Starting phenix.real_space_refine on Wed Feb 14 22:07:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx2_24722/02_2024/7rx2_24722_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx2_24722/02_2024/7rx2_24722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx2_24722/02_2024/7rx2_24722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx2_24722/02_2024/7rx2_24722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx2_24722/02_2024/7rx2_24722_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx2_24722/02_2024/7rx2_24722_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 12 5.49 5 S 38 5.16 5 C 6810 2.51 5 N 1664 2.21 5 O 1850 1.98 5 H 12 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 104": "OE1" <-> "OE2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ARG 642": "NH1" <-> "NH2" Residue "B ARG 647": "NH1" <-> "NH2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B GLU 714": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "A ARG 647": "NH1" <-> "NH2" Residue "A ARG 651": "NH1" <-> "NH2" Residue "A GLU 714": "OE1" <-> "OE2" 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: 10390 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4969 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 30, 'TRANS': 584} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 4969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4969 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 30, 'TRANS': 584} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 217 Unusual residues: {' CA': 2, 'PGW': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 217 Unusual residues: {' CA': 2, 'PGW': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 6.01, per 1000 atoms: 0.58 Number of scatterers: 10390 At special positions: 0 Unit cell: (117.312, 101.058, 98.2313, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 38 16.00 P 12 15.00 O 1850 8.00 N 1664 7.00 C 6810 6.00 H 12 1.00 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: 4.43 Conformation dependent library (CDL) restraints added in 1.8 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 2 sheets defined 65.2% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.872A pdb=" N VAL B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 85 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 175 through 203 removed outlier: 3.592A pdb=" N TYR B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Proline residue: B 194 - end of helix Processing helix chain 'B' and resid 210 through 238 removed outlier: 3.644A pdb=" N GLU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 246 Processing helix chain 'B' and resid 273 through 310 removed outlier: 3.638A pdb=" N ARG B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLN B 283 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Proline residue: B 285 - end of helix removed outlier: 3.624A pdb=" N ILE B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 320 No H-bonds generated for 'chain 'B' and resid 317 through 320' Processing helix chain 'B' and resid 322 through 329 Processing helix chain 'B' and resid 332 through 349 Processing helix chain 'B' and resid 355 through 384 removed outlier: 4.037A pdb=" N VAL B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 425 through 434 Processing helix chain 'B' and resid 436 through 451 removed outlier: 3.527A pdb=" N ALA B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix Processing helix chain 'B' and resid 489 through 502 removed outlier: 4.100A pdb=" N ARG B 492 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE B 493 " --> pdb=" O GLU B 490 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 494 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B 500 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 501 " --> pdb=" O ARG B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 525 removed outlier: 3.509A pdb=" N LEU B 522 " --> pdb=" O GLN B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 553 removed outlier: 3.508A pdb=" N VAL B 542 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 590 removed outlier: 3.519A pdb=" N GLY B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 604 No H-bonds generated for 'chain 'B' and resid 602 through 604' Processing helix chain 'B' and resid 607 through 634 removed outlier: 3.654A pdb=" N LYS B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 657 Processing helix chain 'B' and resid 703 through 705 No H-bonds generated for 'chain 'B' and resid 703 through 705' Processing helix chain 'B' and resid 712 through 725 Processing helix chain 'A' and resid 29 through 45 removed outlier: 3.873A pdb=" N VAL A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 85 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 175 through 203 removed outlier: 3.593A pdb=" N TYR A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 210 through 238 removed outlier: 3.643A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 273 through 310 removed outlier: 3.638A pdb=" N ARG A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLN A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix removed outlier: 3.624A pdb=" N ILE A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 322 through 329 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 355 through 384 removed outlier: 4.037A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 425 through 434 Processing helix chain 'A' and resid 436 through 451 removed outlier: 3.527A pdb=" N ALA A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 489 through 502 removed outlier: 4.099A pdb=" N ARG A 492 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A 493 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 494 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 500 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 501 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 525 removed outlier: 3.509A pdb=" N LEU A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 553 removed outlier: 3.508A pdb=" N VAL A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 590 removed outlier: 3.520A pdb=" N GLY A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 604 No H-bonds generated for 'chain 'A' and resid 602 through 604' Processing helix chain 'A' and resid 607 through 634 removed outlier: 3.654A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 657 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 712 through 725 Processing sheet with id= A, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.551A pdb=" N TYR B 18 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 138 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.551A pdb=" N TYR A 18 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 138 " --> pdb=" O ARG A 21 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1620 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: 2.71 Time building geometry restraints manager: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 12 1.03 - 1.22: 43 1.22 - 1.42: 4415 1.42 - 1.61: 6086 1.61 - 1.81: 72 Bond restraints: 10628 Sorted by residual: bond pdb=" C1 PGW A1508 " pdb=" O01 PGW A1508 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C1 PGW B 807 " pdb=" O01 PGW B 807 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C1 PGW A1504 " pdb=" O01 PGW A1504 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C1 PGW B 803 " pdb=" O01 PGW B 803 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C1 PGW B 805 " pdb=" O01 PGW B 805 " ideal model delta sigma weight residual 1.332 1.419 -0.087 2.00e-02 2.50e+03 1.90e+01 ... (remaining 10623 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.53: 292 106.53 - 113.40: 5862 113.40 - 120.28: 4305 120.28 - 127.15: 3748 127.15 - 134.03: 143 Bond angle restraints: 14350 Sorted by residual: angle pdb=" N ASN A 593 " pdb=" CA ASN A 593 " pdb=" C ASN A 593 " ideal model delta sigma weight residual 113.41 108.17 5.24 1.22e+00 6.72e-01 1.84e+01 angle pdb=" N ASN B 593 " pdb=" CA ASN B 593 " pdb=" C ASN B 593 " ideal model delta sigma weight residual 113.41 108.18 5.23 1.22e+00 6.72e-01 1.84e+01 angle pdb=" C2 PGW B 805 " pdb=" C1 PGW B 805 " pdb=" O01 PGW B 805 " ideal model delta sigma weight residual 110.92 122.12 -11.20 3.00e+00 1.11e-01 1.39e+01 angle pdb=" O11 PGW B 805 " pdb=" P PGW B 805 " pdb=" O12 PGW B 805 " ideal model delta sigma weight residual 98.90 110.10 -11.20 3.00e+00 1.11e-01 1.39e+01 angle pdb=" C2 PGW A1506 " pdb=" C1 PGW A1506 " pdb=" O01 PGW A1506 " ideal model delta sigma weight residual 110.92 122.12 -11.20 3.00e+00 1.11e-01 1.39e+01 ... (remaining 14345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.61: 5968 27.61 - 55.22: 288 55.22 - 82.82: 80 82.82 - 110.43: 14 110.43 - 138.04: 10 Dihedral angle restraints: 6360 sinusoidal: 2738 harmonic: 3622 Sorted by residual: dihedral pdb=" CA ALA B 389 " pdb=" C ALA B 389 " pdb=" N SER B 390 " pdb=" CA SER B 390 " ideal model delta harmonic sigma weight residual 180.00 155.53 24.47 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ALA A 389 " pdb=" C ALA A 389 " pdb=" N SER A 390 " pdb=" CA SER A 390 " ideal model delta harmonic sigma weight residual 180.00 155.56 24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" C15 PGW A1507 " pdb=" C16 PGW A1507 " pdb=" C17 PGW A1507 " pdb=" C18 PGW A1507 " ideal model delta sinusoidal sigma weight residual 178.71 -43.25 -138.04 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 6357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1038 0.048 - 0.095: 445 0.095 - 0.143: 70 0.143 - 0.190: 13 0.190 - 0.238: 4 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CA VAL B 136 " pdb=" N VAL B 136 " pdb=" C VAL B 136 " pdb=" CB VAL B 136 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA VAL A 136 " pdb=" N VAL A 136 " pdb=" C VAL A 136 " pdb=" CB VAL A 136 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C02 PGW B 808 " pdb=" C01 PGW B 808 " pdb=" C03 PGW B 808 " pdb=" O01 PGW B 808 " both_signs ideal model delta sigma weight residual False 2.36 2.55 -0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 1567 not shown) Planarity restraints: 1768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 155 " -0.025 2.00e-02 2.50e+03 1.88e-02 8.85e+00 pdb=" CG TRP A 155 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 155 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 155 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 155 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 155 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 155 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 155 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 155 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 155 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 155 " 0.025 2.00e-02 2.50e+03 1.88e-02 8.80e+00 pdb=" CG TRP B 155 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 155 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 155 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 155 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 155 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 155 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 155 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 155 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 155 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 526 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO B 527 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.033 5.00e-02 4.00e+02 ... (remaining 1765 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 16 2.30 - 2.87: 3814 2.87 - 3.45: 11692 3.45 - 4.02: 20588 4.02 - 4.60: 31238 Nonbonded interactions: 67348 Sorted by model distance: nonbonded pdb=" O PHE B 173 " pdb=" H1 HOH B2301 " model vdw 1.724 1.850 nonbonded pdb=" O PHE A 173 " pdb=" H1 HOH A2301 " model vdw 1.724 1.850 nonbonded pdb=" O PRO A 558 " pdb=" H2 HOH A2302 " model vdw 1.769 1.850 nonbonded pdb=" O PRO B 558 " pdb=" H2 HOH B2302 " model vdw 1.769 1.850 nonbonded pdb=" OH TYR A 312 " pdb=" O PRO A 315 " model vdw 2.196 2.200 ... (remaining 67343 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' and (resid 11 through 727 or resid 1502 or (resid 1504 and (name C01 \ or name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name \ C4 or name C5 or name C6 or name C7 or name C8 or name O01 or name O02 or name \ O03 or name O04 or name O11)) or (resid 1505 and (name C01 or name C02 or name C \ 03 or name C1 or name C19 or name C2 or name C20 or name C21 or name C22 or name \ C23 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )) or resid 1506 or (resid 1507 and (name C01 or name C02 or na \ me C03 or name C06 or name C19 or name C2 or name C20 or name C21 or name C22 or \ name C23 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name O01 or name O02 or name O03 or name O04 or name O11 or name O12 o \ r name O13 or name O14 or name P )) or resid 1508 or (resid 1509 and (name C01 o \ r name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name C21 \ or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or \ name O01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O1 \ 3 or name O14 or name P )))) selection = (chain 'B' and (resid 11 through 727 or resid 802 or (resid 804 and (name C01 or \ name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name O01 or name O02 or name O0 \ 3 or name O04 or name O11)) or (resid 805 and (name C01 or name C02 or name C03 \ or name C1 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name O01 \ or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name \ O14 or name P )) or (resid 806 and (name C01 or name C02 or name C03 or name C1 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C \ 3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 \ or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name \ O14 or name P )) or (resid 807 and (name C01 or name C02 or name C03 or name C06 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name \ C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 \ or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name \ O14 or name P )) or resid 808 through 809)) } 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: 2.760 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: 0.250 Extract box with map and model: 12.530 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 30.680 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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:10.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 0.090 10616 Z= 0.609 Angle : 1.079 11.200 14344 Z= 0.509 Chirality : 0.052 0.238 1570 Planarity : 0.005 0.059 1768 Dihedral : 18.455 138.040 4008 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.19 % Allowed : 4.73 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.19), residues: 1210 helix: -2.88 (0.12), residues: 810 sheet: -0.67 (0.86), residues: 44 loop : -2.97 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 155 HIS 0.006 0.002 HIS B 619 PHE 0.017 0.002 PHE B 61 TYR 0.014 0.003 TYR A 352 ARG 0.010 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 1.245 Fit side-chains REVERT: B 74 ARG cc_start: 0.7520 (tpp-160) cc_final: 0.7311 (ttm-80) REVERT: B 192 MET cc_start: 0.8460 (mtt) cc_final: 0.8116 (mtp) REVERT: B 257 LYS cc_start: 0.6986 (mtpt) cc_final: 0.6620 (mmmm) REVERT: B 289 LEU cc_start: 0.8441 (tt) cc_final: 0.8119 (tt) REVERT: B 626 TYR cc_start: 0.8186 (t80) cc_final: 0.7915 (t80) REVERT: B 641 ARG cc_start: 0.7525 (ttp80) cc_final: 0.7197 (ttp80) REVERT: B 647 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7833 (ttm110) REVERT: B 704 ARG cc_start: 0.7062 (ttm170) cc_final: 0.6819 (mtm-85) REVERT: B 708 ARG cc_start: 0.7018 (tpp-160) cc_final: 0.6702 (ttm-80) REVERT: B 725 LYS cc_start: 0.7818 (tmtt) cc_final: 0.7615 (tmtp) REVERT: A 192 MET cc_start: 0.8484 (mtt) cc_final: 0.8136 (mtp) REVERT: A 257 LYS cc_start: 0.7000 (mtpt) cc_final: 0.6727 (mmmm) REVERT: A 258 GLU cc_start: 0.7438 (tp30) cc_final: 0.7223 (tp30) REVERT: A 289 LEU cc_start: 0.8418 (tt) cc_final: 0.8163 (tt) REVERT: A 626 TYR cc_start: 0.8312 (t80) cc_final: 0.8005 (t80) REVERT: A 641 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7117 (ttp80) REVERT: A 704 ARG cc_start: 0.7030 (ttm170) cc_final: 0.6825 (mtm-85) outliers start: 2 outliers final: 0 residues processed: 150 average time/residue: 1.6006 time to fit residues: 254.9499 Evaluate side-chains 114 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS B 148 ASN B 150 GLN B 370 ASN B 499 ASN B 539 ASN B 639 ASN A 113 HIS A 148 ASN A 150 GLN A 370 ASN A 499 ASN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10616 Z= 0.140 Angle : 0.491 4.423 14344 Z= 0.261 Chirality : 0.039 0.137 1570 Planarity : 0.004 0.045 1768 Dihedral : 16.852 104.393 1696 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.95 % Allowed : 10.78 % Favored : 88.28 % 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: -0.87 (0.23), residues: 1210 helix: 0.24 (0.17), residues: 818 sheet: -0.85 (0.84), residues: 44 loop : -2.41 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 712 HIS 0.003 0.001 HIS A 130 PHE 0.013 0.001 PHE A 61 TYR 0.011 0.001 TYR B 589 ARG 0.005 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.165 Fit side-chains REVERT: B 74 ARG cc_start: 0.7404 (tpp-160) cc_final: 0.7185 (ttm-80) REVERT: B 150 GLN cc_start: 0.7428 (tt0) cc_final: 0.7213 (pt0) REVERT: B 626 TYR cc_start: 0.8188 (t80) cc_final: 0.7946 (t80) REVERT: B 641 ARG cc_start: 0.7092 (ttp80) cc_final: 0.6687 (ttp80) REVERT: B 704 ARG cc_start: 0.7049 (ttm170) cc_final: 0.6844 (mtm-85) REVERT: B 708 ARG cc_start: 0.7045 (tpp-160) cc_final: 0.6826 (ttm-80) REVERT: B 725 LYS cc_start: 0.7732 (tmtt) cc_final: 0.7513 (tmtp) REVERT: A 70 LYS cc_start: 0.7992 (tmmt) cc_final: 0.7357 (mppt) REVERT: A 192 MET cc_start: 0.8430 (mtt) cc_final: 0.8197 (mtp) REVERT: A 626 TYR cc_start: 0.8280 (t80) cc_final: 0.8013 (t80) REVERT: A 641 ARG cc_start: 0.7184 (ttp80) cc_final: 0.6841 (ttt90) REVERT: A 708 ARG cc_start: 0.7195 (tpp-160) cc_final: 0.6992 (ttm-80) outliers start: 10 outliers final: 4 residues processed: 129 average time/residue: 1.3363 time to fit residues: 184.9289 Evaluate side-chains 102 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN A 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 10616 Z= 0.501 Angle : 0.682 8.179 14344 Z= 0.358 Chirality : 0.050 0.164 1570 Planarity : 0.005 0.040 1768 Dihedral : 16.970 106.854 1696 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.40 % Allowed : 12.85 % Favored : 83.74 % 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: -0.12 (0.24), residues: 1210 helix: 0.93 (0.17), residues: 818 sheet: -1.01 (0.79), residues: 48 loop : -2.41 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 155 HIS 0.010 0.002 HIS B 619 PHE 0.026 0.002 PHE A 61 TYR 0.019 0.003 TYR A 212 ARG 0.004 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 99 time to evaluate : 1.216 Fit side-chains REVERT: B 74 ARG cc_start: 0.7405 (tpp-160) cc_final: 0.7199 (ttm-80) REVERT: B 129 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6582 (ptt180) REVERT: B 192 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8346 (mtp) REVERT: B 289 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8335 (tp) REVERT: B 438 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.6241 (mp10) REVERT: B 641 ARG cc_start: 0.7387 (ttp80) cc_final: 0.7005 (ttt90) REVERT: B 704 ARG cc_start: 0.7133 (ttm170) cc_final: 0.6529 (mtt-85) REVERT: B 708 ARG cc_start: 0.7121 (tpp-160) cc_final: 0.6728 (ttm-80) REVERT: A 70 LYS cc_start: 0.8126 (tmmt) cc_final: 0.7376 (mppt) REVERT: A 438 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.6307 (mp10) REVERT: A 641 ARG cc_start: 0.7394 (ttp80) cc_final: 0.6954 (ttt90) REVERT: A 707 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7108 (mtt) REVERT: A 708 ARG cc_start: 0.7121 (tpp-160) cc_final: 0.6826 (ttm-80) outliers start: 36 outliers final: 24 residues processed: 119 average time/residue: 1.4787 time to fit residues: 188.2821 Evaluate side-chains 124 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 74 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 283 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10616 Z= 0.148 Angle : 0.445 3.847 14344 Z= 0.240 Chirality : 0.038 0.138 1570 Planarity : 0.003 0.034 1768 Dihedral : 15.338 96.399 1696 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.89 % Allowed : 15.12 % Favored : 82.99 % 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: 0.97 (0.25), residues: 1210 helix: 1.81 (0.18), residues: 818 sheet: -1.05 (0.82), residues: 44 loop : -2.08 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 227 HIS 0.004 0.001 HIS A 130 PHE 0.012 0.001 PHE A 61 TYR 0.009 0.001 TYR B 589 ARG 0.001 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.098 Fit side-chains REVERT: B 74 ARG cc_start: 0.7296 (tpp-160) cc_final: 0.7094 (ttm-80) REVERT: B 289 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8413 (tp) REVERT: B 641 ARG cc_start: 0.7189 (ttp80) cc_final: 0.6859 (ttp80) REVERT: B 708 ARG cc_start: 0.7096 (tpp-160) cc_final: 0.6869 (ttm-80) REVERT: A 70 LYS cc_start: 0.8067 (tmmt) cc_final: 0.7336 (mppt) REVERT: A 192 MET cc_start: 0.8379 (mtt) cc_final: 0.8171 (mtp) REVERT: A 257 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6742 (mppt) REVERT: A 289 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8400 (tp) REVERT: A 641 ARG cc_start: 0.7187 (ttp80) cc_final: 0.6818 (ttt90) REVERT: A 708 ARG cc_start: 0.7195 (tpp-160) cc_final: 0.6989 (ttm-80) outliers start: 20 outliers final: 10 residues processed: 115 average time/residue: 1.3601 time to fit residues: 167.5854 Evaluate side-chains 116 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 595 HIS ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10616 Z= 0.330 Angle : 0.557 5.579 14344 Z= 0.297 Chirality : 0.045 0.152 1570 Planarity : 0.004 0.034 1768 Dihedral : 15.579 97.767 1696 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.21 % Allowed : 15.31 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1210 helix: 1.76 (0.18), residues: 816 sheet: -1.01 (0.82), residues: 44 loop : -2.21 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 227 HIS 0.008 0.001 HIS B 619 PHE 0.019 0.002 PHE A 61 TYR 0.015 0.002 TYR A 212 ARG 0.003 0.001 ARG B 250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 101 time to evaluate : 1.224 Fit side-chains REVERT: B 74 ARG cc_start: 0.7362 (tpp-160) cc_final: 0.7145 (ttm-80) REVERT: B 129 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6709 (ptt180) REVERT: B 641 ARG cc_start: 0.7308 (ttp80) cc_final: 0.7012 (ttp80) REVERT: B 707 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6789 (mpp) REVERT: B 708 ARG cc_start: 0.7123 (tpp-160) cc_final: 0.6900 (ttm-80) REVERT: A 70 LYS cc_start: 0.8115 (tmmt) cc_final: 0.7380 (mppt) REVERT: A 129 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6727 (ptm160) REVERT: A 192 MET cc_start: 0.8349 (mtt) cc_final: 0.8096 (mtt) REVERT: A 438 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.6157 (mp10) REVERT: A 641 ARG cc_start: 0.7295 (ttp80) cc_final: 0.6981 (ttp80) REVERT: A 708 ARG cc_start: 0.7168 (tpp-160) cc_final: 0.6910 (ttm-80) outliers start: 34 outliers final: 24 residues processed: 122 average time/residue: 1.3908 time to fit residues: 182.0535 Evaluate side-chains 127 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 702 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.0970 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 0.0170 chunk 29 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10616 Z= 0.120 Angle : 0.408 3.617 14344 Z= 0.220 Chirality : 0.037 0.138 1570 Planarity : 0.003 0.033 1768 Dihedral : 14.469 93.251 1696 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.36 % Allowed : 16.16 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.26), residues: 1210 helix: 2.34 (0.19), residues: 820 sheet: -0.89 (0.82), residues: 44 loop : -1.87 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 227 HIS 0.003 0.001 HIS A 130 PHE 0.011 0.001 PHE B 61 TYR 0.008 0.001 TYR B 589 ARG 0.001 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.177 Fit side-chains REVERT: B 129 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6745 (ptt180) REVERT: B 257 LYS cc_start: 0.7118 (mtpp) cc_final: 0.6497 (mptt) REVERT: B 641 ARG cc_start: 0.7147 (ttp80) cc_final: 0.6816 (ttt90) REVERT: B 707 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6732 (mpp) REVERT: A 70 LYS cc_start: 0.8030 (tmmt) cc_final: 0.7340 (mppt) REVERT: A 129 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6495 (ptm160) REVERT: A 257 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6657 (mptt) REVERT: A 641 ARG cc_start: 0.7146 (ttp80) cc_final: 0.6796 (ttt90) outliers start: 25 outliers final: 14 residues processed: 122 average time/residue: 1.3382 time to fit residues: 175.2428 Evaluate side-chains 124 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10616 Z= 0.302 Angle : 0.528 4.741 14344 Z= 0.280 Chirality : 0.043 0.134 1570 Planarity : 0.004 0.031 1768 Dihedral : 15.024 95.440 1696 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.40 % Allowed : 15.88 % Favored : 80.72 % 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: 1.32 (0.25), residues: 1210 helix: 2.11 (0.18), residues: 820 sheet: -0.96 (0.79), residues: 44 loop : -2.04 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 227 HIS 0.008 0.001 HIS A 619 PHE 0.017 0.002 PHE A 61 TYR 0.016 0.002 TYR A 432 ARG 0.003 0.000 ARG A 708 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 106 time to evaluate : 1.273 Fit side-chains REVERT: B 129 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6739 (ptt180) REVERT: B 257 LYS cc_start: 0.7031 (mtpp) cc_final: 0.6350 (mppt) REVERT: B 641 ARG cc_start: 0.7287 (ttp80) cc_final: 0.6974 (ttt90) REVERT: B 707 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6768 (mpp) REVERT: A 70 LYS cc_start: 0.8096 (tmmt) cc_final: 0.7322 (mppt) REVERT: A 129 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6712 (ptm160) REVERT: A 257 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6673 (mptt) REVERT: A 641 ARG cc_start: 0.7271 (ttp80) cc_final: 0.6947 (ttt90) outliers start: 36 outliers final: 24 residues processed: 126 average time/residue: 1.4205 time to fit residues: 191.8184 Evaluate side-chains 134 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 702 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.7980 chunk 70 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10616 Z= 0.127 Angle : 0.408 3.831 14344 Z= 0.219 Chirality : 0.037 0.137 1570 Planarity : 0.003 0.031 1768 Dihedral : 14.147 91.825 1696 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.55 % Allowed : 16.82 % Favored : 80.62 % 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 (0.26), residues: 1210 helix: 2.47 (0.19), residues: 824 sheet: -0.93 (0.77), residues: 44 loop : -1.86 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 712 HIS 0.003 0.001 HIS B 130 PHE 0.011 0.001 PHE B 61 TYR 0.007 0.001 TYR B 589 ARG 0.001 0.000 ARG A 708 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.214 Fit side-chains REVERT: B 129 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6791 (ptt180) REVERT: B 641 ARG cc_start: 0.7175 (ttp80) cc_final: 0.6857 (ttt90) REVERT: A 70 LYS cc_start: 0.8033 (tmmt) cc_final: 0.7347 (mppt) REVERT: A 129 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6535 (ptm160) REVERT: A 257 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6611 (mptt) REVERT: A 641 ARG cc_start: 0.7135 (ttp80) cc_final: 0.6806 (ttt90) outliers start: 27 outliers final: 18 residues processed: 121 average time/residue: 1.4046 time to fit residues: 181.9802 Evaluate side-chains 127 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10616 Z= 0.167 Angle : 0.435 4.153 14344 Z= 0.233 Chirality : 0.039 0.139 1570 Planarity : 0.003 0.032 1768 Dihedral : 14.080 91.099 1696 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.55 % Allowed : 17.39 % Favored : 80.06 % 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 (0.26), residues: 1210 helix: 2.47 (0.19), residues: 828 sheet: -0.91 (0.78), residues: 44 loop : -1.89 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 712 HIS 0.005 0.001 HIS B 619 PHE 0.013 0.001 PHE B 61 TYR 0.009 0.001 TYR A 212 ARG 0.002 0.000 ARG A 708 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.228 Fit side-chains REVERT: B 129 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6796 (ptt180) REVERT: B 641 ARG cc_start: 0.7198 (ttp80) cc_final: 0.6883 (ttt90) REVERT: B 642 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6901 (ttp-170) REVERT: A 70 LYS cc_start: 0.8051 (tmmt) cc_final: 0.7308 (mppt) REVERT: A 129 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6585 (ptm160) REVERT: A 257 LYS cc_start: 0.6898 (OUTLIER) cc_final: 0.6619 (mptt) REVERT: A 438 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.6180 (mp10) REVERT: A 641 ARG cc_start: 0.7182 (ttp80) cc_final: 0.6865 (ttt90) outliers start: 27 outliers final: 22 residues processed: 123 average time/residue: 1.4029 time to fit residues: 184.6234 Evaluate side-chains 131 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 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 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10616 Z= 0.135 Angle : 0.409 3.959 14344 Z= 0.219 Chirality : 0.037 0.138 1570 Planarity : 0.003 0.032 1768 Dihedral : 13.687 88.953 1696 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.55 % Allowed : 17.67 % Favored : 79.77 % 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: 2.03 (0.26), residues: 1210 helix: 2.65 (0.19), residues: 824 sheet: -0.88 (0.77), residues: 44 loop : -1.81 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 712 HIS 0.004 0.001 HIS B 619 PHE 0.012 0.001 PHE B 61 TYR 0.008 0.001 TYR A 589 ARG 0.002 0.000 ARG A 708 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 1.251 Fit side-chains REVERT: B 129 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6784 (ptt180) REVERT: B 150 GLN cc_start: 0.7412 (tt0) cc_final: 0.7197 (tm-30) REVERT: B 641 ARG cc_start: 0.7179 (ttp80) cc_final: 0.6864 (ttt90) REVERT: B 642 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6874 (ttp-170) REVERT: A 70 LYS cc_start: 0.8022 (tmmt) cc_final: 0.7293 (mppt) REVERT: A 129 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6562 (ptm160) REVERT: A 257 LYS cc_start: 0.6873 (OUTLIER) cc_final: 0.6592 (mptt) REVERT: A 438 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.6181 (mp10) REVERT: A 641 ARG cc_start: 0.7131 (ttp80) cc_final: 0.6810 (ttt90) outliers start: 27 outliers final: 20 residues processed: 124 average time/residue: 1.4037 time to fit residues: 186.4238 Evaluate side-chains 133 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 99 optimal weight: 0.0060 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** 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 = 0.3456 r_free = 0.3456 target = 0.127178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.096955 restraints weight = 11516.060| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.53 r_work: 0.2856 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10616 Z= 0.403 Angle : 0.596 5.508 14344 Z= 0.314 Chirality : 0.046 0.143 1570 Planarity : 0.004 0.033 1768 Dihedral : 15.099 95.291 1696 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.84 % Allowed : 17.39 % Favored : 79.77 % 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: 1.23 (0.25), residues: 1210 helix: 2.03 (0.18), residues: 820 sheet: -0.97 (0.78), residues: 44 loop : -2.05 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 155 HIS 0.009 0.001 HIS B 619 PHE 0.023 0.002 PHE B 61 TYR 0.019 0.002 TYR B 432 ARG 0.003 0.001 ARG A 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3951.53 seconds wall clock time: 71 minutes 26.25 seconds (4286.25 seconds total)