Starting phenix.real_space_refine on Fri Nov 17 08:20:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr1_23953/11_2023/7mr1_23953.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr1_23953/11_2023/7mr1_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_23953/11_2023/7mr1_23953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr1_23953/11_2023/7mr1_23953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr1_23953/11_2023/7mr1_23953.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr1_23953/11_2023/7mr1_23953.pdb" } 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 Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 863": "OE1" <-> "OE2" Residue "C GLU 873": "OE1" <-> "OE2" Residue "C TYR 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 45": "OD1" <-> "OD2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 227": "OD1" <-> "OD2" Residue "D ASP 297": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 9.14, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.42 Conformation dependent library (CDL) restraints added in 3.5 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: 1.88 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: 6.88 Time building geometry restraints manager: 7.08 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: 97.84 - 105.10: 396 105.10 - 112.37: 9202 112.37 - 119.64: 6929 119.64 - 126.90: 8787 126.90 - 134.17: 286 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 2.440 nonbonded pdb=" O ALA D 159 " pdb=" OG1 THR D 163 " model vdw 2.276 2.440 nonbonded pdb=" O PHE B 386 " pdb=" OG1 THR B 389 " model vdw 2.289 2.440 nonbonded pdb=" OD1 ASP C1060 " pdb=" OG1 THR C1063 " model vdw 2.291 2.440 nonbonded pdb=" O LYS C 94 " pdb=" OG1 THR C 97 " model vdw 2.296 2.440 ... (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 ========== 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: 0.750 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: 4.330 Check model and map are aligned: 0.230 Set scattering table: 0.170 Process input model: 47.930 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.000 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.968 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2521 time to fit residues: 49.7149 Evaluate side-chains 93 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8904 ------------------------------------------------------------------------------- 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: 3.9990 chunk 96 optimal weight: 9.9990 chunk 59 optimal weight: 0.1980 chunk 117 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 258 ASN B 531 GLN ** B 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN C1018 HIS ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18865 Z= 0.306 Angle : 0.628 10.266 25600 Z= 0.325 Chirality : 0.042 0.159 2830 Planarity : 0.005 0.075 3370 Dihedral : 4.989 40.478 2540 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.42 % Favored : 92.54 % Rotamer: Outliers : 0.05 % Allowed : 6.89 % Favored : 93.06 % 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: -1.13 (0.17), residues: 2306 helix: 0.41 (0.15), residues: 1177 sheet: -0.71 (0.42), residues: 150 loop : -2.26 (0.18), residues: 979 *********************** 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 108 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 2.173 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.2645 time to fit residues: 48.4068 Evaluate side-chains 80 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.029 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0852 ------------------------------------------------------------------------------- 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: 4.9990 chunk 64 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 142 optimal weight: 0.1980 chunk 57 optimal weight: 8.9990 chunk 209 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 186 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN B 455 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS C 510 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18865 Z= 0.340 Angle : 0.652 14.140 25600 Z= 0.336 Chirality : 0.042 0.188 2830 Planarity : 0.005 0.074 3370 Dihedral : 5.112 39.442 2540 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.37 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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: -1.15 (0.17), residues: 2306 helix: 0.47 (0.15), residues: 1175 sheet: -0.83 (0.44), residues: 141 loop : -2.33 (0.18), residues: 990 *********************** 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 104 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 2.405 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2793 time to fit residues: 48.6933 Evaluate side-chains 79 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.975 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9206 ------------------------------------------------------------------------------- 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: 10.0000 chunk 157 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 chunk 222 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 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 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN C 423 GLN C 510 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 18865 Z= 0.418 Angle : 0.730 15.716 25600 Z= 0.375 Chirality : 0.045 0.230 2830 Planarity : 0.005 0.078 3370 Dihedral : 5.433 42.389 2540 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.80 % Favored : 91.15 % Rotamer: Outliers : 0.05 % Allowed : 6.69 % Favored : 93.26 % 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: -1.48 (0.17), residues: 2306 helix: 0.20 (0.15), residues: 1173 sheet: -1.20 (0.45), residues: 133 loop : -2.44 (0.18), residues: 1000 *********************** 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 99 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 3.292 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.2655 time to fit residues: 44.6308 Evaluate side-chains 77 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 2.182 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1660 time to fit residues: 3.2469 ------------------------------------------------------------------------------- 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: 6.9990 chunk 126 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 189 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN B 632 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN C 510 ASN ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18865 Z= 0.144 Angle : 0.551 17.036 25600 Z= 0.282 Chirality : 0.041 0.190 2830 Planarity : 0.004 0.078 3370 Dihedral : 4.828 40.621 2540 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.64 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: -0.65 (0.18), residues: 2306 helix: 0.93 (0.15), residues: 1156 sheet: -0.69 (0.45), residues: 141 loop : -2.09 (0.19), residues: 1009 *********************** 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 115 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2610 time to fit residues: 50.7848 Evaluate side-chains 85 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 2.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9145 ------------------------------------------------------------------------------- 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: 9.9990 chunk 200 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 222 optimal weight: 0.0980 chunk 184 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 228 GLN C 423 GLN C 510 ASN ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18865 Z= 0.218 Angle : 0.583 17.108 25600 Z= 0.297 Chirality : 0.041 0.179 2830 Planarity : 0.004 0.075 3370 Dihedral : 4.799 39.185 2540 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.29 % Favored : 92.67 % Rotamer: Outliers : 0.05 % Allowed : 2.74 % 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: -0.66 (0.18), residues: 2306 helix: 0.93 (0.15), residues: 1167 sheet: -0.65 (0.45), residues: 146 loop : -2.16 (0.19), residues: 993 *********************** 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 104 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 2.220 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.2748 time to fit residues: 48.5238 Evaluate side-chains 83 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1230 ------------------------------------------------------------------------------- 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: 1.9990 chunk 25 optimal weight: 10.0000 chunk 126 optimal weight: 0.3980 chunk 162 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 221 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 594 GLN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN C 510 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18865 Z= 0.150 Angle : 0.553 17.807 25600 Z= 0.279 Chirality : 0.040 0.171 2830 Planarity : 0.004 0.088 3370 Dihedral : 4.638 38.473 2540 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.11 % Favored : 93.84 % Rotamer: Outliers : 0.05 % Allowed : 1.47 % Favored : 98.48 % 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: 1.12 (0.15), residues: 1167 sheet: -0.53 (0.46), residues: 141 loop : -2.06 (0.19), residues: 998 *********************** 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 112 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 2.122 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.2831 time to fit residues: 54.1691 Evaluate side-chains 88 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.286 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0302 ------------------------------------------------------------------------------- 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: 4.9990 chunk 88 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 174 optimal weight: 1.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 510 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 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: 0.8397 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18865 Z= 0.164 Angle : 0.561 17.532 25600 Z= 0.282 Chirality : 0.040 0.177 2830 Planarity : 0.004 0.094 3370 Dihedral : 4.579 37.249 2540 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.29 % Favored : 93.67 % 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: -0.39 (0.18), residues: 2306 helix: 1.16 (0.15), residues: 1170 sheet: -0.37 (0.46), residues: 141 loop : -2.06 (0.19), residues: 995 *********************** 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 107 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.2647 time to fit residues: 47.9228 Evaluate side-chains 86 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 2.134 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8194 ------------------------------------------------------------------------------- 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: 0.8980 chunk 212 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 195 optimal weight: 0.0370 chunk 205 optimal weight: 0.8980 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 455 ASN B 594 GLN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18865 Z= 0.138 Angle : 0.558 17.074 25600 Z= 0.277 Chirality : 0.040 0.187 2830 Planarity : 0.004 0.091 3370 Dihedral : 4.447 37.077 2540 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 0.05 % Allowed : 0.56 % Favored : 99.39 % 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: -0.31 (0.18), residues: 2306 helix: 1.22 (0.16), residues: 1173 sheet: -0.29 (0.46), residues: 142 loop : -2.02 (0.19), residues: 991 *********************** 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 119 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 2.139 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.2706 time to fit residues: 54.2476 Evaluate side-chains 87 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 2.137 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8607 ------------------------------------------------------------------------------- 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: 5.9990 chunk 218 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 229 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 182 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN C 510 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 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: 0.8418 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18865 Z= 0.230 Angle : 0.607 17.394 25600 Z= 0.303 Chirality : 0.042 0.205 2830 Planarity : 0.005 0.102 3370 Dihedral : 4.610 35.906 2540 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.20 % Favored : 92.76 % Rotamer: Outliers : 0.05 % Allowed : 0.30 % 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: -0.46 (0.18), residues: 2306 helix: 1.10 (0.15), residues: 1177 sheet: -0.63 (0.44), residues: 143 loop : -2.07 (0.19), residues: 986 ********************** 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 107 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 2.128 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.2795 time to fit residues: 50.4315 Evaluate side-chains 84 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 2.199 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9848 ------------------------------------------------------------------------------- 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: 1.9990 chunk 194 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 632 ASN ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.059624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.049769 restraints weight = 111180.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050970 restraints weight = 66352.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.051779 restraints weight = 46346.653| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18865 Z= 0.269 Angle : 0.647 18.274 25600 Z= 0.323 Chirality : 0.042 0.206 2830 Planarity : 0.005 0.103 3370 Dihedral : 4.840 36.562 2540 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.59 % Favored : 92.37 % 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: -0.59 (0.18), residues: 2306 helix: 0.98 (0.15), residues: 1177 sheet: -0.72 (0.44), residues: 142 loop : -2.13 (0.19), residues: 987 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2557.39 seconds wall clock time: 48 minutes 23.37 seconds (2903.37 seconds total)