Starting phenix.real_space_refine on Thu Jul 2 13:35:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23ph_69144/07_2026/23ph_69144.cif Found real_map, /net/cci-nas-00/data/ceres_data/23ph_69144/07_2026/23ph_69144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/23ph_69144/07_2026/23ph_69144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23ph_69144/07_2026/23ph_69144.map" model { file = "/net/cci-nas-00/data/ceres_data/23ph_69144/07_2026/23ph_69144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23ph_69144/07_2026/23ph_69144.cif" } resolution = 3.01 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 5500 2.51 5 N 1488 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8580 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4290 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 550} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 4290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4290 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 550} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 1.61, per 1000 atoms: 0.19 Number of scatterers: 8580 At special positions: 0 Unit cell: (89.509, 108.353, 142.676, 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 30 16.00 O 1562 8.00 N 1488 7.00 C 5500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.49 Conformation dependent library (CDL) restraints added in 430.5 milliseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 5 sheets defined 69.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 133 through 169 removed outlier: 3.900A pdb=" N ARG A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 186 through 234 removed outlier: 3.936A pdb=" N ALA A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 246 through 289 removed outlier: 4.651A pdb=" N SER A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Proline residue: A 273 - end of helix Processing helix chain 'A' and resid 290 through 339 removed outlier: 4.201A pdb=" N ALA A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG A 317 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE A 318 " --> pdb=" O TRP A 314 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 removed outlier: 4.048A pdb=" N PHE A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 403 removed outlier: 4.083A pdb=" N LYS A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 419 removed outlier: 3.523A pdb=" N MET A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 Proline residue: A 423 - end of helix No H-bonds generated for 'chain 'A' and resid 420 through 425' Processing helix chain 'A' and resid 426 through 450 removed outlier: 4.170A pdb=" N ARG A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.058A pdb=" N ALA A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 574 through 585 removed outlier: 3.899A pdb=" N LEU A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.815A pdb=" N GLY A 606 " --> pdb=" O GLY A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 626 Processing helix chain 'A' and resid 640 through 653 removed outlier: 4.259A pdb=" N GLY A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.532A pdb=" N LEU A 694 " --> pdb=" O HIS A 691 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 695 " --> pdb=" O GLY A 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 695' Processing helix chain 'A' and resid 699 through 704 Processing helix chain 'B' and resid 133 through 170 removed outlier: 4.011A pdb=" N MET B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) Proline residue: B 158 - end of helix removed outlier: 4.104A pdb=" N GLN B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 234 removed outlier: 3.922A pdb=" N ALA B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'B' and resid 247 through 289 Proline residue: B 273 - end of helix Processing helix chain 'B' and resid 290 through 339 removed outlier: 4.135A pdb=" N ALA B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG B 317 " --> pdb=" O ARG B 313 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE B 318 " --> pdb=" O TRP B 314 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 346 removed outlier: 4.092A pdb=" N PHE B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 403 removed outlier: 4.091A pdb=" N LYS B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 419 removed outlier: 3.516A pdb=" N MET B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 Proline residue: B 423 - end of helix removed outlier: 4.171A pdb=" N PHE B 426 " --> pdb=" O PRO B 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 420 through 426' Processing helix chain 'B' and resid 427 through 450 Processing helix chain 'B' and resid 466 through 470 removed outlier: 3.919A pdb=" N ALA B 470 " --> pdb=" O PRO B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 540 through 546 Processing helix chain 'B' and resid 561 through 568 Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 603 through 607 removed outlier: 4.126A pdb=" N GLY B 606 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 626 Processing helix chain 'B' and resid 640 through 653 removed outlier: 4.195A pdb=" N GLY B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA B 650 " --> pdb=" O THR B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.540A pdb=" N THR B 669 " --> pdb=" O ARG B 666 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 671 " --> pdb=" O SER B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 695 removed outlier: 3.784A pdb=" N LEU B 694 " --> pdb=" O HIS B 691 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 695 " --> pdb=" O GLY B 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 691 through 695' Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.533A pdb=" N MET B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR B 707 " --> pdb=" O GLU B 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 488 through 491 removed outlier: 3.572A pdb=" N PHE A 479 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 490 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 477 " --> pdb=" O GLY A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 491 removed outlier: 3.572A pdb=" N PHE A 479 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 490 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 477 " --> pdb=" O GLY A 490 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 475 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER A 528 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 477 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS A 526 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 548 through 551 removed outlier: 6.406A pdb=" N GLY A 549 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 676 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG A 687 " --> pdb=" O ILE A 676 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 678 " --> pdb=" O ALA A 685 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 488 through 495 removed outlier: 5.032A pdb=" N VAL B 477 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER B 492 " --> pdb=" O ASP B 475 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP B 475 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLU B 494 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA B 473 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 528 " --> pdb=" O ASP B 475 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL B 477 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS B 526 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 548 through 551 removed outlier: 6.420A pdb=" N GLY B 549 " --> pdb=" O LEU B 631 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL B 501 " --> pdb=" O PHE B 662 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 502 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU B 679 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 504 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 676 " --> pdb=" O ARG B 687 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG B 687 " --> pdb=" O ILE B 676 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL B 678 " --> pdb=" O ALA B 685 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1695 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: 1.27 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2624 1.34 - 1.46: 1436 1.46 - 1.57: 4616 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 8734 Sorted by residual: bond pdb=" N VAL A 157 " pdb=" CA VAL A 157 " ideal model delta sigma weight residual 1.463 1.487 -0.024 1.20e-02 6.94e+03 4.07e+00 bond pdb=" CA VAL B 157 " pdb=" C VAL B 157 " ideal model delta sigma weight residual 1.523 1.541 -0.018 9.20e-03 1.18e+04 3.99e+00 bond pdb=" CA VAL A 157 " pdb=" C VAL A 157 " ideal model delta sigma weight residual 1.523 1.541 -0.018 9.20e-03 1.18e+04 3.83e+00 bond pdb=" N VAL B 157 " pdb=" CA VAL B 157 " ideal model delta sigma weight residual 1.463 1.485 -0.022 1.20e-02 6.94e+03 3.25e+00 bond pdb=" C VAL A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.25e-02 6.40e+03 2.91e+00 ... (remaining 8729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 11685 2.78 - 5.57: 131 5.57 - 8.35: 25 8.35 - 11.13: 4 11.13 - 13.92: 3 Bond angle restraints: 11848 Sorted by residual: angle pdb=" CA LEU A 584 " pdb=" CB LEU A 584 " pdb=" CG LEU A 584 " ideal model delta sigma weight residual 116.30 130.22 -13.92 3.50e+00 8.16e-02 1.58e+01 angle pdb=" CB GLU B 208 " pdb=" CG GLU B 208 " pdb=" CD GLU B 208 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.70e+00 3.46e-01 1.46e+01 angle pdb=" CA LEU B 567 " pdb=" CB LEU B 567 " pdb=" CG LEU B 567 " ideal model delta sigma weight residual 116.30 129.39 -13.09 3.50e+00 8.16e-02 1.40e+01 angle pdb=" CA LEU A 567 " pdb=" CB LEU A 567 " pdb=" CG LEU A 567 " ideal model delta sigma weight residual 116.30 129.34 -13.04 3.50e+00 8.16e-02 1.39e+01 angle pdb=" CB GLU A 542 " pdb=" CG GLU A 542 " pdb=" CD GLU A 542 " ideal model delta sigma weight residual 112.60 118.79 -6.19 1.70e+00 3.46e-01 1.33e+01 ... (remaining 11843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4413 17.61 - 35.22: 575 35.22 - 52.83: 157 52.83 - 70.44: 22 70.44 - 88.05: 5 Dihedral angle restraints: 5172 sinusoidal: 1926 harmonic: 3246 Sorted by residual: dihedral pdb=" CG ARG A 658 " pdb=" CD ARG A 658 " pdb=" NE ARG A 658 " pdb=" CZ ARG A 658 " ideal model delta sinusoidal sigma weight residual 180.00 135.30 44.70 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG B 666 " pdb=" CD ARG B 666 " pdb=" NE ARG B 666 " pdb=" CZ ARG B 666 " ideal model delta sinusoidal sigma weight residual 90.00 133.47 -43.47 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG A 666 " pdb=" CD ARG A 666 " pdb=" NE ARG A 666 " pdb=" CZ ARG A 666 " ideal model delta sinusoidal sigma weight residual 90.00 132.37 -42.37 2 1.50e+01 4.44e-03 9.69e+00 ... (remaining 5169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1059 0.050 - 0.101: 273 0.101 - 0.151: 66 0.151 - 0.201: 7 0.201 - 0.252: 1 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CB ILE A 647 " pdb=" CA ILE A 647 " pdb=" CG1 ILE A 647 " pdb=" CG2 ILE A 647 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU A 422 " pdb=" N LEU A 422 " pdb=" C LEU A 422 " pdb=" CB LEU A 422 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA LEU B 422 " pdb=" N LEU B 422 " pdb=" C LEU B 422 " pdb=" CB LEU B 422 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 1403 not shown) Planarity restraints: 1506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 542 " 0.012 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" CD GLU A 542 " -0.044 2.00e-02 2.50e+03 pdb=" OE1 GLU A 542 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU A 542 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 542 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" CD GLU B 542 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU B 542 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 542 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 268 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C VAL B 268 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL B 268 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE B 269 " 0.013 2.00e-02 2.50e+03 ... (remaining 1503 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2563 2.83 - 3.35: 7531 3.35 - 3.86: 13265 3.86 - 4.38: 13507 4.38 - 4.90: 25619 Nonbonded interactions: 62485 Sorted by model distance: nonbonded pdb=" O GLY A 506 " pdb=" OG SER A 509 " model vdw 2.310 3.040 nonbonded pdb=" O GLY B 506 " pdb=" OG SER B 509 " model vdw 2.325 3.040 nonbonded pdb=" O ALA B 186 " pdb=" OG1 THR B 190 " model vdw 2.327 3.040 nonbonded pdb=" O ALA A 186 " pdb=" OG1 THR A 190 " model vdw 2.327 3.040 nonbonded pdb=" OD2 ASP B 640 " pdb=" OG1 THR B 643 " model vdw 2.346 3.040 ... (remaining 62480 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.630 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.005 0.067 8734 Z= 0.279 Angle : 0.834 13.916 11848 Z= 0.445 Chirality : 0.048 0.252 1406 Planarity : 0.006 0.055 1506 Dihedral : 16.686 88.050 3092 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.56 % Allowed : 29.21 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.23), residues: 1122 helix: 0.90 (0.18), residues: 722 sheet: 1.62 (0.67), residues: 66 loop : -2.24 (0.29), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 687 TYR 0.030 0.002 TYR A 286 PHE 0.018 0.002 PHE B 240 TRP 0.008 0.001 TRP A 314 HIS 0.009 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.28 ( 8734) covalent geometry : angle 0.83394 / 0.45 (11848) hydrogen bonds : bond 0.14848 / 10.02 ( 579) hydrogen bonds : angle 4.86643 / 3.59 ( 1695) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.328 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 91 average time/residue: 0.0758 time to fit residues: 9.6718 Evaluate side-chains 89 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 20.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.185321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114498 restraints weight = 10500.560| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.72 r_work: 0.3245 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8734 Z= 0.181 Angle : 0.532 7.724 11848 Z= 0.287 Chirality : 0.040 0.134 1406 Planarity : 0.004 0.034 1506 Dihedral : 4.080 58.991 1233 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.26 % Allowed : 26.29 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.26), residues: 1122 helix: 2.39 (0.19), residues: 724 sheet: 1.32 (0.66), residues: 66 loop : -2.04 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 255 TYR 0.016 0.001 TYR A 304 PHE 0.011 0.001 PHE A 385 TRP 0.008 0.001 TRP B 705 HIS 0.002 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 ( 8734) covalent geometry : angle 0.53183 / 0.29 (11848) hydrogen bonds : bond 0.09979 / 6.90 ( 579) hydrogen bonds : angle 4.18739 / 3.08 ( 1695) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.271 Fit side-chains REVERT: A 385 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7150 (t80) REVERT: B 255 ARG cc_start: 0.7213 (mmm-85) cc_final: 0.6283 (mmp-170) outliers start: 29 outliers final: 18 residues processed: 115 average time/residue: 0.0715 time to fit residues: 11.7085 Evaluate side-chains 114 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 690 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 58 optimal weight: 0.0010 chunk 69 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.0050 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.193264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124738 restraints weight = 10462.558| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.68 r_work: 0.3375 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8734 Z= 0.136 Angle : 0.453 6.977 11848 Z= 0.244 Chirality : 0.037 0.128 1406 Planarity : 0.003 0.027 1506 Dihedral : 3.598 55.262 1228 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.92 % Allowed : 26.74 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.26), residues: 1122 helix: 2.88 (0.19), residues: 728 sheet: 1.76 (0.66), residues: 64 loop : -2.00 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 255 TYR 0.009 0.001 TYR B 196 PHE 0.009 0.001 PHE A 385 TRP 0.006 0.001 TRP B 705 HIS 0.004 0.000 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.14 ( 8734) covalent geometry : angle 0.45317 / 0.24 (11848) hydrogen bonds : bond 0.07597 / 5.27 ( 579) hydrogen bonds : angle 3.76443 / 2.76 ( 1695) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.306 Fit side-chains REVERT: A 385 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7557 (t80) REVERT: A 560 ASN cc_start: 0.8504 (t0) cc_final: 0.8256 (t0) REVERT: B 642 ILE cc_start: 0.5648 (OUTLIER) cc_final: 0.5430 (mp) outliers start: 26 outliers final: 17 residues processed: 113 average time/residue: 0.0684 time to fit residues: 11.4026 Evaluate side-chains 110 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 690 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS B 690 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.186041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115325 restraints weight = 10560.522| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.72 r_work: 0.3254 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8734 Z= 0.179 Angle : 0.508 7.277 11848 Z= 0.271 Chirality : 0.039 0.133 1406 Planarity : 0.003 0.030 1506 Dihedral : 3.264 16.043 1226 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.16 % Allowed : 25.28 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.26), residues: 1122 helix: 2.95 (0.19), residues: 726 sheet: 1.57 (0.66), residues: 64 loop : -1.94 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.015 0.001 TYR A 304 PHE 0.019 0.002 PHE B 240 TRP 0.008 0.001 TRP B 705 HIS 0.002 0.000 HIS B 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 ( 8734) covalent geometry : angle 0.50754 / 0.27 (11848) hydrogen bonds : bond 0.09384 / 6.48 ( 579) hydrogen bonds : angle 3.89040 / 2.87 ( 1695) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.258 Fit side-chains REVERT: A 255 ARG cc_start: 0.7218 (mmm-85) cc_final: 0.6376 (mmp-170) REVERT: A 385 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7281 (t80) REVERT: B 255 ARG cc_start: 0.7194 (mmm-85) cc_final: 0.6349 (mmp-170) REVERT: B 385 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7668 (t80) REVERT: B 642 ILE cc_start: 0.5688 (OUTLIER) cc_final: 0.5471 (mp) outliers start: 37 outliers final: 30 residues processed: 119 average time/residue: 0.0665 time to fit residues: 11.4549 Evaluate side-chains 122 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 690 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 0.0970 chunk 77 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS B 665 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.184482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113348 restraints weight = 10523.836| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.72 r_work: 0.3229 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8734 Z= 0.191 Angle : 0.522 8.147 11848 Z= 0.278 Chirality : 0.040 0.137 1406 Planarity : 0.003 0.030 1506 Dihedral : 3.319 17.582 1226 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.39 % Allowed : 24.61 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.26), residues: 1122 helix: 2.91 (0.19), residues: 726 sheet: 1.32 (0.65), residues: 64 loop : -2.00 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.014 0.001 TYR A 304 PHE 0.013 0.002 PHE A 385 TRP 0.008 0.001 TRP B 705 HIS 0.007 0.001 HIS B 690 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 8734) covalent geometry : angle 0.52196 / 0.28 (11848) hydrogen bonds : bond 0.09812 / 6.79 ( 579) hydrogen bonds : angle 3.95387 / 2.91 ( 1695) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 92 time to evaluate : 0.202 Fit side-chains REVERT: A 255 ARG cc_start: 0.7227 (mmm-85) cc_final: 0.6363 (mmp-170) REVERT: A 385 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7281 (t80) REVERT: B 255 ARG cc_start: 0.7235 (mmm-85) cc_final: 0.6376 (mmp-170) REVERT: B 385 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7621 (t80) REVERT: B 487 VAL cc_start: 0.4472 (OUTLIER) cc_final: 0.4256 (m) REVERT: B 642 ILE cc_start: 0.5669 (OUTLIER) cc_final: 0.5457 (mp) outliers start: 48 outliers final: 37 residues processed: 129 average time/residue: 0.0697 time to fit residues: 12.9076 Evaluate side-chains 131 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 90 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.190344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.120819 restraints weight = 10485.937| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.71 r_work: 0.3323 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8734 Z= 0.142 Angle : 0.460 7.566 11848 Z= 0.246 Chirality : 0.038 0.130 1406 Planarity : 0.003 0.029 1506 Dihedral : 3.195 15.630 1226 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.93 % Allowed : 26.40 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.26), residues: 1122 helix: 3.14 (0.19), residues: 726 sheet: 1.48 (0.65), residues: 64 loop : -1.88 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 255 TYR 0.010 0.001 TYR A 196 PHE 0.024 0.001 PHE B 240 TRP 0.005 0.001 TRP B 705 HIS 0.003 0.000 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 ( 8734) covalent geometry : angle 0.46010 / 0.25 (11848) hydrogen bonds : bond 0.08050 / 5.58 ( 579) hydrogen bonds : angle 3.70629 / 2.72 ( 1695) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.228 Fit side-chains REVERT: A 240 PHE cc_start: 0.6163 (t80) cc_final: 0.5915 (t80) REVERT: A 255 ARG cc_start: 0.7102 (mmm-85) cc_final: 0.6311 (mmp-170) REVERT: A 385 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7451 (t80) REVERT: A 560 ASN cc_start: 0.8477 (t0) cc_final: 0.8221 (t0) REVERT: B 385 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7683 (t80) REVERT: B 642 ILE cc_start: 0.5688 (OUTLIER) cc_final: 0.5470 (mp) outliers start: 35 outliers final: 24 residues processed: 117 average time/residue: 0.0653 time to fit residues: 11.3564 Evaluate side-chains 116 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS B 235 ASN B 665 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.188167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117893 restraints weight = 10577.675| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.72 r_work: 0.3292 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8734 Z= 0.154 Angle : 0.483 6.958 11848 Z= 0.256 Chirality : 0.038 0.132 1406 Planarity : 0.003 0.030 1506 Dihedral : 3.187 16.286 1226 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.04 % Allowed : 25.96 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.26), residues: 1122 helix: 3.16 (0.19), residues: 726 sheet: 1.72 (0.56), residues: 84 loop : -1.93 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.011 0.001 TYR A 304 PHE 0.018 0.001 PHE A 240 TRP 0.006 0.001 TRP B 705 HIS 0.002 0.000 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 ( 8734) covalent geometry : angle 0.48283 / 0.26 (11848) hydrogen bonds : bond 0.08625 / 5.97 ( 579) hydrogen bonds : angle 3.75150 / 2.76 ( 1695) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.303 Fit side-chains REVERT: A 240 PHE cc_start: 0.6282 (t80) cc_final: 0.6050 (t80) REVERT: A 255 ARG cc_start: 0.7207 (mmm-85) cc_final: 0.6374 (mmp-170) REVERT: A 385 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7348 (t80) REVERT: B 385 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7656 (t80) outliers start: 36 outliers final: 31 residues processed: 114 average time/residue: 0.0691 time to fit residues: 11.8475 Evaluate side-chains 119 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 105 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 96 optimal weight: 0.0980 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 45 optimal weight: 0.0270 chunk 50 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS B 665 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.189100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119197 restraints weight = 10426.612| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.69 r_work: 0.3305 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8734 Z= 0.147 Angle : 0.484 9.202 11848 Z= 0.253 Chirality : 0.038 0.131 1406 Planarity : 0.003 0.029 1506 Dihedral : 3.168 15.340 1226 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.93 % Allowed : 26.40 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.26), residues: 1122 helix: 3.18 (0.19), residues: 726 sheet: 1.76 (0.56), residues: 84 loop : -1.89 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 255 TYR 0.010 0.001 TYR A 196 PHE 0.025 0.001 PHE B 240 TRP 0.005 0.001 TRP B 705 HIS 0.002 0.000 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 ( 8734) covalent geometry : angle 0.48408 / 0.25 (11848) hydrogen bonds : bond 0.08353 / 5.79 ( 579) hydrogen bonds : angle 3.70995 / 2.73 ( 1695) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 0.315 Fit side-chains REVERT: A 240 PHE cc_start: 0.6288 (t80) cc_final: 0.6046 (t80) REVERT: A 255 ARG cc_start: 0.7162 (mmm-85) cc_final: 0.6338 (mmp-170) REVERT: A 385 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7404 (t80) REVERT: B 385 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7648 (t80) outliers start: 35 outliers final: 30 residues processed: 116 average time/residue: 0.0594 time to fit residues: 10.2594 Evaluate side-chains 119 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 92 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 59 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS B 270 ASN B 665 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.193710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125385 restraints weight = 10231.100| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.66 r_work: 0.3384 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8734 Z= 0.132 Angle : 0.469 8.370 11848 Z= 0.243 Chirality : 0.037 0.129 1406 Planarity : 0.003 0.026 1506 Dihedral : 3.108 14.498 1226 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.60 % Allowed : 27.08 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.26), residues: 1122 helix: 3.26 (0.19), residues: 730 sheet: 1.85 (0.61), residues: 74 loop : -1.77 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 546 TYR 0.010 0.001 TYR A 196 PHE 0.019 0.001 PHE A 240 TRP 0.004 0.001 TRP B 705 HIS 0.002 0.000 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.13 ( 8734) covalent geometry : angle 0.46939 / 0.24 (11848) hydrogen bonds : bond 0.07229 / 5.01 ( 579) hydrogen bonds : angle 3.56946 / 2.62 ( 1695) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 240 PHE cc_start: 0.6284 (t80) cc_final: 0.6063 (t80) REVERT: A 385 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7539 (t80) REVERT: B 385 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7565 (t80) outliers start: 32 outliers final: 28 residues processed: 108 average time/residue: 0.0597 time to fit residues: 9.7157 Evaluate side-chains 110 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.192469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123825 restraints weight = 10246.650| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.65 r_work: 0.3360 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8734 Z= 0.135 Angle : 0.472 8.449 11848 Z= 0.243 Chirality : 0.037 0.129 1406 Planarity : 0.003 0.023 1506 Dihedral : 3.074 14.454 1226 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.71 % Allowed : 27.19 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.26), residues: 1122 helix: 3.27 (0.19), residues: 730 sheet: 1.85 (0.61), residues: 74 loop : -1.75 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 255 TYR 0.011 0.001 TYR A 196 PHE 0.017 0.001 PHE A 240 TRP 0.005 0.001 TRP B 705 HIS 0.001 0.000 HIS B 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 ( 8734) covalent geometry : angle 0.47216 / 0.24 (11848) hydrogen bonds : bond 0.07549 / 5.24 ( 579) hydrogen bonds : angle 3.57002 / 2.63 ( 1695) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 0.231 Fit side-chains REVERT: A 240 PHE cc_start: 0.6312 (t80) cc_final: 0.6103 (t80) REVERT: A 385 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7472 (t80) REVERT: B 385 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7587 (t80) outliers start: 33 outliers final: 29 residues processed: 111 average time/residue: 0.0559 time to fit residues: 9.3433 Evaluate side-chains 114 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS B 665 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.189781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120137 restraints weight = 10212.384| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.65 r_work: 0.3318 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8734 Z= 0.148 Angle : 0.492 8.076 11848 Z= 0.255 Chirality : 0.038 0.131 1406 Planarity : 0.003 0.025 1506 Dihedral : 3.106 14.774 1226 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.93 % Allowed : 26.85 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.26), residues: 1122 helix: 3.22 (0.19), residues: 730 sheet: 1.80 (0.61), residues: 74 loop : -1.75 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.010 0.001 TYR A 304 PHE 0.017 0.001 PHE A 240 TRP 0.005 0.001 TRP A 705 HIS 0.002 0.000 HIS B 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 ( 8734) covalent geometry : angle 0.49173 / 0.26 (11848) hydrogen bonds : bond 0.08242 / 5.71 ( 579) hydrogen bonds : angle 3.66130 / 2.69 ( 1695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2607.00 seconds wall clock time: 44 minutes 58.36 seconds (2698.36 seconds total)