Starting phenix.real_space_refine (version: dev) on Tue Apr 5 06:23:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/04_2022/7lby_23267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/04_2022/7lby_23267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/04_2022/7lby_23267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/04_2022/7lby_23267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/04_2022/7lby_23267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/04_2022/7lby_23267.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 8800 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 3724 Classifications: {'peptide': 755} Incomplete info: {'truncation_to_alanine': 648} Link IDs: {'PTRANS': 40, 'TRANS': 714} Chain breaks: 2 Unresolved chain link angles: 40 Unresolved non-hydrogen bonds: 2559 Unresolved non-hydrogen angles: 3319 Unresolved non-hydrogen dihedrals: 2205 Unresolved non-hydrogen chiralities: 231 Planarities with less than four sites: {'GLN:plan1': 28, 'ASP:plan': 25, 'TYR:plan': 28, 'ASN:plan1': 28, 'TRP:plan': 22, 'HIS:plan': 24, 'PHE:plan': 40, 'GLU:plan': 32, 'ARG:plan': 54} Unresolved non-hydrogen planarities: 1423 Chain: "B" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5076 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 49, 'TRANS': 612, 'PCIS': 1} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 7.16, per 1000 atoms: 0.81 Number of scatterers: 8800 At special positions: 0 Unit cell: (135, 150.12, 124.2, 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 23 16.00 O 1712 8.00 N 1624 7.00 C 5441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 500 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 1.9 seconds 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 13 sheets defined 40.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 124 through 142 Proline residue: A 129 - end of helix Proline residue: A 133 - end of helix removed outlier: 3.859A pdb=" N HIS A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.510A pdb=" N SER A 152 " --> pdb=" O HIS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 178 through 191 Processing helix chain 'A' and resid 196 through 219 removed outlier: 3.894A pdb=" N MET A 200 " --> pdb=" O TYR A 196 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 228 through 256 Proline residue: A 250 - end of helix Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.576A pdb=" N SER A 300 " --> pdb=" O TRP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.632A pdb=" N SER A 376 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 377 " --> pdb=" O TYR A 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 373 through 377' Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 422 through 430 removed outlier: 3.703A pdb=" N ASN A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 468 removed outlier: 3.825A pdb=" N GLN A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 513 Processing helix chain 'A' and resid 519 through 551 removed outlier: 3.903A pdb=" N THR A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 582 Processing helix chain 'A' and resid 589 through 610 removed outlier: 4.249A pdb=" N GLY A 593 " --> pdb=" O ASN A 589 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 659 Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 663 through 688 Proline residue: A 670 - end of helix Processing helix chain 'A' and resid 791 through 802 removed outlier: 3.822A pdb=" N ARG A 802 " --> pdb=" O ARG A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 831 removed outlier: 3.592A pdb=" N GLY A 830 " --> pdb=" O PHE A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 860 Processing helix chain 'A' and resid 861 through 863 No H-bonds generated for 'chain 'A' and resid 861 through 863' Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.692A pdb=" N LEU B 149 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 259 Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 321 through 335 Processing helix chain 'B' and resid 532 through 538 Processing helix chain 'B' and resid 560 through 578 removed outlier: 3.558A pdb=" N MET B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 615 through 630 removed outlier: 3.907A pdb=" N LEU B 619 " --> pdb=" O LYS B 615 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 620 " --> pdb=" O GLN B 616 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN B 622 " --> pdb=" O ASP B 618 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP B 627 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 697 removed outlier: 3.517A pdb=" N TYR B 688 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP B 697 " --> pdb=" O ASP B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 743 removed outlier: 4.047A pdb=" N VAL B 736 " --> pdb=" O TRP B 732 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP B 737 " --> pdb=" O PHE B 733 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR B 738 " --> pdb=" O GLU B 734 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN B 742 " --> pdb=" O TYR B 738 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS B 743 " --> pdb=" O ALA B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 772 Processing sheet with id=AA1, first strand: chain 'A' and resid 277 through 282 removed outlier: 3.766A pdb=" N ALA A 279 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 311 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 390 through 392 removed outlier: 3.546A pdb=" N PHE A 478 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 700 through 704 removed outlier: 6.586A pdb=" N TYR A 702 " --> pdb=" O THR A 722 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR A 722 " --> pdb=" O TYR A 702 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 704 " --> pdb=" O ASN A 720 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU A 729 " --> pdb=" O VAL A 721 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 716 through 717 Processing sheet with id=AA5, first strand: chain 'B' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'B' and resid 95 through 101 removed outlier: 4.078A pdb=" N PHE B 100 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN B 168 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 173 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 132 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY B 140 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 159 removed outlier: 4.207A pdb=" N THR B 153 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR B 117 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA B 111 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS B 110 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 267 through 269 removed outlier: 4.116A pdb=" N LEU B 268 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 235 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL B 234 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 279 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 316 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 383 through 384 Processing sheet with id=AB1, first strand: chain 'B' and resid 395 through 396 removed outlier: 3.942A pdb=" N LEU B 396 " --> pdb=" O ASN B 480 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN B 480 " --> pdb=" O LEU B 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 437 through 442 removed outlier: 3.880A pdb=" N GLN B 439 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 429 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG B 428 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU B 487 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP B 430 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP B 485 " --> pdb=" O ASP B 430 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 527 through 528 removed outlier: 4.022A pdb=" N ILE B 527 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 727 " --> pdb=" O ILE B 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 586 through 588 removed outlier: 6.163A pdb=" N THR B 553 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B 552 " --> pdb=" O MET B 602 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE B 604 " --> pdb=" O ILE B 552 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL B 554 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE B 601 " --> pdb=" O SER B 676 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 678 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 662 " --> pdb=" O ILE B 711 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 710 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B 717 " --> pdb=" O VAL B 710 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3201 1.34 - 1.46: 1632 1.46 - 1.58: 4037 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 8914 Sorted by residual: bond pdb=" CA VAL A 343 " pdb=" CB VAL A 343 " ideal model delta sigma weight residual 1.537 1.508 0.028 5.00e-03 4.00e+04 3.22e+01 bond pdb=" C THR A 540 " pdb=" O THR A 540 " ideal model delta sigma weight residual 1.236 1.272 -0.036 1.15e-02 7.56e+03 9.71e+00 bond pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.19e-02 7.06e+03 6.89e+00 bond pdb=" N SER A 635 " pdb=" CA SER A 635 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.28e-02 6.10e+03 6.04e+00 bond pdb=" N GLY A 636 " pdb=" CA GLY A 636 " ideal model delta sigma weight residual 1.454 1.481 -0.027 1.24e-02 6.50e+03 4.60e+00 ... (remaining 8909 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 227 107.13 - 113.84: 5011 113.84 - 120.56: 3329 120.56 - 127.27: 3622 127.27 - 133.99: 59 Bond angle restraints: 12248 Sorted by residual: angle pdb=" N PRO A 445 " pdb=" CA PRO A 445 " pdb=" CB PRO A 445 " ideal model delta sigma weight residual 102.25 110.63 -8.38 7.00e-01 2.04e+00 1.43e+02 angle pdb=" N PRO A 764 " pdb=" CA PRO A 764 " pdb=" CB PRO A 764 " ideal model delta sigma weight residual 103.36 110.96 -7.60 8.30e-01 1.45e+00 8.38e+01 angle pdb=" N PRO A 337 " pdb=" CA PRO A 337 " pdb=" CB PRO A 337 " ideal model delta sigma weight residual 103.36 110.62 -7.26 8.30e-01 1.45e+00 7.66e+01 angle pdb=" N PRO A 706 " pdb=" CA PRO A 706 " pdb=" CB PRO A 706 " ideal model delta sigma weight residual 103.25 112.37 -9.12 1.05e+00 9.07e-01 7.55e+01 angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" CB PRO A 763 " ideal model delta sigma weight residual 103.08 111.30 -8.22 9.70e-01 1.06e+00 7.18e+01 ... (remaining 12243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5008 17.93 - 35.86: 233 35.86 - 53.79: 43 53.79 - 71.71: 13 71.71 - 89.64: 7 Dihedral angle restraints: 5304 sinusoidal: 1226 harmonic: 4078 Sorted by residual: dihedral pdb=" N PRO A 342 " pdb=" C PRO A 342 " pdb=" CA PRO A 342 " pdb=" CB PRO A 342 " ideal model delta harmonic sigma weight residual 115.10 124.59 -9.49 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" CB GLU B 183 " pdb=" CG GLU B 183 " pdb=" CD GLU B 183 " pdb=" OE1 GLU B 183 " ideal model delta sinusoidal sigma weight residual 0.00 89.64 -89.64 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" N PRO A 307 " pdb=" C PRO A 307 " pdb=" CA PRO A 307 " pdb=" CB PRO A 307 " ideal model delta harmonic sigma weight residual 115.10 123.23 -8.13 0 2.50e+00 1.60e-01 1.06e+01 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1195 0.052 - 0.104: 227 0.104 - 0.155: 31 0.155 - 0.207: 11 0.207 - 0.259: 33 Chirality restraints: 1497 Sorted by residual: chirality pdb=" CA PRO A 307 " pdb=" N PRO A 307 " pdb=" C PRO A 307 " pdb=" CB PRO A 307 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA PRO A 342 " pdb=" N PRO A 342 " pdb=" C PRO A 342 " pdb=" CB PRO A 342 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA PRO A 660 " pdb=" N PRO A 660 " pdb=" C PRO A 660 " pdb=" CB PRO A 660 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1494 not shown) Planarity restraints: 1689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 83 " -0.047 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO B 84 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 84 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 84 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 538 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C ALA A 538 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA A 538 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS A 539 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 537 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ASP A 537 " 0.029 2.00e-02 2.50e+03 pdb=" O ASP A 537 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A 538 " -0.010 2.00e-02 2.50e+03 ... (remaining 1686 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 174 2.70 - 3.25: 8609 3.25 - 3.80: 13241 3.80 - 4.35: 14118 4.35 - 4.90: 24343 Nonbonded interactions: 60485 Sorted by model distance: nonbonded pdb=" O PHE B 705 " pdb=" OG SER B 718 " model vdw 2.148 2.440 nonbonded pdb=" ND2 ASN B 569 " pdb=" OD1 ASN B 692 " model vdw 2.221 2.520 nonbonded pdb=" OG SER B 432 " pdb=" O ARG B 483 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR B 118 " pdb=" OD1 ASP B 193 " model vdw 2.272 2.440 nonbonded pdb=" O ASN B 67 " pdb=" OH TYR B 311 " model vdw 2.289 2.440 ... (remaining 60480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 5441 2.51 5 N 1624 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 11.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 14.810 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.080 Process input model: 31.870 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8914 Z= 0.212 Angle : 0.780 9.122 12248 Z= 0.603 Chirality : 0.054 0.259 1497 Planarity : 0.003 0.072 1689 Dihedral : 12.333 89.643 2653 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 1.28 % Allowed : 6.19 % Favored : 92.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.24 (0.24), residues: 1406 helix: 2.83 (0.22), residues: 539 sheet: -1.18 (0.40), residues: 194 loop : -2.55 (0.23), residues: 673 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.017 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1681 time to fit residues: 37.7568 Evaluate side-chains 114 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.7980 chunk 106 optimal weight: 0.0010 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN B 244 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 729 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8914 Z= 0.225 Angle : 0.541 5.846 12248 Z= 0.284 Chirality : 0.044 0.148 1497 Planarity : 0.004 0.071 1689 Dihedral : 3.663 19.707 1460 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.69 % Favored : 92.82 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.00 (0.24), residues: 1406 helix: 3.04 (0.22), residues: 556 sheet: -1.05 (0.43), residues: 173 loop : -2.55 (0.22), residues: 677 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.068 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 140 average time/residue: 0.1804 time to fit residues: 36.7412 Evaluate side-chains 111 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0802 time to fit residues: 1.7211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 30.0000 chunk 39 optimal weight: 2.9990 chunk 106 optimal weight: 0.0030 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 0.0050 chunk 127 optimal weight: 0.8980 chunk 43 optimal weight: 40.0000 chunk 102 optimal weight: 0.7980 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8914 Z= 0.137 Angle : 0.500 7.899 12248 Z= 0.254 Chirality : 0.042 0.142 1497 Planarity : 0.003 0.071 1689 Dihedral : 3.371 20.124 1460 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.83 % Favored : 92.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.16 (0.24), residues: 1406 helix: 3.25 (0.22), residues: 562 sheet: -1.25 (0.42), residues: 166 loop : -2.49 (0.22), residues: 678 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.030 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1918 time to fit residues: 39.0528 Evaluate side-chains 110 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 67 optimal weight: 40.0000 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 8914 Z= 0.378 Angle : 0.672 10.085 12248 Z= 0.357 Chirality : 0.046 0.159 1497 Planarity : 0.005 0.071 1689 Dihedral : 4.422 20.898 1460 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.68 % Favored : 90.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.17 (0.24), residues: 1406 helix: 3.07 (0.22), residues: 556 sheet: -1.60 (0.39), residues: 170 loop : -2.67 (0.22), residues: 680 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.158 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1793 time to fit residues: 30.5263 Evaluate side-chains 91 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 50.0000 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 116 optimal weight: 0.0050 chunk 94 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 30.0000 chunk 122 optimal weight: 2.9990 chunk 34 optimal weight: 30.0000 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 8914 Z= 0.313 Angle : 0.619 11.597 12248 Z= 0.323 Chirality : 0.045 0.166 1497 Planarity : 0.004 0.072 1689 Dihedral : 4.273 22.659 1460 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.82 % Favored : 91.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.23 (0.24), residues: 1406 helix: 2.99 (0.22), residues: 562 sheet: -1.67 (0.39), residues: 169 loop : -2.70 (0.22), residues: 675 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1523 time to fit residues: 27.6968 Evaluate side-chains 89 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 136 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 71 optimal weight: 30.0000 chunk 131 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8914 Z= 0.248 Angle : 0.583 8.696 12248 Z= 0.304 Chirality : 0.044 0.186 1497 Planarity : 0.004 0.072 1689 Dihedral : 4.188 24.114 1460 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.68 % Favored : 90.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.09 (0.24), residues: 1406 helix: 3.06 (0.22), residues: 562 sheet: -1.54 (0.41), residues: 162 loop : -2.59 (0.22), residues: 682 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1531 time to fit residues: 27.6289 Evaluate side-chains 90 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 76 optimal weight: 0.0050 chunk 135 optimal weight: 0.0870 chunk 85 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 0.0170 chunk 84 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 overall best weight: 0.3010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8914 Z= 0.129 Angle : 0.531 8.323 12248 Z= 0.270 Chirality : 0.042 0.174 1497 Planarity : 0.004 0.073 1689 Dihedral : 3.789 21.025 1460 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.76 % Favored : 92.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1406 helix: 3.23 (0.22), residues: 556 sheet: -1.20 (0.44), residues: 149 loop : -2.47 (0.22), residues: 701 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.051 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1686 time to fit residues: 31.1157 Evaluate side-chains 94 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 67 optimal weight: 40.0000 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 0.0670 chunk 123 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8914 Z= 0.152 Angle : 0.542 9.541 12248 Z= 0.276 Chirality : 0.043 0.165 1497 Planarity : 0.004 0.074 1689 Dihedral : 3.700 21.168 1460 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.40 % Favored : 93.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1406 helix: 3.25 (0.22), residues: 556 sheet: -1.59 (0.39), residues: 183 loop : -2.39 (0.23), residues: 667 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1440 time to fit residues: 25.7116 Evaluate side-chains 89 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9990 chunk 130 optimal weight: 0.0870 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 38 optimal weight: 50.0000 chunk 114 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.093 8914 Z= 0.174 Angle : 0.538 9.549 12248 Z= 0.279 Chirality : 0.043 0.196 1497 Planarity : 0.004 0.105 1689 Dihedral : 3.695 21.050 1460 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.83 % Favored : 92.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.17 (0.24), residues: 1406 helix: 3.29 (0.22), residues: 556 sheet: -1.39 (0.41), residues: 170 loop : -2.41 (0.23), residues: 680 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.026 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1402 time to fit residues: 25.6385 Evaluate side-chains 92 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 chunk 129 optimal weight: 0.0870 chunk 111 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 34 optimal weight: 30.0000 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.106 8914 Z= 0.176 Angle : 0.539 8.410 12248 Z= 0.277 Chirality : 0.043 0.163 1497 Planarity : 0.005 0.114 1689 Dihedral : 3.672 20.165 1460 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.54 % Favored : 93.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.21 (0.24), residues: 1406 helix: 3.34 (0.22), residues: 557 sheet: -1.55 (0.39), residues: 187 loop : -2.37 (0.23), residues: 662 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.962 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1516 time to fit residues: 28.4593 Evaluate side-chains 93 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 50.0000 chunk 112 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 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 = 0.4195 r_free = 0.4195 target = 0.163346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.149634 restraints weight = 21015.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.147823 restraints weight = 46957.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.144803 restraints weight = 37862.595| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.084 8914 Z= 0.363 Angle : 0.665 8.728 12248 Z= 0.349 Chirality : 0.046 0.174 1497 Planarity : 0.005 0.100 1689 Dihedral : 4.264 26.324 1460 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.32 % Favored : 90.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.03 (0.24), residues: 1406 helix: 3.17 (0.22), residues: 557 sheet: -1.63 (0.41), residues: 163 loop : -2.54 (0.23), residues: 686 =============================================================================== Job complete usr+sys time: 1839.77 seconds wall clock time: 33 minutes 52.20 seconds (2032.20 seconds total)