Starting phenix.real_space_refine on Mon Apr 8 13:55:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hob_34924/04_2024/8hob_34924_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hob_34924/04_2024/8hob_34924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hob_34924/04_2024/8hob_34924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hob_34924/04_2024/8hob_34924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hob_34924/04_2024/8hob_34924_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hob_34924/04_2024/8hob_34924_neut.pdb" } resolution = 2.19 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 8402 2.51 5 N 2190 2.21 5 O 2821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "B PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B GLU 808": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13449 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6558 Classifications: {'peptide': 811} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 781} Chain: "B" Number of atoms: 6558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6558 Classifications: {'peptide': 811} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 781} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 158 Classifications: {'water': 158} Link IDs: {None: 157} Time building chain proxies: 7.44, per 1000 atoms: 0.55 Number of scatterers: 13449 At special positions: 0 Unit cell: (145.25, 95.45, 97.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 2821 8.00 N 2190 7.00 C 8402 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: 5.05 Conformation dependent library (CDL) restraints added in 2.3 seconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 25 sheets defined 33.9% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.811A pdb=" N PHE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 322 through 331 Processing helix chain 'A' and resid 331 through 344 Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.710A pdb=" N LEU A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 388 removed outlier: 3.697A pdb=" N THR A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 433 removed outlier: 3.978A pdb=" N TRP A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 422 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.788A pdb=" N ILE A 437 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 467 removed outlier: 3.989A pdb=" N VAL A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.951A pdb=" N LYS A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 557 Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.719A pdb=" N GLY A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 615 Processing helix chain 'A' and resid 635 through 641 removed outlier: 4.499A pdb=" N ILE A 638 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 641 " --> pdb=" O ILE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 4.067A pdb=" N TRP A 658 " --> pdb=" O HIS A 654 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 680 removed outlier: 3.768A pdb=" N ILE A 679 " --> pdb=" O TYR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 685 Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.557A pdb=" N TRP A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 282 through 292 removed outlier: 3.857A pdb=" N PHE B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 313 Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 331 through 344 Processing helix chain 'B' and resid 360 through 371 removed outlier: 3.710A pdb=" N LEU B 368 " --> pdb=" O ASN B 364 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 removed outlier: 3.693A pdb=" N THR B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 433 removed outlier: 4.007A pdb=" N TRP B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 422 " --> pdb=" O PRO B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.744A pdb=" N ILE B 437 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.991A pdb=" N VAL B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 533 removed outlier: 4.012A pdb=" N LYS B 524 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 557 Processing helix chain 'B' and resid 586 through 595 removed outlier: 3.714A pdb=" N GLY B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 615 Processing helix chain 'B' and resid 635 through 641 removed outlier: 4.514A pdb=" N ILE B 638 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR B 641 " --> pdb=" O ILE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 666 removed outlier: 4.070A pdb=" N TRP B 658 " --> pdb=" O HIS B 654 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 680 removed outlier: 3.763A pdb=" N ILE B 679 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 685 Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.556A pdb=" N TRP B 724 " --> pdb=" O GLY B 720 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.652A pdb=" N SER A 95 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 57 removed outlier: 5.553A pdb=" N ILE A 56 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 55 through 57 removed outlier: 5.553A pdb=" N ILE A 56 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A 208 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 244 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE A 206 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 276 removed outlier: 6.832A pdb=" N VAL A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 316 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 358 through 359 Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 444 removed outlier: 3.970A pdb=" N PHE A 444 " --> pdb=" O LYS A 450 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LYS A 450 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=AB2, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 702 removed outlier: 6.632A pdb=" N ALA A 699 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N SER A 716 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 736 through 739 removed outlier: 3.879A pdb=" N LEU A 743 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 8 removed outlier: 3.649A pdb=" N SER B 95 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 26 through 29 Processing sheet with id=AB7, first strand: chain 'B' and resid 80 through 82 removed outlier: 3.743A pdb=" N HIS B 245 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER B 208 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER B 244 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B 206 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 274 through 276 removed outlier: 6.848A pdb=" N VAL B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 316 through 319 Processing sheet with id=AC1, first strand: chain 'B' and resid 358 through 359 Processing sheet with id=AC2, first strand: chain 'B' and resid 441 through 444 removed outlier: 3.949A pdb=" N PHE B 444 " --> pdb=" O LYS B 450 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LYS B 450 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AC4, first strand: chain 'B' and resid 584 through 585 Processing sheet with id=AC5, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AC6, first strand: chain 'B' and resid 699 through 702 removed outlier: 6.631A pdb=" N ALA B 699 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER B 716 " --> pdb=" O ALA B 699 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 736 through 739 removed outlier: 3.891A pdb=" N LEU B 743 " --> pdb=" O LEU B 796 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1623 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: 5.27 Time building geometry restraints manager: 5.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 0.99: 4 0.99 - 1.20: 4 1.20 - 1.40: 5863 1.40 - 1.61: 7523 1.61 - 1.81: 68 Bond restraints: 13462 Sorted by residual: bond pdb=" C GLN B 166 " pdb=" O GLN B 166 " ideal model delta sigma weight residual 1.236 0.791 0.445 1.18e-02 7.18e+03 1.42e+03 bond pdb=" C ASN B 168 " pdb=" O ASN B 168 " ideal model delta sigma weight residual 1.236 0.822 0.414 1.28e-02 6.10e+03 1.04e+03 bond pdb=" C ARG B 167 " pdb=" O ARG B 167 " ideal model delta sigma weight residual 1.235 0.933 0.301 1.03e-02 9.43e+03 8.56e+02 bond pdb=" C PHE B 165 " pdb=" O PHE B 165 " ideal model delta sigma weight residual 1.236 0.904 0.332 1.26e-02 6.30e+03 6.96e+02 bond pdb=" CA GLN B 166 " pdb=" C GLN B 166 " ideal model delta sigma weight residual 1.523 1.290 0.233 1.35e-02 5.49e+03 2.98e+02 ... (remaining 13457 not shown) Histogram of bond angle deviations from ideal: 80.76 - 93.17: 1 93.17 - 105.58: 190 105.58 - 117.98: 9374 117.98 - 130.39: 8571 130.39 - 142.80: 70 Bond angle restraints: 18206 Sorted by residual: angle pdb=" N GLN B 166 " pdb=" CA GLN B 166 " pdb=" CB GLN B 166 " ideal model delta sigma weight residual 110.06 80.76 29.30 1.50e+00 4.44e-01 3.82e+02 angle pdb=" C GLN B 166 " pdb=" CA GLN B 166 " pdb=" CB GLN B 166 " ideal model delta sigma weight residual 110.68 142.80 -32.12 1.70e+00 3.46e-01 3.57e+02 angle pdb=" CA ASN B 168 " pdb=" CB ASN B 168 " pdb=" CG ASN B 168 " ideal model delta sigma weight residual 112.60 129.82 -17.22 1.00e+00 1.00e+00 2.97e+02 angle pdb=" CA PHE B 165 " pdb=" CB PHE B 165 " pdb=" CG PHE B 165 " ideal model delta sigma weight residual 113.80 128.11 -14.31 1.00e+00 1.00e+00 2.05e+02 angle pdb=" C ASN B 164 " pdb=" N PHE B 165 " pdb=" CA PHE B 165 " ideal model delta sigma weight residual 120.31 142.04 -21.73 1.52e+00 4.33e-01 2.04e+02 ... (remaining 18201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6862 17.93 - 35.86: 730 35.86 - 53.78: 229 53.78 - 71.71: 50 71.71 - 89.64: 21 Dihedral angle restraints: 7892 sinusoidal: 3192 harmonic: 4700 Sorted by residual: dihedral pdb=" C GLN B 166 " pdb=" N GLN B 166 " pdb=" CA GLN B 166 " pdb=" CB GLN B 166 " ideal model delta harmonic sigma weight residual -122.60 -148.42 25.82 0 2.50e+00 1.60e-01 1.07e+02 dihedral pdb=" C ARG B 167 " pdb=" N ARG B 167 " pdb=" CA ARG B 167 " pdb=" CB ARG B 167 " ideal model delta harmonic sigma weight residual -122.60 -144.26 21.66 0 2.50e+00 1.60e-01 7.51e+01 dihedral pdb=" C PHE B 165 " pdb=" N PHE B 165 " pdb=" CA PHE B 165 " pdb=" CB PHE B 165 " ideal model delta harmonic sigma weight residual -122.60 -143.69 21.09 0 2.50e+00 1.60e-01 7.12e+01 ... (remaining 7889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.290: 1854 0.290 - 0.580: 0 0.580 - 0.870: 1 0.870 - 1.160: 2 1.160 - 1.450: 1 Chirality restraints: 1858 Sorted by residual: chirality pdb=" CA GLN B 166 " pdb=" N GLN B 166 " pdb=" C GLN B 166 " pdb=" CB GLN B 166 " both_signs ideal model delta sigma weight residual False 2.51 1.06 1.45 2.00e-01 2.50e+01 5.26e+01 chirality pdb=" CA PHE B 165 " pdb=" N PHE B 165 " pdb=" C PHE B 165 " pdb=" CB PHE B 165 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.36e+01 chirality pdb=" CA ARG B 167 " pdb=" N ARG B 167 " pdb=" C ARG B 167 " pdb=" CB ARG B 167 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.32e+01 ... (remaining 1855 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 168 " 0.030 2.00e-02 2.50e+03 7.53e-02 5.67e+01 pdb=" C ASN B 168 " -0.129 2.00e-02 2.50e+03 pdb=" O ASN B 168 " 0.061 2.00e-02 2.50e+03 pdb=" N PHE B 169 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 165 " 0.019 2.00e-02 2.50e+03 4.30e-02 1.84e+01 pdb=" C PHE B 165 " -0.074 2.00e-02 2.50e+03 pdb=" O PHE B 165 " 0.030 2.00e-02 2.50e+03 pdb=" N GLN B 166 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 165 " 0.004 2.00e-02 2.50e+03 2.88e-02 1.45e+01 pdb=" CG PHE B 165 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 165 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 165 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE B 165 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE B 165 " 0.040 2.00e-02 2.50e+03 pdb=" CZ PHE B 165 " -0.033 2.00e-02 2.50e+03 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2296 2.76 - 3.30: 12140 3.30 - 3.83: 25906 3.83 - 4.37: 32785 4.37 - 4.90: 50930 Nonbonded interactions: 124057 Sorted by model distance: nonbonded pdb=" OD2 ASP A 706 " pdb=" O HOH A 901 " model vdw 2.230 2.440 nonbonded pdb=" OG1 THR B 31 " pdb=" OE2 GLU B 32 " model vdw 2.247 2.440 nonbonded pdb=" OD1 ASP A 209 " pdb=" O HOH A 902 " model vdw 2.262 2.440 nonbonded pdb=" OD1 ASP B 209 " pdb=" O HOH B 901 " model vdw 2.265 2.440 nonbonded pdb=" OD1 ASP A 160 " pdb=" O HOH A 903 " model vdw 2.268 2.440 ... (remaining 124052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 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: 13.810 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 38.490 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 0.445 13462 Z= 0.507 Angle : 0.753 32.118 18206 Z= 0.482 Chirality : 0.066 1.450 1858 Planarity : 0.005 0.083 2372 Dihedral : 17.238 89.641 4916 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.23 % Allowed : 17.05 % Favored : 81.72 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 10.34 % 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: 0.68 (0.21), residues: 1618 helix: 1.14 (0.24), residues: 482 sheet: 1.27 (0.30), residues: 282 loop : -0.19 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 332 HIS 0.003 0.001 HIS A 245 PHE 0.040 0.002 PHE B 165 TYR 0.014 0.001 TYR A 526 ARG 0.054 0.001 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.518 Fit side-chains REVERT: A 258 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: B 167 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7336 (ttt180) outliers start: 17 outliers final: 14 residues processed: 147 average time/residue: 1.8097 time to fit residues: 285.4171 Evaluate side-chains 143 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 363 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 0.0270 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13462 Z= 0.252 Angle : 0.551 6.100 18206 Z= 0.309 Chirality : 0.047 0.151 1858 Planarity : 0.004 0.040 2372 Dihedral : 7.386 79.541 1827 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.73 % Allowed : 17.12 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.67 (0.21), residues: 1618 helix: 1.20 (0.23), residues: 482 sheet: 1.28 (0.30), residues: 282 loop : -0.25 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 332 HIS 0.005 0.001 HIS B 545 PHE 0.022 0.002 PHE B 370 TYR 0.017 0.002 TYR A 526 ARG 0.005 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.645 Fit side-chains REVERT: A 258 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: B 258 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7985 (mt-10) outliers start: 24 outliers final: 13 residues processed: 148 average time/residue: 1.8678 time to fit residues: 295.7730 Evaluate side-chains 138 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 159 optimal weight: 0.0570 chunk 131 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13462 Z= 0.265 Angle : 0.563 5.980 18206 Z= 0.315 Chirality : 0.048 0.143 1858 Planarity : 0.004 0.041 2372 Dihedral : 6.903 77.722 1812 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.38 % Allowed : 16.11 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.59 (0.21), residues: 1618 helix: 1.16 (0.23), residues: 482 sheet: 1.20 (0.29), residues: 292 loop : -0.31 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.005 0.001 HIS B 545 PHE 0.021 0.002 PHE B 370 TYR 0.017 0.002 TYR A 526 ARG 0.007 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.539 Fit side-chains REVERT: A 91 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8048 (mtt180) REVERT: A 258 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: B 138 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: B 258 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: B 600 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7579 (mp0) outliers start: 33 outliers final: 17 residues processed: 147 average time/residue: 1.8713 time to fit residues: 294.5649 Evaluate side-chains 145 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13462 Z= 0.178 Angle : 0.507 5.319 18206 Z= 0.284 Chirality : 0.045 0.142 1858 Planarity : 0.004 0.039 2372 Dihedral : 6.648 73.245 1812 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.24 % Allowed : 15.90 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.71 (0.21), residues: 1618 helix: 1.34 (0.24), residues: 478 sheet: 1.17 (0.30), residues: 284 loop : -0.23 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 332 HIS 0.003 0.001 HIS B 545 PHE 0.021 0.002 PHE A 370 TYR 0.013 0.001 TYR A 14 ARG 0.006 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.452 Fit side-chains REVERT: A 91 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8041 (mtt180) REVERT: A 258 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: B 91 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7813 (mtt180) REVERT: B 138 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: B 258 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: B 600 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7569 (mp0) outliers start: 31 outliers final: 15 residues processed: 150 average time/residue: 1.9411 time to fit residues: 311.3718 Evaluate side-chains 149 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 0.0570 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 457 HIS B 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 13462 Z= 0.139 Angle : 0.476 5.070 18206 Z= 0.266 Chirality : 0.044 0.140 1858 Planarity : 0.004 0.039 2372 Dihedral : 6.342 67.468 1810 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.66 % Allowed : 16.62 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.79 (0.21), residues: 1618 helix: 1.47 (0.24), residues: 478 sheet: 1.18 (0.30), residues: 284 loop : -0.20 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 332 HIS 0.003 0.001 HIS B 245 PHE 0.020 0.001 PHE B 370 TYR 0.012 0.001 TYR A 14 ARG 0.009 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.590 Fit side-chains REVERT: A 91 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8021 (mtt180) REVERT: A 270 ASP cc_start: 0.8547 (m-30) cc_final: 0.8223 (m-30) REVERT: B 138 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: B 258 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: B 600 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7526 (mp0) outliers start: 23 outliers final: 15 residues processed: 146 average time/residue: 1.8945 time to fit residues: 295.2097 Evaluate side-chains 145 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 737 LYS Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13462 Z= 0.247 Angle : 0.546 5.402 18206 Z= 0.305 Chirality : 0.047 0.144 1858 Planarity : 0.004 0.039 2372 Dihedral : 6.262 57.581 1807 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.66 % Allowed : 16.47 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.69 (0.21), residues: 1618 helix: 1.27 (0.23), residues: 482 sheet: 1.25 (0.30), residues: 282 loop : -0.25 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 332 HIS 0.005 0.001 HIS B 545 PHE 0.021 0.002 PHE B 370 TYR 0.017 0.002 TYR A 526 ARG 0.006 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.468 Fit side-chains REVERT: A 91 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8061 (mtt180) REVERT: B 138 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: B 258 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: B 600 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7537 (mp0) outliers start: 23 outliers final: 14 residues processed: 146 average time/residue: 1.8986 time to fit residues: 296.2364 Evaluate side-chains 144 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 737 LYS Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13462 Z= 0.326 Angle : 0.599 6.317 18206 Z= 0.335 Chirality : 0.049 0.150 1858 Planarity : 0.005 0.042 2372 Dihedral : 6.499 57.822 1807 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.81 % Allowed : 16.47 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.58 (0.21), residues: 1618 helix: 1.12 (0.23), residues: 482 sheet: 1.21 (0.29), residues: 292 loop : -0.31 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 332 HIS 0.005 0.001 HIS B 545 PHE 0.021 0.002 PHE A 370 TYR 0.019 0.002 TYR A 526 ARG 0.004 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 1.581 Fit side-chains REVERT: A 91 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8075 (mtt180) REVERT: A 258 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: B 138 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: B 258 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: B 600 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7586 (mp0) outliers start: 25 outliers final: 16 residues processed: 147 average time/residue: 1.9011 time to fit residues: 298.9082 Evaluate side-chains 147 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 737 LYS Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 77 optimal weight: 0.0050 chunk 14 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13462 Z= 0.134 Angle : 0.481 5.234 18206 Z= 0.269 Chirality : 0.044 0.142 1858 Planarity : 0.004 0.039 2372 Dihedral : 6.097 58.069 1807 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.23 % Allowed : 17.12 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.78 (0.21), residues: 1618 helix: 1.43 (0.24), residues: 478 sheet: 1.18 (0.30), residues: 284 loop : -0.19 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 332 HIS 0.003 0.001 HIS B 245 PHE 0.020 0.001 PHE A 370 TYR 0.011 0.001 TYR A 14 ARG 0.006 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.536 Fit side-chains REVERT: A 91 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8019 (mtt180) REVERT: B 138 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7864 (mt-10) outliers start: 17 outliers final: 13 residues processed: 141 average time/residue: 1.9753 time to fit residues: 297.2506 Evaluate side-chains 142 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 737 LYS Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 0.0670 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13462 Z= 0.216 Angle : 0.531 5.860 18206 Z= 0.296 Chirality : 0.046 0.143 1858 Planarity : 0.004 0.039 2372 Dihedral : 6.215 57.056 1807 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.37 % Allowed : 17.05 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.72 (0.21), residues: 1618 helix: 1.33 (0.23), residues: 482 sheet: 1.20 (0.30), residues: 284 loop : -0.23 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 332 HIS 0.004 0.001 HIS B 545 PHE 0.020 0.002 PHE B 370 TYR 0.015 0.002 TYR B 526 ARG 0.009 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.668 Fit side-chains REVERT: A 91 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8053 (mtt180) REVERT: B 138 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: B 258 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7942 (mt-10) outliers start: 19 outliers final: 14 residues processed: 143 average time/residue: 1.8786 time to fit residues: 287.8630 Evaluate side-chains 142 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 737 LYS Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13462 Z= 0.265 Angle : 0.566 6.239 18206 Z= 0.316 Chirality : 0.047 0.144 1858 Planarity : 0.004 0.041 2372 Dihedral : 6.360 57.033 1807 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.23 % Allowed : 17.12 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.63 (0.21), residues: 1618 helix: 1.22 (0.23), residues: 482 sheet: 1.19 (0.29), residues: 292 loop : -0.30 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 332 HIS 0.004 0.001 HIS B 545 PHE 0.021 0.002 PHE B 370 TYR 0.017 0.002 TYR B 526 ARG 0.008 0.001 ARG A 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.594 Fit side-chains REVERT: A 91 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8068 (mtt180) REVERT: B 138 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: B 258 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7962 (mt-10) outliers start: 17 outliers final: 14 residues processed: 144 average time/residue: 1.9208 time to fit residues: 295.6993 Evaluate side-chains 143 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 737 LYS Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.098747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.086535 restraints weight = 14325.312| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.26 r_work: 0.2902 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13462 Z= 0.212 Angle : 0.536 5.483 18206 Z= 0.299 Chirality : 0.046 0.143 1858 Planarity : 0.004 0.041 2372 Dihedral : 6.283 57.524 1807 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.59 % Allowed : 16.76 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.65 (0.21), residues: 1618 helix: 1.26 (0.23), residues: 482 sheet: 1.11 (0.29), residues: 294 loop : -0.26 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 332 HIS 0.004 0.001 HIS B 545 PHE 0.020 0.002 PHE B 370 TYR 0.014 0.001 TYR A 526 ARG 0.008 0.001 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5297.97 seconds wall clock time: 95 minutes 46.58 seconds (5746.58 seconds total)