= 0.146 Angle : 0.621 7.502 15412 Z= 0.299 Chirality : 0.041 0.163 1726 Planarity : 0.005 0.042 1978 Dihedral : 4.724 29.681 1528 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.18 % Favored : 91.68 % Rotamer: Outliers : 2.97 % Allowed : 20.00 % Favored : 77.03 % 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: 0.35 (0.25), residues: 1382 helix: 3.11 (0.24), residues: 486 sheet: 0.04 (0.32), residues: 260 loop : -2.17 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 167 HIS 0.002 0.000 HIS B 532 PHE 0.014 0.001 PHE B 312 TYR 0.027 0.001 TYR E 423 ARG 0.004 0.000 ARG A 160 *********************** 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 228 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 1.380 Fit side-chains REVERT: A 362 ILE cc_start: 0.9117 (mt) cc_final: 0.8767 (tt) REVERT: B 109 MET cc_start: 0.2118 (OUTLIER) cc_final: 0.1458 (tmm) REVERT: B 165 ASP cc_start: 0.8485 (m-30) cc_final: 0.8247 (m-30) REVERT: B 185 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7089 (t0) REVERT: B 512 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7064 (ttt90) REVERT: B 557 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8703 (tp30) REVERT: B 649 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7624 (pp) REVERT: D 362 ILE cc_start: 0.9115 (mt) cc_final: 0.8775 (tt) REVERT: E 109 MET cc_start: 0.4181 (mtm) cc_final: 0.3194 (tmm) REVERT: E 131 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7599 (pp) REVERT: E 136 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8210 (p) REVERT: E 165 ASP cc_start: 0.8480 (m-30) cc_final: 0.8247 (m-30) REVERT: E 512 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.6970 (ttt90) REVERT: E 543 ILE cc_start: 0.8238 (tp) cc_final: 0.8021 (tp) REVERT: E 557 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8833 (tp30) REVERT: E 649 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7642 (pp) outliers start: 35 outliers final: 22 residues processed: 213 average time/residue: 0.1831 time to fit residues: 59.4367 Evaluate side-chains 217 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 400 TRP Chi-restraints excluded: chain E residue 512 ARG Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 674 ASP Chi-restraints excluded: chain E residue 723 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 118 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7794 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11296 Z= 0.167 Angle : 0.623 7.582 15412 Z= 0.300 Chirality : 0.041 0.164 1726 Planarity : 0.005 0.040 1978 Dihedral : 4.645 29.056 1528 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.39 % Favored : 91.46 % Rotamer: Outliers : 2.80 % Allowed : 20.34 % Favored : 76.86 % 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: 0.43 (0.25), residues: 1382 helix: 3.16 (0.24), residues: 486 sheet: 0.06 (0.32), residues: 260 loop : -2.09 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 400 HIS 0.002 0.001 HIS E 648 PHE 0.014 0.001 PHE B 312 TYR 0.025 0.001 TYR E 423 ARG 0.004 0.000 ARG B 417 ********************** 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 224 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 1.246 Fit side-chains REVERT: A 362 ILE cc_start: 0.9124 (mt) cc_final: 0.8778 (tt) REVERT: B 109 MET cc_start: 0.1987 (OUTLIER) cc_final: 0.1355 (tmm) REVERT: B 165 ASP cc_start: 0.8488 (m-30) cc_final: 0.8259 (m-30) REVERT: B 185 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7114 (t0) REVERT: B 512 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7048 (ttt90) REVERT: B 557 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8712 (tp30) REVERT: B 649 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7641 (pp) REVERT: D 362 ILE cc_start: 0.9125 (mt) cc_final: 0.8791 (tt) REVERT: E 109 MET cc_start: 0.4213 (mtm) cc_final: 0.3254 (tmm) REVERT: E 131 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7686 (pp) REVERT: E 136 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8201 (p) REVERT: E 165 ASP cc_start: 0.8473 (m-30) cc_final: 0.8236 (m-30) REVERT: E 512 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6942 (ttt90) REVERT: E 543 ILE cc_start: 0.8314 (tp) cc_final: 0.8063 (tp) REVERT: E 546 MET cc_start: 0.8731 (mmm) cc_final: 0.8449 (mmm) REVERT: E 557 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8820 (tp30) REVERT: E 649 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7651 (pp) outliers start: 33 outliers final: 22 residues processed: 208 average time/residue: 0.1901 time to fit residues: 59.4078 Evaluate side-chains 218 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 400 TRP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 381 TYR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 400 TRP Chi-restraints excluded: chain E residue 512 ARG Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 674 ASP Chi-restraints excluded: chain E residue 723 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.078563 restraints weight = 19448.769| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.17 r_work: 0.2950 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 73 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11296 Z= 0.309 Angle : 0.683 9.746 15412 Z= 0.336 Chirality : 0.043 0.167 1726 Planarity : 0.006 0.042 1978 Dihedral : 4.788 31.288 1528 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.35 % Favored : 89.51 % Rotamer: Outliers : 2.88 % Allowed : 20.42 % Favored : 76.69 % 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: 0.22 (0.24), residues: 1382 helix: 2.96 (0.24), residues: 486 sheet: -0.19 (0.31), residues: 260 loop : -2.12 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 171 HIS 0.005 0.001 HIS E 648 PHE 0.013 0.002 PHE D 107 TYR 0.024 0.002 TYR E 423 ARG 0.003 0.000 ARG A 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2488.15 seconds wall clock time: 45 minutes 16.38 seconds (2716.38 seconds total)