Starting phenix.real_space_refine on Thu Sep 26 00:16:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d14_30543/09_2024/7d14_30543_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d14_30543/09_2024/7d14_30543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d14_30543/09_2024/7d14_30543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d14_30543/09_2024/7d14_30543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d14_30543/09_2024/7d14_30543_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d14_30543/09_2024/7d14_30543_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 84 5.16 5 C 7462 2.51 5 N 2010 2.21 5 O 2080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11636 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 5818 Classifications: {'peptide': 850} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 30, 'TRANS': 819} Chain breaks: 11 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 822 Unresolved non-hydrogen angles: 1044 Unresolved non-hydrogen dihedrals: 687 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 9, 'TYR:plan': 10, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 9, 'GLU:plan': 24, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 493 Restraints were copied for chains: B Time building chain proxies: 12.25, per 1000 atoms: 1.05 Number of scatterers: 11636 At special positions: 0 Unit cell: (118.919, 103.645, 147.285, 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 84 16.00 O 2080 8.00 N 2010 7.00 C 7462 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: 2.83 Conformation dependent library (CDL) restraints added in 1.7 seconds 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3100 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 50.5% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 98 through 107 removed outlier: 4.060A pdb=" N ALA A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.805A pdb=" N LEU A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix removed outlier: 3.796A pdb=" N ASN A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 151 through 177 removed outlier: 4.233A pdb=" N CYS A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 166 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A 169 " --> pdb=" O CYS A 165 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 221 removed outlier: 3.954A pdb=" N MET A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) Proline residue: A 197 - end of helix removed outlier: 3.609A pdb=" N GLY A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 247 through 270 removed outlier: 3.569A pdb=" N ASN A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 268 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 4.068A pdb=" N VAL A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 removed outlier: 3.609A pdb=" N VAL A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER A 289 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.906A pdb=" N GLY A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.607A pdb=" N SER A 441 " --> pdb=" O MET A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 458 through 476 removed outlier: 4.197A pdb=" N THR A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 473 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 539 removed outlier: 4.747A pdb=" N PHE A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 526 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) Proline residue: A 530 - end of helix removed outlier: 3.904A pdb=" N ASP A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 removed outlier: 3.938A pdb=" N GLY A 549 " --> pdb=" O GLN A 546 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 550 " --> pdb=" O VAL A 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 546 through 550' Processing helix chain 'A' and resid 558 through 573 removed outlier: 4.199A pdb=" N GLY A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 605 removed outlier: 3.691A pdb=" N ALA A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Proline residue: A 582 - end of helix removed outlier: 4.202A pdb=" N MET A 586 " --> pdb=" O PRO A 582 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 595 " --> pdb=" O CYS A 591 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N THR A 603 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 637 removed outlier: 3.730A pdb=" N CYS A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 637 " --> pdb=" O MET A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 661 removed outlier: 4.167A pdb=" N VAL A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 682 removed outlier: 4.048A pdb=" N SER A 672 " --> pdb=" O ILE A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 723 removed outlier: 4.175A pdb=" N LEU A 715 " --> pdb=" O HIS A 711 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 722 " --> pdb=" O THR A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 759 Proline residue: A 743 - end of helix removed outlier: 3.662A pdb=" N GLU A 757 " --> pdb=" O ARG A 753 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 758 " --> pdb=" O ARG A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 824 Processing helix chain 'A' and resid 859 through 869 removed outlier: 3.593A pdb=" N LEU A 864 " --> pdb=" O MET A 860 " (cutoff:3.500A) Proline residue: A 865 - end of helix Processing helix chain 'A' and resid 893 through 905 Processing helix chain 'A' and resid 927 through 937 removed outlier: 3.700A pdb=" N GLU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1113 removed outlier: 3.532A pdb=" N PHE A1112 " --> pdb=" O ASN A1108 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A1113 " --> pdb=" O TYR A1109 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1108 through 1113' Processing helix chain 'B' and resid 98 through 107 removed outlier: 4.060A pdb=" N ALA B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 133 removed outlier: 3.806A pdb=" N LEU B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) Proline residue: B 129 - end of helix removed outlier: 3.795A pdb=" N ASN B 133 " --> pdb=" O PRO B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 149 Processing helix chain 'B' and resid 151 through 177 removed outlier: 4.233A pdb=" N CYS B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 166 " --> pdb=" O CYS B 162 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR B 169 " --> pdb=" O CYS B 165 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 221 removed outlier: 3.954A pdb=" N MET B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) Proline residue: B 197 - end of helix removed outlier: 3.608A pdb=" N GLY B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS B 206 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 247 through 270 removed outlier: 3.569A pdb=" N ASN B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 268 " --> pdb=" O MET B 264 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 removed outlier: 4.068A pdb=" N VAL B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 removed outlier: 3.609A pdb=" N VAL B 286 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER B 289 " --> pdb=" O CYS B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 431 removed outlier: 3.906A pdb=" N GLY B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.607A pdb=" N SER B 441 " --> pdb=" O MET B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 458 through 476 removed outlier: 4.197A pdb=" N THR B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 468 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 473 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 539 removed outlier: 4.747A pdb=" N PHE B 515 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 516 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 526 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA B 529 " --> pdb=" O SER B 525 " (cutoff:3.500A) Proline residue: B 530 - end of helix removed outlier: 3.904A pdb=" N ASP B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 removed outlier: 3.938A pdb=" N GLY B 549 " --> pdb=" O GLN B 546 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS B 550 " --> pdb=" O VAL B 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 546 through 550' Processing helix chain 'B' and resid 558 through 573 removed outlier: 4.198A pdb=" N GLY B 571 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 605 removed outlier: 3.690A pdb=" N ALA B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Proline residue: B 582 - end of helix removed outlier: 4.201A pdb=" N MET B 586 " --> pdb=" O PRO B 582 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 595 " --> pdb=" O CYS B 591 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 596 " --> pdb=" O TYR B 592 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N THR B 603 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 604 " --> pdb=" O ALA B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 637 removed outlier: 3.730A pdb=" N CYS B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 637 " --> pdb=" O MET B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 661 removed outlier: 4.167A pdb=" N VAL B 643 " --> pdb=" O TYR B 639 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS B 653 " --> pdb=" O GLY B 649 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 682 removed outlier: 4.047A pdb=" N SER B 672 " --> pdb=" O ILE B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 723 removed outlier: 4.175A pdb=" N LEU B 715 " --> pdb=" O HIS B 711 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B 720 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 722 " --> pdb=" O THR B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 759 Proline residue: B 743 - end of helix removed outlier: 3.662A pdb=" N GLU B 757 " --> pdb=" O ARG B 753 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 758 " --> pdb=" O ARG B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 824 Processing helix chain 'B' and resid 859 through 869 removed outlier: 3.593A pdb=" N LEU B 864 " --> pdb=" O MET B 860 " (cutoff:3.500A) Proline residue: B 865 - end of helix Processing helix chain 'B' and resid 893 through 905 Processing helix chain 'B' and resid 927 through 937 removed outlier: 3.700A pdb=" N GLU B 933 " --> pdb=" O THR B 929 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1113 removed outlier: 3.533A pdb=" N PHE B1112 " --> pdb=" O ASN B1108 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B1113 " --> pdb=" O TYR B1109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1108 through 1113' Processing sheet with id=AA1, first strand: chain 'A' and resid 764 through 768 removed outlier: 3.606A pdb=" N VAL A 768 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 697 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLY A 731 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 699 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL A 733 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 698 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY A 797 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU A 700 " --> pdb=" O GLY A 797 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 794 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR A 831 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 796 " --> pdb=" O THR A 831 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A1092 " --> pdb=" O MET A1124 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A1126 " --> pdb=" O VAL A1092 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A1094 " --> pdb=" O VAL A1126 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN A1095 " --> pdb=" O TRP A 852 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 764 through 768 removed outlier: 3.605A pdb=" N VAL B 768 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 697 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLY B 731 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL B 699 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL B 733 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU B 698 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLY B 797 " --> pdb=" O LEU B 698 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU B 700 " --> pdb=" O GLY B 797 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 794 " --> pdb=" O LEU B 829 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR B 831 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 796 " --> pdb=" O THR B 831 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B1092 " --> pdb=" O MET B1124 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL B1126 " --> pdb=" O VAL B1092 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU B1094 " --> pdb=" O VAL B1126 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN B1095 " --> pdb=" O TRP B 852 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 3.32 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: 3723 1.34 - 1.46: 1805 1.46 - 1.57: 6164 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 11824 Sorted by residual: bond pdb=" C ILE B 454 " pdb=" N PRO B 455 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.43e+00 bond pdb=" C ILE A 454 " pdb=" N PRO A 455 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.37e+00 bond pdb=" CA VAL B 913 " pdb=" CB VAL B 913 " ideal model delta sigma weight residual 1.541 1.519 0.023 1.28e-02 6.10e+03 3.15e+00 bond pdb=" CA VAL A 913 " pdb=" CB VAL A 913 " ideal model delta sigma weight residual 1.541 1.519 0.022 1.28e-02 6.10e+03 3.02e+00 bond pdb=" CA VAL B 914 " pdb=" CB VAL B 914 " ideal model delta sigma weight residual 1.537 1.519 0.018 1.17e-02 7.31e+03 2.43e+00 ... (remaining 11819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 15245 2.07 - 4.15: 731 4.15 - 6.22: 110 6.22 - 8.29: 42 8.29 - 10.37: 6 Bond angle restraints: 16134 Sorted by residual: angle pdb=" N PRO A 407 " pdb=" CA PRO A 407 " pdb=" CB PRO A 407 " ideal model delta sigma weight residual 103.15 110.73 -7.58 9.70e-01 1.06e+00 6.11e+01 angle pdb=" N PRO B 407 " pdb=" CA PRO B 407 " pdb=" CB PRO B 407 " ideal model delta sigma weight residual 103.15 110.70 -7.55 9.70e-01 1.06e+00 6.05e+01 angle pdb=" N PRO A 370 " pdb=" CA PRO A 370 " pdb=" CB PRO A 370 " ideal model delta sigma weight residual 103.25 111.19 -7.94 1.05e+00 9.07e-01 5.72e+01 angle pdb=" N PRO B 370 " pdb=" CA PRO B 370 " pdb=" CB PRO B 370 " ideal model delta sigma weight residual 103.25 111.17 -7.92 1.05e+00 9.07e-01 5.69e+01 angle pdb=" N PRO A 308 " pdb=" CA PRO A 308 " pdb=" CB PRO A 308 " ideal model delta sigma weight residual 103.25 111.13 -7.88 1.05e+00 9.07e-01 5.63e+01 ... (remaining 16129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 6494 15.46 - 30.93: 293 30.93 - 46.39: 65 46.39 - 61.85: 6 61.85 - 77.31: 8 Dihedral angle restraints: 6866 sinusoidal: 2052 harmonic: 4814 Sorted by residual: dihedral pdb=" CA VAL B 182 " pdb=" C VAL B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ILE A 138 " pdb=" C ILE A 138 " pdb=" N LEU A 139 " pdb=" CA LEU A 139 " ideal model delta harmonic sigma weight residual 180.00 153.78 26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ILE B 138 " pdb=" C ILE B 138 " pdb=" N LEU B 139 " pdb=" CA LEU B 139 " ideal model delta harmonic sigma weight residual 180.00 153.78 26.22 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 6863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1617 0.075 - 0.150: 325 0.150 - 0.224: 40 0.224 - 0.299: 4 0.299 - 0.374: 2 Chirality restraints: 1988 Sorted by residual: chirality pdb=" CB ILE A1134 " pdb=" CA ILE A1134 " pdb=" CG1 ILE A1134 " pdb=" CG2 ILE A1134 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CB ILE B1134 " pdb=" CA ILE B1134 " pdb=" CG1 ILE B1134 " pdb=" CG2 ILE B1134 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA PRO B 398 " pdb=" N PRO B 398 " pdb=" C PRO B 398 " pdb=" CB PRO B 398 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 1985 not shown) Planarity restraints: 2044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 853 " 0.020 2.00e-02 2.50e+03 1.94e-02 9.40e+00 pdb=" CG TRP B 853 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 853 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 853 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 853 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 853 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 853 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 853 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 853 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 853 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 853 " -0.020 2.00e-02 2.50e+03 1.94e-02 9.38e+00 pdb=" CG TRP A 853 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 853 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 853 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 853 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 853 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 853 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 853 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 853 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 853 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 431 " -0.046 5.00e-02 4.00e+02 6.86e-02 7.54e+00 pdb=" N PRO B 432 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " -0.039 5.00e-02 4.00e+02 ... (remaining 2041 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3392 2.81 - 3.33: 10475 3.33 - 3.86: 17674 3.86 - 4.38: 19224 4.38 - 4.90: 33681 Nonbonded interactions: 84446 Sorted by model distance: nonbonded pdb=" OE2 GLU A 102 " pdb=" NH2 ARG A 538 " model vdw 2.291 3.120 nonbonded pdb=" OE2 GLU B 102 " pdb=" NH2 ARG B 538 " model vdw 2.291 3.120 nonbonded pdb=" O THR B 211 " pdb=" OG SER B 525 " model vdw 2.304 3.040 nonbonded pdb=" O THR A 211 " pdb=" OG SER A 525 " model vdw 2.304 3.040 nonbonded pdb=" ND2 ASN A 833 " pdb=" O ASP A1121 " model vdw 2.360 3.120 ... (remaining 84441 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.670 Find NCS groups from input model: 0.300 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.006 0.059 11824 Z= 0.394 Angle : 1.045 10.366 16134 Z= 0.607 Chirality : 0.061 0.374 1988 Planarity : 0.007 0.069 2044 Dihedral : 10.350 77.313 3766 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.38 % Favored : 88.01 % Rotamer: Outliers : 0.40 % Allowed : 5.42 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.55 (0.15), residues: 1652 helix: -3.32 (0.12), residues: 836 sheet: -2.22 (0.43), residues: 142 loop : -4.44 (0.18), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 853 HIS 0.006 0.002 HIS A 870 PHE 0.027 0.003 PHE B 476 TYR 0.020 0.003 TYR B 678 ARG 0.004 0.001 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 233 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.8370 (tpt) cc_final: 0.8168 (tpp) REVERT: A 430 TYR cc_start: 0.8921 (t80) cc_final: 0.8709 (t80) REVERT: A 511 VAL cc_start: 0.9263 (m) cc_final: 0.8964 (t) REVERT: A 579 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6598 (mt-10) REVERT: A 850 ASP cc_start: 0.8092 (m-30) cc_final: 0.7837 (m-30) REVERT: B 511 VAL cc_start: 0.9290 (m) cc_final: 0.9031 (t) REVERT: B 645 MET cc_start: 0.8349 (ttp) cc_final: 0.8145 (ttm) outliers start: 4 outliers final: 2 residues processed: 235 average time/residue: 0.2090 time to fit residues: 72.4605 Evaluate side-chains 136 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 697 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS A 840 ASN B 618 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11824 Z= 0.183 Angle : 0.615 8.270 16134 Z= 0.325 Chirality : 0.044 0.216 1988 Planarity : 0.004 0.058 2044 Dihedral : 5.678 25.391 1772 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.69 % Favored : 90.07 % Rotamer: Outliers : 3.41 % Allowed : 10.94 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.18), residues: 1652 helix: -1.90 (0.16), residues: 834 sheet: -2.29 (0.42), residues: 166 loop : -3.97 (0.21), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 853 HIS 0.003 0.001 HIS A 742 PHE 0.012 0.001 PHE B 544 TYR 0.014 0.001 TYR B 422 ARG 0.005 0.000 ARG A 754 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.487 Fit side-chains REVERT: A 511 VAL cc_start: 0.9334 (m) cc_final: 0.9084 (t) REVERT: A 678 TYR cc_start: 0.7766 (m-80) cc_final: 0.7500 (t80) REVERT: B 190 MET cc_start: 0.7611 (ttm) cc_final: 0.7368 (mtp) REVERT: B 511 VAL cc_start: 0.9229 (m) cc_final: 0.9014 (t) REVERT: B 512 ILE cc_start: 0.9234 (pp) cc_final: 0.8706 (mm) REVERT: B 579 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6888 (mt-10) REVERT: B 678 TYR cc_start: 0.7662 (m-80) cc_final: 0.7267 (t80) REVERT: B 820 GLU cc_start: 0.8590 (tp30) cc_final: 0.8383 (tt0) REVERT: B 863 LEU cc_start: 0.8902 (tp) cc_final: 0.8698 (tp) outliers start: 34 outliers final: 17 residues processed: 197 average time/residue: 0.2124 time to fit residues: 61.7550 Evaluate side-chains 158 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1095 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11824 Z= 0.191 Angle : 0.570 6.903 16134 Z= 0.301 Chirality : 0.043 0.218 1988 Planarity : 0.004 0.051 2044 Dihedral : 5.147 24.475 1772 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.08 % Favored : 90.68 % Rotamer: Outliers : 2.51 % Allowed : 14.16 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.20), residues: 1652 helix: -1.26 (0.17), residues: 852 sheet: -2.13 (0.41), residues: 166 loop : -3.89 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 853 HIS 0.004 0.001 HIS A 742 PHE 0.013 0.001 PHE B 623 TYR 0.010 0.001 TYR A 422 ARG 0.008 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 1.230 Fit side-chains REVERT: A 446 ASP cc_start: 0.8188 (m-30) cc_final: 0.7938 (m-30) REVERT: A 511 VAL cc_start: 0.9351 (m) cc_final: 0.9140 (t) REVERT: A 678 TYR cc_start: 0.7793 (m-80) cc_final: 0.7507 (t80) REVERT: B 217 MET cc_start: 0.9183 (ttp) cc_final: 0.8815 (ttt) REVERT: B 511 VAL cc_start: 0.9211 (m) cc_final: 0.9007 (t) REVERT: B 512 ILE cc_start: 0.9253 (pp) cc_final: 0.8710 (mm) REVERT: B 579 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6901 (mt-10) REVERT: B 678 TYR cc_start: 0.7695 (m-80) cc_final: 0.7359 (t80) outliers start: 25 outliers final: 16 residues processed: 182 average time/residue: 0.1994 time to fit residues: 55.4037 Evaluate side-chains 154 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11824 Z= 0.300 Angle : 0.621 5.696 16134 Z= 0.325 Chirality : 0.045 0.215 1988 Planarity : 0.004 0.044 2044 Dihedral : 5.182 26.746 1770 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.93 % Favored : 89.83 % Rotamer: Outliers : 3.82 % Allowed : 13.86 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.20), residues: 1652 helix: -1.05 (0.18), residues: 846 sheet: -2.16 (0.40), residues: 166 loop : -3.78 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 853 HIS 0.004 0.001 HIS A 742 PHE 0.011 0.001 PHE B 431 TYR 0.012 0.001 TYR B 422 ARG 0.007 0.001 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 1.294 Fit side-chains REVERT: A 446 ASP cc_start: 0.8298 (m-30) cc_final: 0.8076 (m-30) REVERT: A 511 VAL cc_start: 0.9370 (m) cc_final: 0.9147 (t) REVERT: A 633 MET cc_start: 0.8858 (ttm) cc_final: 0.8658 (ttm) REVERT: B 217 MET cc_start: 0.9191 (ttp) cc_final: 0.8949 (ttt) REVERT: B 511 VAL cc_start: 0.9231 (m) cc_final: 0.9007 (t) REVERT: B 512 ILE cc_start: 0.9270 (pp) cc_final: 0.8663 (mm) REVERT: B 567 ILE cc_start: 0.9271 (mt) cc_final: 0.9068 (mm) REVERT: B 579 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6929 (mt-10) outliers start: 38 outliers final: 24 residues processed: 171 average time/residue: 0.1843 time to fit residues: 49.2421 Evaluate side-chains 159 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 0.2980 chunk 113 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 83 optimal weight: 0.0060 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11824 Z= 0.248 Angle : 0.588 6.467 16134 Z= 0.307 Chirality : 0.044 0.216 1988 Planarity : 0.004 0.043 2044 Dihedral : 4.914 23.262 1768 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.05 % Favored : 89.71 % Rotamer: Outliers : 3.31 % Allowed : 15.26 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.20), residues: 1652 helix: -0.87 (0.18), residues: 856 sheet: -2.05 (0.40), residues: 166 loop : -3.85 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 853 HIS 0.004 0.001 HIS B 742 PHE 0.011 0.001 PHE B 544 TYR 0.011 0.001 TYR B 422 ARG 0.007 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 1.286 Fit side-chains REVERT: A 511 VAL cc_start: 0.9356 (m) cc_final: 0.9147 (t) REVERT: B 579 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6899 (mt-10) outliers start: 33 outliers final: 27 residues processed: 171 average time/residue: 0.1693 time to fit residues: 46.7400 Evaluate side-chains 166 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 164 optimal weight: 0.0050 chunk 136 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.3952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN A 609 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 GLN B 720 GLN B 791 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11824 Z= 0.146 Angle : 0.537 6.107 16134 Z= 0.281 Chirality : 0.042 0.218 1988 Planarity : 0.003 0.040 2044 Dihedral : 4.516 21.426 1768 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.96 % Favored : 90.80 % Rotamer: Outliers : 3.21 % Allowed : 16.77 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.20), residues: 1652 helix: -0.61 (0.18), residues: 864 sheet: -1.87 (0.41), residues: 166 loop : -3.74 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 619 HIS 0.004 0.001 HIS B 742 PHE 0.013 0.001 PHE A 544 TYR 0.009 0.001 TYR A 422 ARG 0.004 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.333 Fit side-chains REVERT: B 264 MET cc_start: 0.8755 (ptm) cc_final: 0.8427 (ptp) REVERT: B 512 ILE cc_start: 0.9226 (pp) cc_final: 0.8616 (mm) REVERT: B 532 LEU cc_start: 0.8991 (tp) cc_final: 0.8740 (tt) REVERT: B 579 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6739 (mt-10) REVERT: B 775 ASP cc_start: 0.8667 (p0) cc_final: 0.8309 (p0) outliers start: 32 outliers final: 24 residues processed: 186 average time/residue: 0.1758 time to fit residues: 51.2043 Evaluate side-chains 171 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 138 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 163 optimal weight: 0.0670 chunk 102 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11824 Z= 0.337 Angle : 0.628 6.419 16134 Z= 0.326 Chirality : 0.046 0.223 1988 Planarity : 0.004 0.036 2044 Dihedral : 4.826 24.240 1768 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.47 % Favored : 89.29 % Rotamer: Outliers : 3.92 % Allowed : 17.77 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.20), residues: 1652 helix: -0.65 (0.18), residues: 858 sheet: -1.84 (0.41), residues: 166 loop : -3.71 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 853 HIS 0.005 0.001 HIS B 742 PHE 0.011 0.001 PHE B 431 TYR 0.011 0.001 TYR A 422 ARG 0.005 0.001 ARG A1127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 140 time to evaluate : 1.419 Fit side-chains REVERT: A 633 MET cc_start: 0.8895 (ttp) cc_final: 0.8585 (ttm) REVERT: B 264 MET cc_start: 0.8782 (ptm) cc_final: 0.8489 (ptp) REVERT: B 579 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6859 (mt-10) REVERT: B 590 MET cc_start: 0.8681 (tpp) cc_final: 0.8246 (mtt) REVERT: B 633 MET cc_start: 0.8581 (ttm) cc_final: 0.8127 (mtt) outliers start: 39 outliers final: 28 residues processed: 167 average time/residue: 0.1780 time to fit residues: 46.9242 Evaluate side-chains 165 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 0.0000 chunk 81 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11824 Z= 0.166 Angle : 0.558 6.439 16134 Z= 0.289 Chirality : 0.043 0.227 1988 Planarity : 0.003 0.038 2044 Dihedral : 4.496 23.362 1768 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.26 % Favored : 90.50 % Rotamer: Outliers : 3.11 % Allowed : 18.88 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.21), residues: 1652 helix: -0.40 (0.18), residues: 860 sheet: -1.77 (0.41), residues: 166 loop : -3.58 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 798 HIS 0.004 0.001 HIS B 742 PHE 0.027 0.001 PHE A 156 TYR 0.009 0.001 TYR A 422 ARG 0.003 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 1.299 Fit side-chains REVERT: B 264 MET cc_start: 0.8706 (ptm) cc_final: 0.8481 (ptp) REVERT: B 579 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6780 (mt-10) REVERT: B 633 MET cc_start: 0.8329 (ttm) cc_final: 0.7925 (mtt) outliers start: 31 outliers final: 25 residues processed: 174 average time/residue: 0.1725 time to fit residues: 47.7853 Evaluate side-chains 164 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 0.0670 chunk 144 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 161 optimal weight: 10.0000 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11824 Z= 0.173 Angle : 0.565 6.923 16134 Z= 0.293 Chirality : 0.043 0.220 1988 Planarity : 0.003 0.037 2044 Dihedral : 4.363 23.057 1768 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.14 % Favored : 90.62 % Rotamer: Outliers : 3.01 % Allowed : 18.98 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.21), residues: 1652 helix: -0.30 (0.18), residues: 862 sheet: -1.70 (0.42), residues: 166 loop : -3.58 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 559 HIS 0.004 0.001 HIS B 742 PHE 0.026 0.001 PHE A 156 TYR 0.008 0.001 TYR B 127 ARG 0.006 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.287 Fit side-chains REVERT: A 590 MET cc_start: 0.8535 (tpp) cc_final: 0.8248 (mtt) REVERT: B 198 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7456 (mt-10) REVERT: B 579 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6787 (mt-10) REVERT: B 633 MET cc_start: 0.8202 (ttm) cc_final: 0.7914 (mtt) outliers start: 30 outliers final: 26 residues processed: 172 average time/residue: 0.1748 time to fit residues: 47.7792 Evaluate side-chains 173 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 143 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11824 Z= 0.210 Angle : 0.580 6.808 16134 Z= 0.299 Chirality : 0.044 0.227 1988 Planarity : 0.003 0.034 2044 Dihedral : 4.423 23.303 1768 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.50 % Favored : 90.25 % Rotamer: Outliers : 3.01 % Allowed : 19.28 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.21), residues: 1652 helix: -0.23 (0.18), residues: 862 sheet: -1.74 (0.41), residues: 166 loop : -3.57 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 853 HIS 0.004 0.001 HIS B 742 PHE 0.026 0.001 PHE A 156 TYR 0.008 0.001 TYR A 422 ARG 0.006 0.000 ARG A 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.475 Fit side-chains REVERT: A 249 MET cc_start: 0.8441 (tpp) cc_final: 0.8168 (tpp) REVERT: B 579 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6799 (mt-10) REVERT: B 633 MET cc_start: 0.8324 (ttm) cc_final: 0.8090 (mtt) outliers start: 30 outliers final: 26 residues processed: 171 average time/residue: 0.1812 time to fit residues: 49.3457 Evaluate side-chains 172 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 4.9990 chunk 124 optimal weight: 0.0060 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097656 restraints weight = 24410.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098903 restraints weight = 15601.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099906 restraints weight = 12133.644| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11824 Z= 0.182 Angle : 0.567 6.689 16134 Z= 0.292 Chirality : 0.044 0.320 1988 Planarity : 0.003 0.048 2044 Dihedral : 4.305 23.002 1768 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.14 % Favored : 90.62 % Rotamer: Outliers : 2.71 % Allowed : 19.58 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.21), residues: 1652 helix: -0.19 (0.18), residues: 862 sheet: -1.72 (0.41), residues: 166 loop : -3.53 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 853 HIS 0.003 0.001 HIS B 742 PHE 0.025 0.001 PHE A 156 TYR 0.008 0.001 TYR A 422 ARG 0.009 0.000 ARG A 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.79 seconds wall clock time: 40 minutes 22.48 seconds (2422.48 seconds total)