Starting phenix.real_space_refine on Wed Feb 14 17:44:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwj_24717/02_2024/7rwj_24717_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwj_24717/02_2024/7rwj_24717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwj_24717/02_2024/7rwj_24717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwj_24717/02_2024/7rwj_24717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwj_24717/02_2024/7rwj_24717_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rwj_24717/02_2024/7rwj_24717_updated.pdb" } resolution = 3.5 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= 0.002 sd= 0.052 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 38 5.16 5 C 6486 2.51 5 N 1628 2.21 5 O 1746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B GLU 601": "OE1" <-> "OE2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ARG 647": "NH1" <-> "NH2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 647": "NH1" <-> "NH2" Residue "A ARG 651": "NH1" <-> "NH2" 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: 9906 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4885 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 29, 'TRANS': 576} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4885 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 29, 'TRANS': 576} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 68 Unusual residues: {' CA': 2, 'PGW': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 68 Unusual residues: {' CA': 2, 'PGW': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 5.65, per 1000 atoms: 0.57 Number of scatterers: 9906 At special positions: 0 Unit cell: (127.2, 79.5, 98.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 38 16.00 P 4 15.00 O 1746 8.00 N 1628 7.00 C 6486 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: 3.83 Conformation dependent library (CDL) restraints added in 1.8 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 2 sheets defined 63.0% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'B' and resid 29 through 44 removed outlier: 3.743A pdb=" N GLU B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 85 removed outlier: 3.573A pdb=" N SER B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) 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 155 Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 174 through 188 removed outlier: 3.600A pdb=" N GLY B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 210 through 237 Processing helix chain 'B' and resid 243 through 246 Processing helix chain 'B' and resid 273 through 310 removed outlier: 4.526A pdb=" N LEU B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLN B 283 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Proline residue: B 285 - end of helix Processing helix chain 'B' and resid 323 through 347 Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 355 through 382 removed outlier: 4.314A pdb=" N VAL B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.227A 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 389 through 393 Processing helix chain 'B' and resid 425 through 446 removed outlier: 4.491A pdb=" N ALA B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.644A pdb=" N THR B 495 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 524 Processing helix chain 'B' and resid 532 through 553 removed outlier: 3.999A pdb=" N ARG B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 590 removed outlier: 3.805A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 634 removed outlier: 3.846A pdb=" N LEU B 611 " --> pdb=" O CYS B 607 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 612 " --> pdb=" O TRP B 608 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 646 through 657 removed outlier: 4.284A pdb=" N ARG B 651 " --> pdb=" O ARG B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 723 Processing helix chain 'A' and resid 29 through 44 removed outlier: 3.743A pdb=" N GLU A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 85 removed outlier: 3.573A pdb=" N SER A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) 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 155 Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 174 through 188 removed outlier: 3.600A pdb=" N GLY A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 210 through 237 Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 273 through 310 removed outlier: 4.526A pdb=" N LEU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLN A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 323 through 347 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 355 through 382 removed outlier: 4.315A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.227A 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 389 through 393 Processing helix chain 'A' and resid 425 through 446 removed outlier: 4.492A pdb=" N ALA A 437 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.645A pdb=" N THR A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 524 Processing helix chain 'A' and resid 532 through 553 removed outlier: 3.999A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 590 removed outlier: 3.804A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 634 removed outlier: 3.846A pdb=" N LEU A 611 " --> pdb=" O CYS A 607 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 612 " --> pdb=" O TRP A 608 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 Processing helix chain 'A' and resid 646 through 657 removed outlier: 4.284A pdb=" N ARG A 651 " --> pdb=" O ARG A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 Processing sheet with id= A, first strand: chain 'B' and resid 139 through 141 Processing sheet with id= B, first strand: chain 'A' and resid 139 through 141 533 hydrogen bonds defined for protein. 1575 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: 2.78 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1530 1.27 - 1.41: 2725 1.41 - 1.54: 5691 1.54 - 1.67: 154 1.67 - 1.81: 56 Bond restraints: 10156 Sorted by residual: bond pdb=" C ILE B 605 " pdb=" O ILE B 605 " ideal model delta sigma weight residual 1.236 1.140 0.096 9.80e-03 1.04e+04 9.51e+01 bond pdb=" C ILE A 605 " pdb=" O ILE A 605 " ideal model delta sigma weight residual 1.236 1.140 0.096 9.80e-03 1.04e+04 9.51e+01 bond pdb=" C LEU A 380 " pdb=" O LEU A 380 " ideal model delta sigma weight residual 1.236 1.139 0.098 1.15e-02 7.56e+03 7.23e+01 bond pdb=" C LEU B 380 " pdb=" O LEU B 380 " ideal model delta sigma weight residual 1.236 1.139 0.097 1.15e-02 7.56e+03 7.11e+01 bond pdb=" C ILE B 379 " pdb=" O ILE B 379 " ideal model delta sigma weight residual 1.236 1.153 0.084 1.10e-02 8.26e+03 5.77e+01 ... (remaining 10151 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.54: 322 106.54 - 113.50: 5473 113.50 - 120.47: 4441 120.47 - 127.43: 3434 127.43 - 134.40: 116 Bond angle restraints: 13786 Sorted by residual: angle pdb=" N PRO B 387 " pdb=" CA PRO B 387 " pdb=" C PRO B 387 " ideal model delta sigma weight residual 113.65 123.85 -10.20 1.35e+00 5.49e-01 5.71e+01 angle pdb=" N PRO A 387 " pdb=" CA PRO A 387 " pdb=" C PRO A 387 " ideal model delta sigma weight residual 113.65 123.85 -10.20 1.35e+00 5.49e-01 5.70e+01 angle pdb=" CA PHE A 383 " pdb=" CB PHE A 383 " pdb=" CG PHE A 383 " ideal model delta sigma weight residual 113.80 107.31 6.49 1.00e+00 1.00e+00 4.21e+01 angle pdb=" CA PHE B 383 " pdb=" CB PHE B 383 " pdb=" CG PHE B 383 " ideal model delta sigma weight residual 113.80 107.32 6.48 1.00e+00 1.00e+00 4.20e+01 angle pdb=" C PHE B 388 " pdb=" CA PHE B 388 " pdb=" CB PHE B 388 " ideal model delta sigma weight residual 114.52 103.43 11.09 1.81e+00 3.05e-01 3.75e+01 ... (remaining 13781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.19: 5820 33.19 - 66.38: 168 66.38 - 99.58: 14 99.58 - 132.77: 4 132.77 - 165.96: 4 Dihedral angle restraints: 6010 sinusoidal: 2442 harmonic: 3568 Sorted by residual: dihedral pdb=" CA HIS B 130 " pdb=" C HIS B 130 " pdb=" N GLY B 131 " pdb=" CA GLY B 131 " ideal model delta harmonic sigma weight residual 180.00 -152.59 -27.41 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA HIS A 130 " pdb=" C HIS A 130 " pdb=" N GLY A 131 " pdb=" CA GLY A 131 " ideal model delta harmonic sigma weight residual -180.00 -152.62 -27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" C VAL A 386 " pdb=" N VAL A 386 " pdb=" CA VAL A 386 " pdb=" CB VAL A 386 " ideal model delta harmonic sigma weight residual -122.00 -135.03 13.03 0 2.50e+00 1.60e-01 2.71e+01 ... (remaining 6007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1392 0.103 - 0.205: 132 0.205 - 0.308: 10 0.308 - 0.410: 6 0.410 - 0.513: 2 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA ILE B 605 " pdb=" N ILE B 605 " pdb=" C ILE B 605 " pdb=" CB ILE B 605 " both_signs ideal model delta sigma weight residual False 2.43 2.95 -0.51 2.00e-01 2.50e+01 6.57e+00 chirality pdb=" CA ILE A 605 " pdb=" N ILE A 605 " pdb=" C ILE A 605 " pdb=" CB ILE A 605 " both_signs ideal model delta sigma weight residual False 2.43 2.95 -0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" CA PRO A 387 " pdb=" N PRO A 387 " pdb=" C PRO A 387 " pdb=" CB PRO A 387 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.40 2.00e-01 2.50e+01 4.10e+00 ... (remaining 1539 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 388 " 0.021 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C PHE B 388 " -0.075 2.00e-02 2.50e+03 pdb=" O PHE B 388 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA B 389 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 388 " -0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C PHE A 388 " 0.075 2.00e-02 2.50e+03 pdb=" O PHE A 388 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA A 389 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 592 " -0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C SER B 592 " 0.068 2.00e-02 2.50e+03 pdb=" O SER B 592 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN B 593 " -0.023 2.00e-02 2.50e+03 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2358 2.79 - 3.31: 9169 3.31 - 3.84: 16672 3.84 - 4.37: 18975 4.37 - 4.90: 33438 Nonbonded interactions: 80612 Sorted by model distance: nonbonded pdb=" N GLU B 601 " pdb=" OE1 GLU B 601 " model vdw 2.258 2.520 nonbonded pdb=" N GLU A 601 " pdb=" OE1 GLU A 601 " model vdw 2.258 2.520 nonbonded pdb=" O CYS B 607 " pdb=" SG CYS B 607 " model vdw 2.260 3.400 nonbonded pdb=" O CYS A 607 " pdb=" SG CYS A 607 " model vdw 2.261 3.400 nonbonded pdb=" OH TYR A 180 " pdb=" OD2 ASP A 547 " model vdw 2.274 2.440 ... (remaining 80607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.080 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: 5.220 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.950 Find NCS groups from input model: 0.560 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.008 0.100 10156 Z= 0.521 Angle : 1.166 11.620 13786 Z= 0.666 Chirality : 0.068 0.513 1542 Planarity : 0.008 0.058 1714 Dihedral : 16.668 165.959 3690 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.05 % Favored : 94.61 % Rotamer: Outliers : 1.35 % Allowed : 6.74 % Favored : 91.91 % Cbeta Deviations : 0.34 % 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: -3.76 (0.20), residues: 1188 helix: -2.24 (0.14), residues: 802 sheet: -1.45 (0.81), residues: 40 loop : -2.79 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 227 HIS 0.008 0.002 HIS A 130 PHE 0.023 0.002 PHE B 367 TYR 0.027 0.002 TYR B 654 ARG 0.008 0.001 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 VAL cc_start: 0.8809 (t) cc_final: 0.8600 (t) REVERT: B 121 GLU cc_start: 0.7116 (pp20) cc_final: 0.6798 (pt0) REVERT: B 281 LEU cc_start: 0.8182 (mt) cc_final: 0.7949 (tp) REVERT: B 515 MET cc_start: 0.7998 (mmp) cc_final: 0.7760 (mmt) REVERT: A 121 GLU cc_start: 0.7158 (pp20) cc_final: 0.6813 (pt0) REVERT: A 224 ILE cc_start: 0.8843 (mm) cc_final: 0.8562 (mt) REVERT: A 515 MET cc_start: 0.7948 (mmp) cc_final: 0.7714 (mmt) outliers start: 14 outliers final: 7 residues processed: 143 average time/residue: 0.2778 time to fit residues: 52.7822 Evaluate side-chains 95 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 605 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.4980 chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.0020 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 171 ASN B 216 ASN B 230 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 ASN A 148 ASN A 171 ASN A 185 GLN A 216 ASN A 230 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10156 Z= 0.188 Angle : 0.587 6.972 13786 Z= 0.303 Chirality : 0.041 0.219 1542 Planarity : 0.005 0.049 1714 Dihedral : 12.664 155.044 1450 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.87 % Favored : 95.96 % Rotamer: Outliers : 1.16 % Allowed : 11.46 % Favored : 87.38 % 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: -1.38 (0.23), residues: 1188 helix: -0.24 (0.17), residues: 802 sheet: -1.15 (0.77), residues: 40 loop : -2.32 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 578 HIS 0.005 0.001 HIS A 130 PHE 0.015 0.001 PHE B 61 TYR 0.012 0.001 TYR B 589 ARG 0.004 0.000 ARG B 644 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: B 224 ILE cc_start: 0.8779 (mm) cc_final: 0.8474 (mt) REVERT: B 500 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 504 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7716 (pm20) REVERT: B 515 MET cc_start: 0.8122 (mmp) cc_final: 0.7882 (mmp) REVERT: B 629 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6749 (ttp-110) REVERT: B 647 ARG cc_start: 0.8398 (tmm160) cc_final: 0.8162 (tmm-80) REVERT: B 649 MET cc_start: 0.8253 (mmm) cc_final: 0.7782 (mmm) REVERT: A 117 VAL cc_start: 0.8855 (t) cc_final: 0.8480 (p) REVERT: A 224 ILE cc_start: 0.8717 (mm) cc_final: 0.8399 (mt) REVERT: A 504 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: A 515 MET cc_start: 0.8125 (mmp) cc_final: 0.7892 (mmp) outliers start: 12 outliers final: 5 residues processed: 101 average time/residue: 0.2576 time to fit residues: 35.6935 Evaluate side-chains 92 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10156 Z= 0.206 Angle : 0.575 6.552 13786 Z= 0.293 Chirality : 0.041 0.198 1542 Planarity : 0.004 0.038 1714 Dihedral : 11.562 143.935 1440 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.80 % Favored : 95.03 % Rotamer: Outliers : 2.12 % Allowed : 12.91 % Favored : 84.97 % 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: -0.39 (0.25), residues: 1188 helix: 0.64 (0.19), residues: 790 sheet: -1.09 (0.77), residues: 40 loop : -2.13 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 155 HIS 0.004 0.001 HIS A 130 PHE 0.017 0.001 PHE A 61 TYR 0.011 0.001 TYR A 654 ARG 0.004 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: B 224 ILE cc_start: 0.8777 (mm) cc_final: 0.8483 (mt) REVERT: B 447 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7677 (pt) REVERT: B 500 GLU cc_start: 0.8234 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 504 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: B 647 ARG cc_start: 0.8301 (tmm160) cc_final: 0.8100 (tmm-80) REVERT: A 224 ILE cc_start: 0.8746 (mm) cc_final: 0.8483 (mt) REVERT: A 504 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7632 (pm20) outliers start: 22 outliers final: 13 residues processed: 106 average time/residue: 0.2456 time to fit residues: 36.2442 Evaluate side-chains 98 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.9990 chunk 82 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10156 Z= 0.172 Angle : 0.548 6.466 13786 Z= 0.278 Chirality : 0.041 0.232 1542 Planarity : 0.004 0.034 1714 Dihedral : 10.519 122.708 1440 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.29 % Favored : 95.54 % Rotamer: Outliers : 2.22 % Allowed : 13.49 % Favored : 84.30 % 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 (0.25), residues: 1188 helix: 1.05 (0.19), residues: 790 sheet: -0.91 (0.78), residues: 40 loop : -1.92 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 155 HIS 0.004 0.001 HIS A 130 PHE 0.015 0.001 PHE A 61 TYR 0.011 0.001 TYR B 589 ARG 0.003 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.169 Fit side-chains REVERT: B 224 ILE cc_start: 0.8756 (mm) cc_final: 0.8471 (mt) REVERT: B 504 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: A 224 ILE cc_start: 0.8709 (mm) cc_final: 0.8362 (mt) REVERT: A 504 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7677 (pm20) outliers start: 23 outliers final: 13 residues processed: 107 average time/residue: 0.2449 time to fit residues: 37.0147 Evaluate side-chains 100 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 565 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 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 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 438 GLN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10156 Z= 0.191 Angle : 0.554 6.404 13786 Z= 0.282 Chirality : 0.042 0.215 1542 Planarity : 0.004 0.033 1714 Dihedral : 10.044 134.740 1440 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.80 % Favored : 95.03 % Rotamer: Outliers : 2.70 % Allowed : 14.07 % Favored : 83.24 % 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: 0.28 (0.25), residues: 1188 helix: 1.14 (0.19), residues: 796 sheet: -0.90 (0.76), residues: 40 loop : -1.89 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 155 HIS 0.004 0.001 HIS B 130 PHE 0.016 0.001 PHE A 61 TYR 0.010 0.001 TYR B 589 ARG 0.003 0.000 ARG B 250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 1.039 Fit side-chains REVERT: B 224 ILE cc_start: 0.8727 (mm) cc_final: 0.8458 (mt) REVERT: B 504 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: B 601 GLU cc_start: 0.7831 (pm20) cc_final: 0.7432 (pm20) REVERT: B 707 MET cc_start: 0.7078 (tpt) cc_final: 0.6791 (tpt) REVERT: A 224 ILE cc_start: 0.8712 (mm) cc_final: 0.8426 (mt) REVERT: A 504 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7696 (pm20) outliers start: 28 outliers final: 19 residues processed: 111 average time/residue: 0.2355 time to fit residues: 36.4237 Evaluate side-chains 108 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 499 ASN ** 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: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10156 Z= 0.212 Angle : 0.565 7.780 13786 Z= 0.287 Chirality : 0.042 0.214 1542 Planarity : 0.004 0.033 1714 Dihedral : 9.967 144.594 1440 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.95 % Rotamer: Outliers : 2.70 % Allowed : 14.55 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1188 helix: 1.19 (0.19), residues: 794 sheet: -0.84 (0.75), residues: 40 loop : -1.82 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 155 HIS 0.004 0.001 HIS A 619 PHE 0.019 0.001 PHE A 22 TYR 0.010 0.001 TYR B 589 ARG 0.004 0.000 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 1.220 Fit side-chains REVERT: B 224 ILE cc_start: 0.8733 (mm) cc_final: 0.8450 (mt) REVERT: B 504 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: B 601 GLU cc_start: 0.7822 (pm20) cc_final: 0.7485 (pm20) REVERT: B 707 MET cc_start: 0.7129 (tpt) cc_final: 0.6925 (tpt) REVERT: A 224 ILE cc_start: 0.8744 (mm) cc_final: 0.8466 (mt) REVERT: A 504 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7728 (pm20) outliers start: 28 outliers final: 22 residues processed: 112 average time/residue: 0.2360 time to fit residues: 37.0921 Evaluate side-chains 112 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 64 optimal weight: 0.0980 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 280 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN A 148 ASN A 280 GLN A 370 ASN A 438 GLN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10156 Z= 0.363 Angle : 0.657 6.812 13786 Z= 0.336 Chirality : 0.046 0.215 1542 Planarity : 0.004 0.034 1714 Dihedral : 10.755 167.425 1440 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.56 % Favored : 94.28 % Rotamer: Outliers : 3.28 % Allowed : 15.41 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1188 helix: 0.83 (0.19), residues: 808 sheet: -1.16 (0.74), residues: 40 loop : -1.74 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 155 HIS 0.007 0.002 HIS B 619 PHE 0.020 0.002 PHE A 61 TYR 0.011 0.002 TYR A 654 ARG 0.005 0.000 ARG A 647 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 88 time to evaluate : 1.222 Fit side-chains REVERT: B 224 ILE cc_start: 0.8814 (mm) cc_final: 0.8560 (mt) REVERT: B 601 GLU cc_start: 0.8092 (pm20) cc_final: 0.7674 (pm20) REVERT: A 224 ILE cc_start: 0.8806 (mm) cc_final: 0.8555 (mt) outliers start: 34 outliers final: 24 residues processed: 114 average time/residue: 0.2420 time to fit residues: 38.4892 Evaluate side-chains 112 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 438 GLN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10156 Z= 0.252 Angle : 0.607 7.968 13786 Z= 0.309 Chirality : 0.044 0.216 1542 Planarity : 0.004 0.032 1714 Dihedral : 10.226 158.255 1440 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.53 % Rotamer: Outliers : 2.70 % Allowed : 16.47 % Favored : 80.83 % 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 (0.25), residues: 1188 helix: 0.99 (0.19), residues: 808 sheet: -1.09 (0.74), residues: 40 loop : -1.69 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 155 HIS 0.004 0.001 HIS B 619 PHE 0.020 0.001 PHE A 22 TYR 0.009 0.001 TYR B 654 ARG 0.003 0.000 ARG B 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 1.849 Fit side-chains REVERT: B 129 ARG cc_start: 0.7083 (ttp80) cc_final: 0.6818 (ptp90) REVERT: B 224 ILE cc_start: 0.8767 (mm) cc_final: 0.8477 (mt) REVERT: B 359 LYS cc_start: 0.7908 (tppt) cc_final: 0.7087 (tptm) REVERT: B 601 GLU cc_start: 0.7978 (pm20) cc_final: 0.7635 (pm20) REVERT: A 224 ILE cc_start: 0.8760 (mm) cc_final: 0.8472 (mt) REVERT: A 359 LYS cc_start: 0.7915 (tppt) cc_final: 0.7074 (tptm) outliers start: 28 outliers final: 24 residues processed: 111 average time/residue: 0.2709 time to fit residues: 41.9979 Evaluate side-chains 114 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.0470 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 370 ASN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10156 Z= 0.178 Angle : 0.567 7.803 13786 Z= 0.286 Chirality : 0.042 0.209 1542 Planarity : 0.004 0.032 1714 Dihedral : 9.594 174.128 1440 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.97 % Favored : 94.87 % Rotamer: Outliers : 2.41 % Allowed : 16.86 % Favored : 80.73 % 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: 0.51 (0.25), residues: 1188 helix: 1.31 (0.19), residues: 794 sheet: -1.14 (0.91), residues: 28 loop : -1.72 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 155 HIS 0.004 0.001 HIS A 130 PHE 0.022 0.001 PHE B 22 TYR 0.010 0.001 TYR B 589 ARG 0.003 0.000 ARG B 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 1.064 Fit side-chains REVERT: B 129 ARG cc_start: 0.6986 (ttp80) cc_final: 0.6664 (ptp90) REVERT: B 224 ILE cc_start: 0.8725 (mm) cc_final: 0.8450 (mt) REVERT: B 601 GLU cc_start: 0.7795 (pm20) cc_final: 0.7509 (pm20) REVERT: A 224 ILE cc_start: 0.8729 (mm) cc_final: 0.8466 (mt) outliers start: 25 outliers final: 24 residues processed: 107 average time/residue: 0.2391 time to fit residues: 35.9383 Evaluate side-chains 115 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 119 optimal weight: 0.3980 chunk 110 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10156 Z= 0.151 Angle : 0.549 7.835 13786 Z= 0.276 Chirality : 0.041 0.205 1542 Planarity : 0.003 0.032 1714 Dihedral : 8.454 121.617 1440 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.95 % Rotamer: Outliers : 2.41 % Allowed : 16.96 % Favored : 80.64 % 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: 0.76 (0.25), residues: 1188 helix: 1.49 (0.19), residues: 796 sheet: -0.99 (0.91), residues: 28 loop : -1.62 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 155 HIS 0.004 0.001 HIS A 130 PHE 0.024 0.001 PHE A 22 TYR 0.010 0.001 TYR A 589 ARG 0.003 0.000 ARG A 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 1.001 Fit side-chains REVERT: B 129 ARG cc_start: 0.6905 (ttp80) cc_final: 0.6604 (ptp90) REVERT: B 224 ILE cc_start: 0.8720 (mm) cc_final: 0.8437 (mt) REVERT: B 601 GLU cc_start: 0.7571 (pm20) cc_final: 0.6566 (tt0) REVERT: A 224 ILE cc_start: 0.8730 (mm) cc_final: 0.8412 (mt) outliers start: 25 outliers final: 21 residues processed: 110 average time/residue: 0.2339 time to fit residues: 36.0998 Evaluate side-chains 113 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.8980 chunk 14 optimal weight: 0.0020 chunk 26 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.139230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120450 restraints weight = 14643.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123211 restraints weight = 9076.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125085 restraints weight = 6582.373| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10156 Z= 0.232 Angle : 0.583 7.845 13786 Z= 0.295 Chirality : 0.043 0.213 1542 Planarity : 0.004 0.032 1714 Dihedral : 8.678 117.628 1440 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.05 % Favored : 94.78 % Rotamer: Outliers : 2.12 % Allowed : 17.24 % Favored : 80.64 % 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: 0.70 (0.25), residues: 1188 helix: 1.36 (0.19), residues: 808 sheet: -1.11 (0.92), residues: 28 loop : -1.50 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 155 HIS 0.004 0.001 HIS B 619 PHE 0.022 0.001 PHE B 22 TYR 0.009 0.001 TYR B 187 ARG 0.003 0.000 ARG B 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1871.14 seconds wall clock time: 35 minutes 5.17 seconds (2105.17 seconds total)