Starting phenix.real_space_refine on Sat Sep 28 07:13:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr1_23953/09_2024/7mr1_23953.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr1_23953/09_2024/7mr1_23953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr1_23953/09_2024/7mr1_23953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr1_23953/09_2024/7mr1_23953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr1_23953/09_2024/7mr1_23953.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr1_23953/09_2024/7mr1_23953.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 87 5.16 5 C 11667 2.51 5 N 3264 2.21 5 O 3455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18473 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 6852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6852 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 34, 'TRANS': 823} Chain breaks: 1 Chain: "C" Number of atoms: 8915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8915 Classifications: {'peptide': 1101} Link IDs: {'PCIS': 1, 'PTRANS': 64, 'TRANS': 1035} Chain breaks: 1 Chain: "D" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2706 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 16, 'TRANS': 340} Time building chain proxies: 9.78, per 1000 atoms: 0.53 Number of scatterers: 18473 At special positions: 0 Unit cell: (141.25, 126.56, 166.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 3455 8.00 N 3264 7.00 C 11667 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: 4.15 Conformation dependent library (CDL) restraints added in 2.1 seconds 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4386 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 15 sheets defined 55.9% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'B' and resid 9 through 13 removed outlier: 3.778A pdb=" N LEU B 13 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 43 removed outlier: 3.544A pdb=" N ILE B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.845A pdb=" N ALA B 49 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.526A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 removed outlier: 3.554A pdb=" N GLU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.701A pdb=" N LEU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.687A pdb=" N GLU B 123 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 140 Processing helix chain 'B' and resid 157 through 173 removed outlier: 3.608A pdb=" N ASP B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 5.245A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.710A pdb=" N ARG B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.567A pdb=" N LEU B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 197 through 202' Processing helix chain 'B' and resid 217 through 240 removed outlier: 3.718A pdb=" N THR B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG B 237 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASP B 238 " --> pdb=" O GLN B 234 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 266 removed outlier: 3.979A pdb=" N LYS B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 281 removed outlier: 3.859A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.635A pdb=" N GLU B 287 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 317 removed outlier: 3.741A pdb=" N ILE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP B 314 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.026A pdb=" N ALA B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 364 removed outlier: 3.623A pdb=" N ALA B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 378 removed outlier: 3.503A pdb=" N ARG B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 402 removed outlier: 3.658A pdb=" N HIS B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 4.356A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER B 435 " --> pdb=" O MET B 431 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 460 Processing helix chain 'B' and resid 510 through 517 removed outlier: 3.625A pdb=" N TYR B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 535 removed outlier: 4.214A pdb=" N CYS B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 573 removed outlier: 4.358A pdb=" N ALA B 565 " --> pdb=" O ARG B 561 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN B 566 " --> pdb=" O GLN B 562 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA B 570 " --> pdb=" O GLN B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 removed outlier: 3.531A pdb=" N GLU B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 589' Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.975A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP B 598 " --> pdb=" O GLN B 594 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.679A pdb=" N ARG B 613 " --> pdb=" O GLU B 609 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER B 614 " --> pdb=" O ASN B 610 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 removed outlier: 3.801A pdb=" N LEU B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B 634 " --> pdb=" O THR B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 655 removed outlier: 3.943A pdb=" N VAL B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 642 " --> pdb=" O TRP B 638 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU B 643 " --> pdb=" O ASP B 639 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU B 644 " --> pdb=" O VAL B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.622A pdb=" N ALA B 663 " --> pdb=" O PRO B 659 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 removed outlier: 3.832A pdb=" N THR B 677 " --> pdb=" O ASN B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 701 removed outlier: 3.592A pdb=" N ARG B 683 " --> pdb=" O GLY B 679 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 685 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B 687 " --> pdb=" O ARG B 683 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 688 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 695 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 717 removed outlier: 4.089A pdb=" N ARG B 709 " --> pdb=" O HIS B 705 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 716 " --> pdb=" O SER B 712 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU B 717 " --> pdb=" O GLN B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 805 removed outlier: 3.548A pdb=" N LEU B 789 " --> pdb=" O GLU B 785 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 794 " --> pdb=" O ALA B 790 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 799 " --> pdb=" O LEU B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 835 Processing helix chain 'B' and resid 836 through 843 removed outlier: 3.834A pdb=" N ARG B 840 " --> pdb=" O SER B 836 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 4.441A pdb=" N THR B 855 " --> pdb=" O ALA B 851 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N CYS B 856 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.521A pdb=" N ARG C 75 " --> pdb=" O ASP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 103 Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.809A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 185 through 199 removed outlier: 3.578A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.675A pdb=" N LEU C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.811A pdb=" N LEU C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.546A pdb=" N LEU C 345 " --> pdb=" O ASP C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 381 through 400 Processing helix chain 'C' and resid 414 through 417 removed outlier: 3.561A pdb=" N SER C 417 " --> pdb=" O ASP C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 417' Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.779A pdb=" N LEU C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 463 Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.626A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 501 removed outlier: 3.806A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 501 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.840A pdb=" N LEU C 514 " --> pdb=" O ASN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.797A pdb=" N GLY C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 589 through 599 Processing helix chain 'C' and resid 605 through 626 Processing helix chain 'C' and resid 633 through 646 removed outlier: 4.216A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 removed outlier: 3.794A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 834 through 843 removed outlier: 4.128A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 874 through 889 removed outlier: 4.723A pdb=" N ILE C 880 " --> pdb=" O SER C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 910 through 933 removed outlier: 4.232A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 990 Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 4.021A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1049 Processing helix chain 'C' and resid 1060 through 1076 Processing helix chain 'C' and resid 1087 through 1094 Processing helix chain 'C' and resid 1098 through 1120 Proline residue: C1115 - end of helix Processing helix chain 'D' and resid 3 through 13 removed outlier: 4.211A pdb=" N ALA D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 32 through 49 removed outlier: 3.832A pdb=" N THR D 36 " --> pdb=" O HIS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 66 through 72 Processing helix chain 'D' and resid 80 through 87 Processing helix chain 'D' and resid 110 through 127 removed outlier: 3.836A pdb=" N VAL D 126 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN D 127 " --> pdb=" O PHE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 205 through 223 Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 240 through 245 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.664A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.816A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 320 removed outlier: 3.627A pdb=" N ALA D 319 " --> pdb=" O TYR D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 334 Processing helix chain 'D' and resid 345 through 351 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.911A pdb=" N GLU B 6 " --> pdb=" O HIS B 440 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.778A pdb=" N GLN B 151 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.638A pdb=" N VAL B 777 " --> pdb=" O TYR B 768 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR B 768 " --> pdb=" O VAL B 777 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 491 removed outlier: 3.709A pdb=" N ARG B 488 " --> pdb=" O MET B 541 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET B 541 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 490 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 502 Processing sheet with id=AA6, first strand: chain 'B' and resid 555 through 558 removed outlier: 3.843A pdb=" N VAL B 739 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 558 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 61 removed outlier: 3.607A pdb=" N ASP C 61 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU C 2 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU C 323 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL C 4 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG C 265 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 264 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.492A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 437 through 439 removed outlier: 6.693A pdb=" N ALA C 438 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N THR C 663 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS C 662 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS C 676 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL C 675 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 730 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR C 375 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 729 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 731 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS C 379 " --> pdb=" O TYR C 731 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS C 782 " --> pdb=" O PHE C 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 442 through 443 Processing sheet with id=AB2, first strand: chain 'C' and resid 831 through 833 removed outlier: 3.793A pdb=" N THR C 953 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN C 951 " --> pdb=" O CYS C 947 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N CYS C 947 " --> pdb=" O GLN C 951 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N THR C 953 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU C 945 " --> pdb=" O THR C 953 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TRP C 955 " --> pdb=" O ILE C 943 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE C 943 " --> pdb=" O TRP C 955 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET C 941 " --> pdb=" O PRO C 957 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 963 through 967 removed outlier: 6.125A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER C 996 " --> pdb=" O PHE C1008 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE C1008 " --> pdb=" O SER C 996 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1050 through 1051 removed outlier: 3.658A pdb=" N ALA C1056 " --> pdb=" O ASP C1051 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.625A pdb=" N LEU D 53 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D 107 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 166 through 170 removed outlier: 6.675A pdb=" N SER D 167 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLY D 296 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE D 169 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU D 266 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU D 295 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 268 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG D 200 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL D 267 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 202 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 802 hydrogen bonds defined for protein. 2358 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.82 Time building geometry restraints manager: 4.88 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: 6143 1.34 - 1.46: 3479 1.46 - 1.58: 9099 1.58 - 1.70: 1 1.70 - 1.82: 143 Bond restraints: 18865 Sorted by residual: bond pdb=" CA ASP B 155 " pdb=" CB ASP B 155 " ideal model delta sigma weight residual 1.526 1.605 -0.079 1.76e-02 3.23e+03 2.02e+01 bond pdb=" CA ARG C 433 " pdb=" CB ARG C 433 " ideal model delta sigma weight residual 1.528 1.552 -0.024 1.39e-02 5.18e+03 2.90e+00 bond pdb=" CB GLN B 281 " pdb=" CG GLN B 281 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.32e+00 bond pdb=" C LEU D 276 " pdb=" N PRO D 277 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.28e-02 6.10e+03 2.02e+00 bond pdb=" CG GLN B 281 " pdb=" CD GLN B 281 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.78e+00 ... (remaining 18860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 25133 2.46 - 4.92: 371 4.92 - 7.38: 78 7.38 - 9.84: 15 9.84 - 12.29: 3 Bond angle restraints: 25600 Sorted by residual: angle pdb=" CA ARG B 259 " pdb=" CB ARG B 259 " pdb=" CG ARG B 259 " ideal model delta sigma weight residual 114.10 124.53 -10.43 2.00e+00 2.50e-01 2.72e+01 angle pdb=" CB MET B 136 " pdb=" CG MET B 136 " pdb=" SD MET B 136 " ideal model delta sigma weight residual 112.70 124.99 -12.29 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C PHE C 277 " pdb=" N ARG C 278 " pdb=" CA ARG C 278 " ideal model delta sigma weight residual 122.46 115.16 7.30 1.80e+00 3.09e-01 1.64e+01 angle pdb=" C LEU D 8 " pdb=" N GLU D 9 " pdb=" CA GLU D 9 " ideal model delta sigma weight residual 121.14 114.10 7.04 1.75e+00 3.27e-01 1.62e+01 angle pdb=" C ASP B 384 " pdb=" N GLU B 385 " pdb=" CA GLU B 385 " ideal model delta sigma weight residual 121.54 129.19 -7.65 1.91e+00 2.74e-01 1.61e+01 ... (remaining 25595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10191 17.99 - 35.97: 1042 35.97 - 53.96: 163 53.96 - 71.95: 42 71.95 - 89.94: 16 Dihedral angle restraints: 11454 sinusoidal: 4706 harmonic: 6748 Sorted by residual: dihedral pdb=" CA GLN B 417 " pdb=" C GLN B 417 " pdb=" N ALA B 418 " pdb=" CA ALA B 418 " ideal model delta harmonic sigma weight residual 180.00 138.82 41.18 0 5.00e+00 4.00e-02 6.78e+01 dihedral pdb=" CA LEU C 460 " pdb=" C LEU C 460 " pdb=" N PRO C 461 " pdb=" CA PRO C 461 " ideal model delta harmonic sigma weight residual -180.00 -153.73 -26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ASP B 414 " pdb=" C ASP B 414 " pdb=" N PRO B 415 " pdb=" CA PRO B 415 " ideal model delta harmonic sigma weight residual -180.00 -154.12 -25.88 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 11451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2266 0.055 - 0.110: 465 0.110 - 0.165: 89 0.165 - 0.220: 8 0.220 - 0.275: 2 Chirality restraints: 2830 Sorted by residual: chirality pdb=" CB THR C 402 " pdb=" CA THR C 402 " pdb=" OG1 THR C 402 " pdb=" CG2 THR C 402 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ARG B 259 " pdb=" N ARG B 259 " pdb=" C ARG B 259 " pdb=" CB ARG B 259 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB ILE C 557 " pdb=" CA ILE C 557 " pdb=" CG1 ILE C 557 " pdb=" CG2 ILE C 557 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2827 not shown) Planarity restraints: 3370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 65 " -0.059 5.00e-02 4.00e+02 9.04e-02 1.31e+01 pdb=" N PRO D 66 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 66 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 66 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO C 658 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 259 " 0.219 9.50e-02 1.11e+02 9.86e-02 7.18e+00 pdb=" NE ARG B 259 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 259 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 259 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 259 " 0.001 2.00e-02 2.50e+03 ... (remaining 3367 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3178 2.77 - 3.30: 17185 3.30 - 3.83: 29823 3.83 - 4.37: 31373 4.37 - 4.90: 53838 Nonbonded interactions: 135397 Sorted by model distance: nonbonded pdb=" O SER B 24 " pdb=" OG1 THR B 27 " model vdw 2.237 3.040 nonbonded pdb=" O ALA D 159 " pdb=" OG1 THR D 163 " model vdw 2.276 3.040 nonbonded pdb=" O PHE B 386 " pdb=" OG1 THR B 389 " model vdw 2.289 3.040 nonbonded pdb=" OD1 ASP C1060 " pdb=" OG1 THR C1063 " model vdw 2.291 3.040 nonbonded pdb=" O LYS C 94 " pdb=" OG1 THR C 97 " model vdw 2.296 3.040 ... (remaining 135392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 18865 Z= 0.212 Angle : 0.784 12.294 25600 Z= 0.406 Chirality : 0.047 0.275 2830 Planarity : 0.006 0.099 3370 Dihedral : 14.913 89.936 7068 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.46 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.78 (0.16), residues: 2306 helix: -0.34 (0.14), residues: 1148 sheet: -0.65 (0.43), residues: 157 loop : -2.27 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 447 HIS 0.008 0.001 HIS D 255 PHE 0.040 0.002 PHE C 73 TYR 0.033 0.002 TYR C 190 ARG 0.019 0.001 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.168 Fit side-chains REVERT: B 453 MET cc_start: 0.8857 (mmm) cc_final: 0.8448 (mmt) REVERT: B 469 MET cc_start: 0.8679 (mmm) cc_final: 0.8462 (mmm) REVERT: B 509 CYS cc_start: 0.6816 (p) cc_final: 0.6508 (p) REVERT: B 621 MET cc_start: 0.8552 (tpt) cc_final: 0.8347 (mmm) REVERT: C 190 TYR cc_start: 0.8034 (p90) cc_final: 0.7808 (p90) REVERT: C 396 MET cc_start: 0.8560 (mtm) cc_final: 0.8008 (mtt) REVERT: C 537 MET cc_start: 0.8696 (ptp) cc_final: 0.8431 (ptp) REVERT: C 787 MET cc_start: 0.8985 (mmp) cc_final: 0.8476 (mmm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2554 time to fit residues: 50.6726 Evaluate side-chains 94 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 59 optimal weight: 0.0060 chunk 117 optimal weight: 20.0000 chunk 93 optimal weight: 0.0970 chunk 180 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 overall best weight: 2.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN B 689 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN C 699 GLN D 110 ASN D 255 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18865 Z= 0.198 Angle : 0.551 11.386 25600 Z= 0.288 Chirality : 0.040 0.154 2830 Planarity : 0.005 0.079 3370 Dihedral : 4.755 41.127 2540 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.11 % Favored : 93.84 % Rotamer: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2306 helix: 0.52 (0.15), residues: 1170 sheet: -0.25 (0.45), residues: 142 loop : -2.15 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 447 HIS 0.003 0.001 HIS B 307 PHE 0.016 0.001 PHE C 73 TYR 0.014 0.001 TYR C1027 ARG 0.005 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 453 MET cc_start: 0.8817 (mmm) cc_final: 0.8445 (mmt) REVERT: B 469 MET cc_start: 0.8728 (mmm) cc_final: 0.8491 (mmm) REVERT: B 509 CYS cc_start: 0.7049 (p) cc_final: 0.6711 (p) REVERT: B 594 GLN cc_start: 0.9128 (tp-100) cc_final: 0.8925 (tp-100) REVERT: B 620 MET cc_start: 0.8774 (tpt) cc_final: 0.8557 (tpt) REVERT: C 190 TYR cc_start: 0.8005 (p90) cc_final: 0.7440 (p90) REVERT: C 396 MET cc_start: 0.8568 (mtm) cc_final: 0.8011 (mtt) REVERT: C 667 MET cc_start: 0.4149 (mmm) cc_final: 0.3495 (mmm) REVERT: C 680 MET cc_start: 0.9169 (mmm) cc_final: 0.8852 (mmm) REVERT: C 1031 MET cc_start: 0.8043 (ptp) cc_final: 0.7803 (ptp) REVERT: D 270 GLU cc_start: 0.8783 (tp30) cc_final: 0.8244 (tp30) REVERT: D 273 MET cc_start: 0.8058 (mtt) cc_final: 0.7432 (mtt) REVERT: D 279 MET cc_start: 0.9283 (mmt) cc_final: 0.9059 (tpp) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.2506 time to fit residues: 48.4545 Evaluate side-chains 88 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 226 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 531 GLN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS C 510 ASN C 979 GLN C1018 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18865 Z= 0.333 Angle : 0.662 14.556 25600 Z= 0.340 Chirality : 0.043 0.213 2830 Planarity : 0.005 0.078 3370 Dihedral : 4.992 39.775 2540 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.46 % Favored : 92.50 % Rotamer: Outliers : 0.05 % Allowed : 5.63 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.02 (0.17), residues: 2306 helix: 0.57 (0.15), residues: 1174 sheet: -0.66 (0.44), residues: 139 loop : -2.27 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 272 HIS 0.006 0.001 HIS C 267 PHE 0.016 0.002 PHE D 123 TYR 0.013 0.002 TYR C 492 ARG 0.009 0.001 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 2.115 Fit side-chains revert: symmetry clash REVERT: B 453 MET cc_start: 0.8809 (mmm) cc_final: 0.8264 (mmt) REVERT: B 469 MET cc_start: 0.8884 (mmm) cc_final: 0.8657 (mmm) REVERT: B 620 MET cc_start: 0.8803 (tpt) cc_final: 0.8538 (tpt) REVERT: B 627 ASP cc_start: 0.8519 (m-30) cc_final: 0.8278 (t0) REVERT: C 190 TYR cc_start: 0.8073 (p90) cc_final: 0.7509 (p90) REVERT: C 396 MET cc_start: 0.8575 (mtm) cc_final: 0.8041 (mtt) REVERT: D 270 GLU cc_start: 0.8882 (tp30) cc_final: 0.8279 (tp30) REVERT: D 273 MET cc_start: 0.8063 (mtt) cc_final: 0.7299 (mtt) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.2787 time to fit residues: 49.3121 Evaluate side-chains 79 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 209 optimal weight: 20.0000 chunk 222 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 510 ASN D 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18865 Z= 0.216 Angle : 0.568 15.348 25600 Z= 0.292 Chirality : 0.041 0.220 2830 Planarity : 0.004 0.082 3370 Dihedral : 4.808 43.414 2540 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.20 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.17), residues: 2306 helix: 0.83 (0.15), residues: 1168 sheet: -0.37 (0.46), residues: 129 loop : -2.11 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.004 0.001 HIS C 522 PHE 0.013 0.001 PHE D 123 TYR 0.018 0.001 TYR C1027 ARG 0.010 0.000 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.085 Fit side-chains revert: symmetry clash REVERT: B 453 MET cc_start: 0.8804 (mmm) cc_final: 0.8246 (mmt) REVERT: B 469 MET cc_start: 0.8811 (mmm) cc_final: 0.8592 (mmm) REVERT: B 499 MET cc_start: 0.8488 (tmm) cc_final: 0.8212 (tmm) REVERT: C 190 TYR cc_start: 0.8026 (p90) cc_final: 0.7460 (p90) REVERT: C 396 MET cc_start: 0.8580 (mtm) cc_final: 0.8004 (mtt) REVERT: C 1031 MET cc_start: 0.8135 (ptp) cc_final: 0.7479 (ppp) REVERT: D 270 GLU cc_start: 0.8812 (tp30) cc_final: 0.8166 (tp30) REVERT: D 273 MET cc_start: 0.8154 (mtt) cc_final: 0.7421 (mtt) REVERT: D 279 MET cc_start: 0.9374 (mmp) cc_final: 0.9138 (tpp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2658 time to fit residues: 49.9409 Evaluate side-chains 81 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18865 Z= 0.268 Angle : 0.607 15.855 25600 Z= 0.311 Chirality : 0.042 0.175 2830 Planarity : 0.005 0.079 3370 Dihedral : 4.879 42.363 2540 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.63 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2306 helix: 0.80 (0.15), residues: 1172 sheet: -0.82 (0.43), residues: 151 loop : -2.16 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 574 HIS 0.005 0.001 HIS C 267 PHE 0.015 0.001 PHE D 123 TYR 0.012 0.001 TYR C 310 ARG 0.006 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.274 Fit side-chains revert: symmetry clash REVERT: B 453 MET cc_start: 0.8777 (mmm) cc_final: 0.8525 (tpp) REVERT: B 469 MET cc_start: 0.8891 (mmm) cc_final: 0.8667 (mmm) REVERT: B 499 MET cc_start: 0.8559 (tmm) cc_final: 0.8270 (tmm) REVERT: C 190 TYR cc_start: 0.7949 (p90) cc_final: 0.7478 (p90) REVERT: C 396 MET cc_start: 0.8550 (mtm) cc_final: 0.8006 (mtt) REVERT: C 1031 MET cc_start: 0.8230 (ptp) cc_final: 0.7704 (ppp) REVERT: D 270 GLU cc_start: 0.8789 (tp30) cc_final: 0.8536 (tp30) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2809 time to fit residues: 49.9373 Evaluate side-chains 81 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN C 510 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18865 Z= 0.313 Angle : 0.642 16.682 25600 Z= 0.329 Chirality : 0.043 0.231 2830 Planarity : 0.005 0.080 3370 Dihedral : 5.018 41.626 2540 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.02 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2306 helix: 0.69 (0.15), residues: 1179 sheet: -0.72 (0.44), residues: 139 loop : -2.29 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 187 HIS 0.005 0.001 HIS B 438 PHE 0.025 0.002 PHE D 123 TYR 0.013 0.001 TYR C 310 ARG 0.006 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.068 Fit side-chains REVERT: B 453 MET cc_start: 0.8892 (mmm) cc_final: 0.8610 (tpp) REVERT: B 469 MET cc_start: 0.8942 (mmm) cc_final: 0.8727 (mmm) REVERT: B 499 MET cc_start: 0.8618 (tmm) cc_final: 0.8289 (tmm) REVERT: B 501 MET cc_start: 0.8945 (ppp) cc_final: 0.8631 (ppp) REVERT: C 190 TYR cc_start: 0.7970 (p90) cc_final: 0.7527 (p90) REVERT: C 396 MET cc_start: 0.8560 (mtm) cc_final: 0.8078 (mtt) REVERT: C 941 MET cc_start: 0.8573 (ppp) cc_final: 0.8194 (ppp) REVERT: C 1031 MET cc_start: 0.8212 (ptp) cc_final: 0.7717 (ppp) REVERT: D 270 GLU cc_start: 0.8788 (tp30) cc_final: 0.8136 (tp30) REVERT: D 273 MET cc_start: 0.8037 (mtt) cc_final: 0.7307 (mtt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2797 time to fit residues: 46.1638 Evaluate side-chains 79 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 221 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 632 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN C 510 ASN D 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18865 Z= 0.165 Angle : 0.564 16.715 25600 Z= 0.285 Chirality : 0.041 0.180 2830 Planarity : 0.004 0.081 3370 Dihedral : 4.714 39.585 2540 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2306 helix: 1.10 (0.15), residues: 1160 sheet: -0.60 (0.44), residues: 137 loop : -1.98 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 187 HIS 0.005 0.001 HIS C 522 PHE 0.017 0.001 PHE C 901 TYR 0.009 0.001 TYR C 434 ARG 0.006 0.000 ARG C 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.080 Fit side-chains REVERT: B 453 MET cc_start: 0.8878 (mmm) cc_final: 0.8544 (tpp) REVERT: B 469 MET cc_start: 0.8886 (mmm) cc_final: 0.8654 (mmm) REVERT: B 499 MET cc_start: 0.8531 (tmm) cc_final: 0.8202 (tmm) REVERT: B 501 MET cc_start: 0.8871 (ppp) cc_final: 0.8556 (ppp) REVERT: C 190 TYR cc_start: 0.7860 (p90) cc_final: 0.7445 (p90) REVERT: C 396 MET cc_start: 0.8528 (mtm) cc_final: 0.8030 (mtt) REVERT: C 941 MET cc_start: 0.8497 (ppp) cc_final: 0.8129 (ppp) REVERT: D 270 GLU cc_start: 0.8725 (tp30) cc_final: 0.8480 (tp30) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2640 time to fit residues: 47.3423 Evaluate side-chains 85 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 66 optimal weight: 0.0470 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS C 510 ASN C 739 ASN D 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18865 Z= 0.210 Angle : 0.587 16.087 25600 Z= 0.297 Chirality : 0.041 0.199 2830 Planarity : 0.004 0.083 3370 Dihedral : 4.711 38.749 2540 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.94 % Favored : 93.02 % Rotamer: Outliers : 0.05 % Allowed : 1.06 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.18), residues: 2306 helix: 1.07 (0.15), residues: 1168 sheet: -0.58 (0.44), residues: 136 loop : -2.00 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 187 HIS 0.004 0.001 HIS C 522 PHE 0.019 0.001 PHE D 123 TYR 0.010 0.001 TYR C 310 ARG 0.007 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 2.311 Fit side-chains REVERT: B 469 MET cc_start: 0.8879 (mmm) cc_final: 0.8652 (mmm) REVERT: B 499 MET cc_start: 0.8566 (tmm) cc_final: 0.8222 (tmm) REVERT: B 501 MET cc_start: 0.8916 (ppp) cc_final: 0.8544 (ppp) REVERT: C 190 TYR cc_start: 0.7853 (p90) cc_final: 0.7545 (p90) REVERT: C 396 MET cc_start: 0.8527 (mtm) cc_final: 0.8029 (mtt) REVERT: D 270 GLU cc_start: 0.8778 (tp30) cc_final: 0.8570 (tp30) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.2780 time to fit residues: 48.9445 Evaluate side-chains 85 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 195 optimal weight: 0.0970 chunk 205 optimal weight: 6.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN C 739 ASN D 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18865 Z= 0.150 Angle : 0.569 16.063 25600 Z= 0.285 Chirality : 0.040 0.178 2830 Planarity : 0.004 0.081 3370 Dihedral : 4.567 37.312 2540 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.05 % Allowed : 0.51 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.18), residues: 2306 helix: 1.21 (0.16), residues: 1163 sheet: -0.59 (0.43), residues: 147 loop : -1.92 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 710 HIS 0.004 0.001 HIS C 522 PHE 0.040 0.001 PHE C 73 TYR 0.013 0.001 TYR C 310 ARG 0.006 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 2.169 Fit side-chains revert: symmetry clash REVERT: B 59 LEU cc_start: 0.9477 (mt) cc_final: 0.9220 (mm) REVERT: B 469 MET cc_start: 0.8804 (mmm) cc_final: 0.8579 (mmm) REVERT: B 499 MET cc_start: 0.8539 (tmm) cc_final: 0.8201 (tmm) REVERT: B 501 MET cc_start: 0.8861 (ppp) cc_final: 0.8516 (ppp) REVERT: C 190 TYR cc_start: 0.7906 (p90) cc_final: 0.7654 (p90) REVERT: C 396 MET cc_start: 0.8523 (mtm) cc_final: 0.8015 (mtt) REVERT: D 270 GLU cc_start: 0.8716 (tp30) cc_final: 0.8186 (tp30) REVERT: D 273 MET cc_start: 0.8193 (mtt) cc_final: 0.7506 (mtt) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.2956 time to fit residues: 54.1393 Evaluate side-chains 91 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 229 optimal weight: 20.0000 chunk 210 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 HIS B 632 ASN ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** C 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 18865 Z= 0.418 Angle : 0.759 17.322 25600 Z= 0.385 Chirality : 0.045 0.196 2830 Planarity : 0.005 0.078 3370 Dihedral : 5.181 39.254 2540 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.67 % Favored : 91.28 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2306 helix: 0.61 (0.15), residues: 1176 sheet: -0.92 (0.44), residues: 140 loop : -2.23 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 504 HIS 0.006 0.002 HIS B 438 PHE 0.040 0.002 PHE C 73 TYR 0.019 0.002 TYR C1027 ARG 0.007 0.001 ARG B 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4612 Ramachandran restraints generated. 2306 Oldfield, 0 Emsley, 2306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 2.104 Fit side-chains revert: symmetry clash REVERT: B 469 MET cc_start: 0.8976 (mmm) cc_final: 0.8747 (mmm) REVERT: B 499 MET cc_start: 0.8607 (tmm) cc_final: 0.8306 (tmm) REVERT: B 501 MET cc_start: 0.8979 (ppp) cc_final: 0.8599 (ppp) REVERT: C 190 TYR cc_start: 0.7971 (p90) cc_final: 0.7683 (p90) REVERT: C 216 ILE cc_start: 0.8263 (tp) cc_final: 0.8015 (tp) REVERT: C 396 MET cc_start: 0.8531 (mtm) cc_final: 0.8012 (mtt) REVERT: C 739 ASN cc_start: 0.9334 (OUTLIER) cc_final: 0.9122 (t0) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.2716 time to fit residues: 45.2495 Evaluate side-chains 81 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 182 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 510 ASN D 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.065513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.054873 restraints weight = 118987.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056104 restraints weight = 70929.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.056938 restraints weight = 49503.662| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18865 Z= 0.226 Angle : 0.625 17.378 25600 Z= 0.316 Chirality : 0.042 0.189 2830 Planarity : 0.004 0.081 3370 Dihedral : 4.963 38.076 2540 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.16 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.17), residues: 2306 helix: 0.86 (0.15), residues: 1170 sheet: -0.61 (0.45), residues: 130 loop : -2.08 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 811 HIS 0.003 0.001 HIS D 255 PHE 0.039 0.001 PHE C 73 TYR 0.015 0.001 TYR C1027 ARG 0.007 0.000 ARG B 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2587.40 seconds wall clock time: 48 minutes 38.00 seconds (2918.00 seconds total)