Starting phenix.real_space_refine on Wed Sep 25 18:24:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/09_2024/7lby_23267.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/09_2024/7lby_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_23267/09_2024/7lby_23267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/09_2024/7lby_23267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/09_2024/7lby_23267.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/09_2024/7lby_23267.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2664 atoms to isotropic. 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 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. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 612} 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: 6.56, per 1000 atoms: 0.75 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 - 3.00 Amino acid : True - 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: 1.90 Conformation dependent library (CDL) restraints added in 1.1 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: 1.04 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: 2.67 Time building geometry restraints manager: 2.20 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: 0.00 - 1.82: 11846 1.82 - 3.65: 307 3.65 - 5.47: 45 5.47 - 7.30: 37 7.30 - 9.12: 13 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 3.040 nonbonded pdb=" ND2 ASN B 569 " pdb=" OD1 ASN B 692 " model vdw 2.221 3.120 nonbonded pdb=" OG SER B 432 " pdb=" O ARG B 483 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR B 118 " pdb=" OD1 ASP B 193 " model vdw 2.272 3.040 nonbonded pdb=" O ASN B 67 " pdb=" OH TYR B 311 " model vdw 2.289 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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 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: 2.790 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.320 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 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 % Allowed : 0.00 % Favored : 100.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.000 TRP B 253 HIS 0.001 0.000 HIS B 509 PHE 0.024 0.001 PHE B 289 TYR 0.005 0.001 TYR B 524 ARG 0.005 0.000 ARG B 257 *********************** 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 : 0.981 Fit side-chains revert: symmetry clash REVERT: B 172 LEU cc_start: 0.8714 (mp) cc_final: 0.8465 (mt) REVERT: B 338 LEU cc_start: 0.8362 (pt) cc_final: 0.7991 (pp) REVERT: B 429 MET cc_start: 0.8745 (tmm) cc_final: 0.8237 (tmm) REVERT: B 482 LEU cc_start: 0.8744 (tp) cc_final: 0.8481 (tt) REVERT: B 676 SER cc_start: 0.8473 (p) cc_final: 0.7910 (p) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1708 time to fit residues: 38.7812 Evaluate side-chains 115 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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: 1.9990 chunk 106 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 67 optimal weight: 0.0470 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 729 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8914 Z= 0.231 Angle : 0.537 5.437 12248 Z= 0.286 Chirality : 0.043 0.149 1497 Planarity : 0.004 0.071 1689 Dihedral : 3.556 18.022 1460 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.26 % Favored : 93.24 % Rotamer: Outliers : 0.18 % Allowed : 5.54 % Favored : 94.28 % 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: 3.14 (0.22), residues: 556 sheet: -1.18 (0.44), residues: 165 loop : -2.54 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 737 HIS 0.003 0.001 HIS B 177 PHE 0.017 0.001 PHE B 221 TYR 0.010 0.001 TYR B 416 ARG 0.003 0.001 ARG B 675 *********************** 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 136 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.925 Fit side-chains REVERT: B 88 VAL cc_start: 0.8304 (t) cc_final: 0.8054 (m) REVERT: B 258 SER cc_start: 0.8883 (t) cc_final: 0.8544 (t) REVERT: B 338 LEU cc_start: 0.8339 (pt) cc_final: 0.8033 (pp) REVERT: B 372 PHE cc_start: 0.7394 (m-80) cc_final: 0.6964 (m-80) REVERT: B 466 LYS cc_start: 0.7696 (mmmt) cc_final: 0.7027 (ttmm) REVERT: B 482 LEU cc_start: 0.8919 (tp) cc_final: 0.8683 (tt) outliers start: 1 outliers final: 1 residues processed: 136 average time/residue: 0.1728 time to fit residues: 34.0531 Evaluate side-chains 114 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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: 20.0000 chunk 39 optimal weight: 7.9990 chunk 106 optimal weight: 0.0020 chunk 87 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 128 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 127 optimal weight: 6.9990 chunk 43 optimal weight: 30.0000 chunk 102 optimal weight: 0.0570 overall best weight: 0.4908 ------------------------------------------------------------------------------- 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 305 ASN B 509 HIS ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8914 Z= 0.139 Angle : 0.495 7.724 12248 Z= 0.256 Chirality : 0.042 0.139 1497 Planarity : 0.004 0.071 1689 Dihedral : 3.398 21.606 1460 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.83 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: 0.11 (0.24), residues: 1406 helix: 3.17 (0.22), residues: 562 sheet: -1.15 (0.43), residues: 163 loop : -2.52 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 627 HIS 0.002 0.001 HIS B 509 PHE 0.019 0.001 PHE B 254 TYR 0.012 0.001 TYR B 378 ARG 0.002 0.000 ARG B 257 *********************** 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 143 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.998 Fit side-chains REVERT: B 88 VAL cc_start: 0.8200 (t) cc_final: 0.7993 (m) REVERT: B 95 ASN cc_start: 0.7829 (p0) cc_final: 0.7520 (p0) REVERT: B 112 MET cc_start: 0.7509 (tpp) cc_final: 0.7250 (mtp) REVERT: B 338 LEU cc_start: 0.8314 (pt) cc_final: 0.7982 (pp) REVERT: B 372 PHE cc_start: 0.7440 (m-80) cc_final: 0.7132 (m-10) REVERT: B 378 TYR cc_start: 0.5890 (t80) cc_final: 0.5659 (t80) REVERT: B 429 MET cc_start: 0.8674 (tmm) cc_final: 0.8307 (tmm) REVERT: B 466 LYS cc_start: 0.7623 (mmmt) cc_final: 0.7025 (ttmm) REVERT: B 482 LEU cc_start: 0.8883 (tp) cc_final: 0.8597 (tt) REVERT: B 580 PHE cc_start: 0.8352 (t80) cc_final: 0.8152 (t80) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1774 time to fit residues: 36.5397 Evaluate side-chains 110 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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: 0.0670 chunk 96 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 61 optimal weight: 30.0000 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 67 optimal weight: 40.0000 chunk 122 optimal weight: 0.9990 chunk 36 optimal weight: 40.0000 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8914 Z= 0.172 Angle : 0.500 5.899 12248 Z= 0.262 Chirality : 0.042 0.141 1497 Planarity : 0.004 0.070 1689 Dihedral : 3.496 20.129 1460 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.12 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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: 0.13 (0.24), residues: 1406 helix: 3.20 (0.22), residues: 563 sheet: -1.34 (0.41), residues: 172 loop : -2.47 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 191 HIS 0.002 0.001 HIS B 509 PHE 0.017 0.001 PHE B 221 TYR 0.008 0.001 TYR B 725 ARG 0.003 0.000 ARG B 675 *********************** 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 135 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.906 Fit side-chains REVERT: B 88 VAL cc_start: 0.8322 (t) cc_final: 0.8109 (m) REVERT: B 338 LEU cc_start: 0.8255 (pt) cc_final: 0.7968 (pp) REVERT: B 429 MET cc_start: 0.8748 (tmm) cc_final: 0.8452 (tmm) REVERT: B 466 LYS cc_start: 0.7820 (mmmt) cc_final: 0.7342 (ttmm) REVERT: B 482 LEU cc_start: 0.8939 (tp) cc_final: 0.8660 (tt) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1662 time to fit residues: 33.1541 Evaluate side-chains 109 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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: 7.9990 chunk 77 optimal weight: 0.0270 chunk 1 optimal weight: 50.0000 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 40.0000 chunk 122 optimal weight: 0.8980 chunk 34 optimal weight: 30.0000 overall best weight: 1.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8914 Z= 0.311 Angle : 0.605 6.676 12248 Z= 0.321 Chirality : 0.045 0.185 1497 Planarity : 0.004 0.071 1689 Dihedral : 4.063 21.113 1460 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.32 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: -0.06 (0.24), residues: 1406 helix: 3.13 (0.22), residues: 563 sheet: -1.73 (0.40), residues: 171 loop : -2.58 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 191 HIS 0.005 0.001 HIS B 729 PHE 0.017 0.002 PHE B 580 TYR 0.018 0.001 TYR B 378 ARG 0.006 0.001 ARG B 368 *********************** 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 125 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.948 Fit side-chains REVERT: B 88 VAL cc_start: 0.8689 (t) cc_final: 0.8487 (m) REVERT: B 210 LYS cc_start: 0.7884 (pttp) cc_final: 0.7440 (tppt) REVERT: B 466 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7740 (ttmm) REVERT: B 547 ASP cc_start: 0.8269 (p0) cc_final: 0.8058 (p0) REVERT: B 565 GLU cc_start: 0.7862 (pp20) cc_final: 0.7645 (pp20) REVERT: B 690 MET cc_start: 0.7309 (ptt) cc_final: 0.7082 (ptt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1894 time to fit residues: 35.0440 Evaluate side-chains 100 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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: 7.9990 chunk 122 optimal weight: 0.0010 chunk 26 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 30.0000 chunk 131 optimal weight: 5.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 8914 Z= 0.515 Angle : 0.810 16.550 12248 Z= 0.431 Chirality : 0.050 0.198 1497 Planarity : 0.006 0.071 1689 Dihedral : 5.264 28.736 1460 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.17 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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: -0.63 (0.24), residues: 1406 helix: 2.64 (0.23), residues: 559 sheet: -2.38 (0.37), residues: 162 loop : -2.73 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 191 HIS 0.009 0.002 HIS B 509 PHE 0.028 0.003 PHE B 580 TYR 0.028 0.003 TYR B 378 ARG 0.011 0.001 ARG B 196 *********************** 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 : 0.901 Fit side-chains revert: symmetry clash REVERT: B 88 VAL cc_start: 0.8904 (t) cc_final: 0.8674 (m) REVERT: B 210 LYS cc_start: 0.7819 (pttp) cc_final: 0.7537 (tppt) REVERT: B 340 ARG cc_start: 0.7800 (ptt180) cc_final: 0.7199 (ttt180) REVERT: B 565 GLU cc_start: 0.7889 (pp20) cc_final: 0.7658 (pp20) REVERT: B 627 TRP cc_start: 0.8924 (t-100) cc_final: 0.8686 (t-100) REVERT: B 675 ARG cc_start: 0.7054 (mmt90) cc_final: 0.6549 (mmt180) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1619 time to fit residues: 27.7612 Evaluate side-chains 90 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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: 9.9990 chunk 77 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 114 optimal weight: 7.9990 chunk 76 optimal weight: 0.3980 chunk 135 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.7217 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8914 Z= 0.233 Angle : 0.616 9.206 12248 Z= 0.323 Chirality : 0.045 0.188 1497 Planarity : 0.004 0.038 1689 Dihedral : 4.523 25.519 1460 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.11 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -0.34 (0.24), residues: 1406 helix: 2.90 (0.23), residues: 560 sheet: -2.14 (0.38), residues: 157 loop : -2.63 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 732 HIS 0.004 0.001 HIS B 306 PHE 0.019 0.002 PHE B 540 TYR 0.032 0.002 TYR B 378 ARG 0.008 0.001 ARG B 196 *********************** 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 : 0.735 Fit side-chains REVERT: B 88 VAL cc_start: 0.8823 (t) cc_final: 0.8620 (m) REVERT: B 340 ARG cc_start: 0.7850 (ptt180) cc_final: 0.7186 (mtp85) REVERT: B 395 SER cc_start: 0.8401 (m) cc_final: 0.7330 (m) REVERT: B 412 MET cc_start: 0.8429 (mmm) cc_final: 0.8195 (mmp) REVERT: B 627 TRP cc_start: 0.8839 (t-100) cc_final: 0.8605 (t-100) REVERT: B 675 ARG cc_start: 0.6876 (mmt90) cc_final: 0.6268 (mmt180) REVERT: B 681 LEU cc_start: 0.8340 (tp) cc_final: 0.8079 (tp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1274 time to fit residues: 22.3232 Evaluate side-chains 96 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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: 0.4980 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 0.0670 chunk 92 optimal weight: 0.0570 chunk 67 optimal weight: 40.0000 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 130 optimal weight: 0.0030 chunk 118 optimal weight: 0.5980 overall best weight: 0.2446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 244 GLN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3737 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= 0.145 Angle : 0.583 9.758 12248 Z= 0.298 Chirality : 0.044 0.173 1497 Planarity : 0.004 0.040 1689 Dihedral : 4.074 22.050 1460 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.69 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: -0.15 (0.24), residues: 1406 helix: 3.09 (0.22), residues: 554 sheet: -1.83 (0.41), residues: 138 loop : -2.55 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 760 HIS 0.002 0.000 HIS B 306 PHE 0.012 0.001 PHE B 540 TYR 0.028 0.001 TYR B 378 ARG 0.004 0.000 ARG B 368 *********************** 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 122 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.048 Fit side-chains REVERT: B 253 TRP cc_start: 0.9078 (t60) cc_final: 0.8592 (t60) REVERT: B 547 ASP cc_start: 0.8265 (p0) cc_final: 0.8042 (p0) REVERT: B 627 TRP cc_start: 0.8796 (t-100) cc_final: 0.8587 (t-100) REVERT: B 681 LEU cc_start: 0.8249 (tp) cc_final: 0.7953 (tp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1601 time to fit residues: 29.3408 Evaluate side-chains 102 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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: 1.9990 chunk 130 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7158 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8914 Z= 0.193 Angle : 0.591 11.589 12248 Z= 0.302 Chirality : 0.044 0.170 1497 Planarity : 0.004 0.040 1689 Dihedral : 4.083 23.599 1460 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.33 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.14 (0.24), residues: 1406 helix: 3.11 (0.22), residues: 555 sheet: -1.93 (0.38), residues: 168 loop : -2.54 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 760 HIS 0.004 0.001 HIS B 177 PHE 0.025 0.002 PHE B 540 TYR 0.026 0.001 TYR B 378 ARG 0.004 0.001 ARG B 196 *********************** 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 118 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: B 627 TRP cc_start: 0.8849 (t-100) cc_final: 0.8630 (t-100) REVERT: B 681 LEU cc_start: 0.8301 (tp) cc_final: 0.8017 (tp) REVERT: B 690 MET cc_start: 0.7409 (ptt) cc_final: 0.7049 (ptt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1481 time to fit residues: 26.9108 Evaluate side-chains 99 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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: 10.0000 chunk 93 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 119 optimal weight: 0.0470 chunk 34 optimal weight: 30.0000 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 GLN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8914 Z= 0.228 Angle : 0.604 9.274 12248 Z= 0.312 Chirality : 0.044 0.171 1497 Planarity : 0.004 0.037 1689 Dihedral : 4.170 25.184 1460 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.54 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -0.14 (0.24), residues: 1406 helix: 3.12 (0.22), residues: 555 sheet: -1.99 (0.36), residues: 187 loop : -2.53 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 760 HIS 0.004 0.001 HIS B 306 PHE 0.027 0.002 PHE B 540 TYR 0.024 0.001 TYR B 378 ARG 0.003 0.001 ARG B 368 ********************** 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 114 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: B 112 MET cc_start: 0.7443 (tpt) cc_final: 0.6934 (tpt) REVERT: B 675 ARG cc_start: 0.6680 (mmt90) cc_final: 0.6159 (mmt180) REVERT: B 690 MET cc_start: 0.7461 (ptt) cc_final: 0.7046 (ptt) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1485 time to fit residues: 26.1228 Evaluate side-chains 95 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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: 0.6980 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 50.0000 chunk 112 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 115 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 481 GLN ** B 668 GLN ** 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 = 0.4234 r_free = 0.4234 target = 0.166367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.150136 restraints weight = 20893.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.147841 restraints weight = 43093.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.148011 restraints weight = 48885.159| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8914 Z= 0.217 Angle : 0.597 9.588 12248 Z= 0.307 Chirality : 0.044 0.168 1497 Planarity : 0.004 0.037 1689 Dihedral : 4.137 24.979 1460 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.33 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -0.11 (0.24), residues: 1406 helix: 3.11 (0.22), residues: 555 sheet: -1.72 (0.39), residues: 157 loop : -2.56 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 732 HIS 0.003 0.001 HIS B 306 PHE 0.027 0.002 PHE B 540 TYR 0.025 0.001 TYR B 378 ARG 0.004 0.001 ARG B 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1903.90 seconds wall clock time: 37 minutes 23.78 seconds (2243.78 seconds total)