Starting phenix.real_space_refine on Sat Nov 16 11:08:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/11_2024/8jcv_36166.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/11_2024/8jcv_36166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/11_2024/8jcv_36166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/11_2024/8jcv_36166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/11_2024/8jcv_36166.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/11_2024/8jcv_36166.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 62 5.16 5 C 6682 2.51 5 N 1891 2.21 5 O 2032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10667 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5283 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 37, 'TRANS': 725} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 885 Unresolved non-hydrogen dihedrals: 575 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 10, 'ASN:plan1': 5, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 12, 'GLU:plan': 12, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 369 Chain: "3" Number of atoms: 5304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5304 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PTRANS': 29, 'TRANS': 721} Chain breaks: 3 Unresolved non-hydrogen bonds: 682 Unresolved non-hydrogen angles: 874 Unresolved non-hydrogen dihedrals: 583 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 16, 'GLU:plan': 8, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 355 Chain: "2" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.56, per 1000 atoms: 0.71 Number of scatterers: 10667 At special positions: 0 Unit cell: (84.609, 122.094, 183.141, 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 62 16.00 O 2032 8.00 N 1891 7.00 C 6682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS 2 50 " - pdb=" SG CYS 2 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 234 " - pdb=" SG CYS 2 518 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 355 " - pdb=" SG CYS 2 362 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 400 " - pdb=" SG CYS 2 407 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 500 " - pdb=" SG CYS 2 519 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 504 " - pdb=" SG CYS 2 522 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 525 " - pdb=" SG CYS 2 537 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 540 " - pdb=" SG CYS 2 553 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 57 " - pdb=" SG CYS 3 99 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 361 " - pdb=" SG CYS 3 373 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 412 " - pdb=" SG CYS 3 419 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 509 " - pdb=" SG CYS 3 528 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 549 " - pdb=" SG CYS 3 562 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 641 " - pdb=" SG CYS 3 730 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG 22001 " - " ASN 2 203 " " NAG 32001 " - " ASN 3 209 " Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.6 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2842 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 48.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain '2' and resid 58 through 75 Processing helix chain '2' and resid 94 through 103 Processing helix chain '2' and resid 104 through 106 No H-bonds generated for 'chain '2' and resid 104 through 106' Processing helix chain '2' and resid 145 through 159 removed outlier: 4.296A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE 2 158 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) Processing helix chain '2' and resid 170 through 174 Processing helix chain '2' and resid 189 through 202 Processing helix chain '2' and resid 218 through 231 removed outlier: 3.517A pdb=" N GLU 2 222 " --> pdb=" O GLU 2 218 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA 2 230 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG 2 231 " --> pdb=" O GLU 2 227 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 260 removed outlier: 4.285A pdb=" N LYS 2 260 " --> pdb=" O ALA 2 256 " (cutoff:3.500A) Processing helix chain '2' and resid 271 through 285 Processing helix chain '2' and resid 300 through 305 removed outlier: 4.103A pdb=" N VAL 2 304 " --> pdb=" O LEU 2 300 " (cutoff:3.500A) Processing helix chain '2' and resid 324 through 332 Processing helix chain '2' and resid 344 through 353 Processing helix chain '2' and resid 360 through 364 removed outlier: 3.517A pdb=" N ALA 2 363 " --> pdb=" O ARG 2 360 " (cutoff:3.500A) Processing helix chain '2' and resid 375 through 377 No H-bonds generated for 'chain '2' and resid 375 through 377' Processing helix chain '2' and resid 378 through 400 removed outlier: 3.570A pdb=" N VAL 2 382 " --> pdb=" O ILE 2 378 " (cutoff:3.500A) Processing helix chain '2' and resid 407 through 411 removed outlier: 3.814A pdb=" N MET 2 410 " --> pdb=" O CYS 2 407 " (cutoff:3.500A) Processing helix chain '2' and resid 414 through 422 removed outlier: 3.697A pdb=" N LEU 2 418 " --> pdb=" O ASN 2 414 " (cutoff:3.500A) Processing helix chain '2' and resid 423 through 426 removed outlier: 3.990A pdb=" N VAL 2 426 " --> pdb=" O VAL 2 423 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 423 through 426' Processing helix chain '2' and resid 482 through 485 Processing helix chain '2' and resid 568 through 592 removed outlier: 3.848A pdb=" N THR 2 573 " --> pdb=" O VAL 2 569 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL 2 588 " --> pdb=" O PHE 2 584 " (cutoff:3.500A) Processing helix chain '2' and resid 595 through 601 removed outlier: 3.502A pdb=" N ALA 2 600 " --> pdb=" O PRO 2 596 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER 2 601 " --> pdb=" O VAL 2 597 " (cutoff:3.500A) Processing helix chain '2' and resid 602 through 623 Processing helix chain '2' and resid 631 through 660 removed outlier: 4.333A pdb=" N ARG 2 656 " --> pdb=" O THR 2 652 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE 2 657 " --> pdb=" O LYS 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 676 through 702 removed outlier: 3.974A pdb=" N VAL 2 699 " --> pdb=" O VAL 2 695 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA 2 702 " --> pdb=" O LEU 2 698 " (cutoff:3.500A) Processing helix chain '2' and resid 723 through 749 removed outlier: 3.776A pdb=" N SER 2 727 " --> pdb=" O HIS 2 723 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY 2 730 " --> pdb=" O ALA 2 726 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER 2 731 " --> pdb=" O SER 2 727 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS 2 748 " --> pdb=" O LEU 2 744 " (cutoff:3.500A) Processing helix chain '2' and resid 757 through 784 removed outlier: 4.264A pdb=" N PHE 2 761 " --> pdb=" O ASN 2 757 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE 2 771 " --> pdb=" O TYR 2 767 " (cutoff:3.500A) Proline residue: 2 778 - end of helix Processing helix chain '2' and resid 786 through 818 removed outlier: 4.017A pdb=" N ALA 2 811 " --> pdb=" O GLY 2 807 " (cutoff:3.500A) Proline residue: 2 812 - end of helix Processing helix chain '3' and resid 65 through 82 Processing helix chain '3' and resid 101 through 109 Processing helix chain '3' and resid 109 through 115 removed outlier: 3.760A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA 3 115 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 150 through 164 removed outlier: 3.996A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE 3 164 " --> pdb=" O LEU 3 160 " (cutoff:3.500A) Processing helix chain '3' and resid 176 through 180 Processing helix chain '3' and resid 194 through 208 removed outlier: 3.673A pdb=" N ALA 3 198 " --> pdb=" O ASP 3 194 " (cutoff:3.500A) Processing helix chain '3' and resid 220 through 238 removed outlier: 3.715A pdb=" N LEU 3 236 " --> pdb=" O GLN 3 232 " (cutoff:3.500A) Processing helix chain '3' and resid 252 through 265 removed outlier: 3.557A pdb=" N GLN 3 265 " --> pdb=" O ARG 3 261 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 290 removed outlier: 4.057A pdb=" N ARG 3 282 " --> pdb=" O SER 3 278 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU 3 283 " --> pdb=" O ASP 3 279 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG 3 290 " --> pdb=" O ALA 3 286 " (cutoff:3.500A) Processing helix chain '3' and resid 330 through 339 removed outlier: 3.604A pdb=" N ASP 3 334 " --> pdb=" O VAL 3 330 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG 3 335 " --> pdb=" O ARG 3 331 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER 3 339 " --> pdb=" O ARG 3 335 " (cutoff:3.500A) Processing helix chain '3' and resid 349 through 360 removed outlier: 4.308A pdb=" N ASP 3 353 " --> pdb=" O PRO 3 349 " (cutoff:3.500A) Processing helix chain '3' and resid 380 through 384 removed outlier: 3.520A pdb=" N ASN 3 383 " --> pdb=" O ASP 3 380 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR 3 384 " --> pdb=" O SER 3 381 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 380 through 384' Processing helix chain '3' and resid 389 through 412 removed outlier: 3.712A pdb=" N MET 3 400 " --> pdb=" O ALA 3 396 " (cutoff:3.500A) Processing helix chain '3' and resid 426 through 433 removed outlier: 3.515A pdb=" N ASP 3 433 " --> pdb=" O LYS 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 577 through 601 Processing helix chain '3' and resid 614 through 632 removed outlier: 3.501A pdb=" N CYS 3 627 " --> pdb=" O GLY 3 623 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR 3 629 " --> pdb=" O SER 3 625 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE 3 632 " --> pdb=" O MET 3 628 " (cutoff:3.500A) Processing helix chain '3' and resid 639 through 665 removed outlier: 4.100A pdb=" N LEU 3 659 " --> pdb=" O CYS 3 655 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU 3 660 " --> pdb=" O TYR 3 656 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR 3 661 " --> pdb=" O SER 3 657 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS 3 662 " --> pdb=" O ALA 3 658 " (cutoff:3.500A) Processing helix chain '3' and resid 685 through 706 removed outlier: 3.757A pdb=" N VAL 3 703 " --> pdb=" O GLN 3 699 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER 3 704 " --> pdb=" O ILE 3 700 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP 3 706 " --> pdb=" O MET 3 702 " (cutoff:3.500A) Processing helix chain '3' and resid 732 through 759 removed outlier: 3.765A pdb=" N SER 3 736 " --> pdb=" O VAL 3 732 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE 3 739 " --> pdb=" O SER 3 735 " (cutoff:3.500A) Processing helix chain '3' and resid 764 through 791 Proline residue: 3 787 - end of helix removed outlier: 3.526A pdb=" N TYR 3 790 " --> pdb=" O LEU 3 786 " (cutoff:3.500A) Processing helix chain '3' and resid 797 through 825 removed outlier: 3.598A pdb=" N ALA 3 820 " --> pdb=" O GLY 3 816 " (cutoff:3.500A) Proline residue: 3 821 - end of helix Processing sheet with id=AA1, first strand: chain '2' and resid 26 through 27 removed outlier: 6.611A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 162 through 164 Processing sheet with id=AA3, first strand: chain '2' and resid 234 through 235 removed outlier: 3.906A pdb=" N VAL 2 207 " --> pdb=" O CYS 2 234 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR 2 206 " --> pdb=" O VAL 2 265 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL 2 267 " --> pdb=" O TYR 2 206 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER 2 208 " --> pdb=" O VAL 2 267 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA 2 266 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TRP 2 291 " --> pdb=" O ILE 2 315 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE 2 317 " --> pdb=" O TRP 2 291 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA 2 293 " --> pdb=" O ILE 2 317 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N LEU 2 319 " --> pdb=" O ALA 2 293 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY 2 472 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR 2 479 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 428 through 429 removed outlier: 3.830A pdb=" N PHE 2 428 " --> pdb=" O VAL 2 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 32 through 35 removed outlier: 3.610A pdb=" N ILE 3 33 " --> pdb=" O ILE 3 95 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL 3 93 " --> pdb=" O ILE 3 35 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY 3 144 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU 3 44 " --> pdb=" O ILE 3 146 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL 3 145 " --> pdb=" O ILE 3 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 48 through 50 removed outlier: 4.794A pdb=" N ARG 3 59 " --> pdb=" O GLU 3 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3' and resid 240 through 247 removed outlier: 9.647A pdb=" N VAL 3 213 " --> pdb=" O THR 3 243 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N GLU 3 245 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR 3 215 " --> pdb=" O GLU 3 245 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL 3 247 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA 3 217 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TYR 3 212 " --> pdb=" O VAL 3 271 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N VAL 3 273 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER 3 214 " --> pdb=" O VAL 3 273 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE 3 275 " --> pdb=" O SER 3 214 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL 3 216 " --> pdb=" O PHE 3 275 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL 3 272 " --> pdb=" O VAL 3 298 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain '3' and resid 321 through 325 removed outlier: 6.564A pdb=" N TYR 3 466 " --> pdb=" O HIS 3 485 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N HIS 3 485 " --> pdb=" O TYR 3 466 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL 3 468 " --> pdb=" O VAL 3 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 440 through 441 removed outlier: 3.721A pdb=" N PHE 3 440 " --> pdb=" O VAL 3 454 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 518 through 521 removed outlier: 3.785A pdb=" N ILE 3 530 " --> pdb=" O MET 3 521 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3431 1.34 - 1.46: 1997 1.46 - 1.58: 5374 1.58 - 1.70: 0 1.70 - 1.83: 78 Bond restraints: 10880 Sorted by residual: bond pdb=" CAT Z99 22101 " pdb=" OAP Z99 22101 " ideal model delta sigma weight residual 1.364 1.451 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CAT Z99 32101 " pdb=" OAP Z99 32101 " ideal model delta sigma weight residual 1.364 1.450 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" CAS Z99 22101 " pdb=" OAP Z99 22101 " ideal model delta sigma weight residual 1.369 1.452 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" CAS Z99 32101 " pdb=" OAP Z99 32101 " ideal model delta sigma weight residual 1.369 1.449 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" CA ALA 3 172 " pdb=" CB ALA 3 172 " ideal model delta sigma weight residual 1.535 1.498 0.037 1.64e-02 3.72e+03 5.06e+00 ... (remaining 10875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 14503 1.50 - 3.00: 280 3.00 - 4.50: 50 4.50 - 6.00: 25 6.00 - 7.50: 12 Bond angle restraints: 14870 Sorted by residual: angle pdb=" C ARG 2 358 " pdb=" N GLN 2 359 " pdb=" CA GLN 2 359 " ideal model delta sigma weight residual 121.40 126.72 -5.32 1.52e+00 4.33e-01 1.23e+01 angle pdb=" N ARG 2 360 " pdb=" CA ARG 2 360 " pdb=" C ARG 2 360 " ideal model delta sigma weight residual 107.73 112.25 -4.52 1.34e+00 5.57e-01 1.14e+01 angle pdb=" C SER 2 340 " pdb=" N ARG 2 341 " pdb=" CA ARG 2 341 " ideal model delta sigma weight residual 120.38 124.95 -4.57 1.37e+00 5.33e-01 1.11e+01 angle pdb=" C ASP 2 215 " pdb=" N TYR 2 216 " pdb=" CA TYR 2 216 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.95e+00 angle pdb=" CA PRO 2 76 " pdb=" C PRO 2 76 " pdb=" N HIS 2 77 " ideal model delta sigma weight residual 116.45 118.78 -2.33 8.50e-01 1.38e+00 7.49e+00 ... (remaining 14865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 6411 34.55 - 69.09: 117 69.09 - 103.64: 20 103.64 - 138.19: 7 138.19 - 172.73: 2 Dihedral angle restraints: 6557 sinusoidal: 2167 harmonic: 4390 Sorted by residual: dihedral pdb=" CB CYS 2 234 " pdb=" SG CYS 2 234 " pdb=" SG CYS 2 518 " pdb=" CB CYS 2 518 " ideal model delta sinusoidal sigma weight residual -86.00 -161.06 75.06 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS 3 57 " pdb=" SG CYS 3 57 " pdb=" SG CYS 3 99 " pdb=" CB CYS 3 99 " ideal model delta sinusoidal sigma weight residual 93.00 26.23 66.77 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS 2 500 " pdb=" SG CYS 2 500 " pdb=" SG CYS 2 519 " pdb=" CB CYS 2 519 " ideal model delta sinusoidal sigma weight residual 93.00 29.54 63.46 1 1.00e+01 1.00e-02 5.31e+01 ... (remaining 6554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.071: 1723 1.071 - 2.143: 0 2.143 - 3.214: 0 3.214 - 4.286: 0 4.286 - 5.357: 2 Chirality restraints: 1725 Sorted by residual: chirality pdb=" CAW Z99 32101 " pdb=" CAN Z99 32101 " pdb=" CAU Z99 32101 " pdb=" CAV Z99 32101 " both_signs ideal model delta sigma weight residual False 2.61 -2.75 5.36 2.00e-01 2.50e+01 7.18e+02 chirality pdb=" CAW Z99 22101 " pdb=" CAN Z99 22101 " pdb=" CAU Z99 22101 " pdb=" CAV Z99 22101 " both_signs ideal model delta sigma weight residual False 2.61 -2.64 5.25 2.00e-01 2.50e+01 6.89e+02 chirality pdb=" CAZ Z99 22101 " pdb=" CAO Z99 22101 " pdb=" CAX Z99 22101 " pdb=" CAY Z99 22101 " both_signs ideal model delta sigma weight residual True 2.39 -2.74 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 1722 not shown) Planarity restraints: 1971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP 2 75 " 0.063 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO 2 76 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO 2 76 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO 2 76 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL 2 370 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO 2 371 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO 2 371 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO 2 371 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 74 " -0.110 9.50e-02 1.11e+02 4.94e-02 1.81e+00 pdb=" NE ARG 2 74 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG 2 74 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 74 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 74 " -0.001 2.00e-02 2.50e+03 ... (remaining 1968 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3235 2.82 - 3.34: 10329 3.34 - 3.86: 16956 3.86 - 4.38: 18372 4.38 - 4.90: 32263 Nonbonded interactions: 81155 Sorted by model distance: nonbonded pdb=" NE2 GLN 3 508 " pdb=" O CYS 3 509 " model vdw 2.300 3.120 nonbonded pdb=" NH1 ARG 2 460 " pdb=" O ALA 2 461 " model vdw 2.307 3.120 nonbonded pdb=" O LEU 3 39 " pdb=" N GLY 3 92 " model vdw 2.314 3.120 nonbonded pdb=" NH2 ARG 2 200 " pdb=" O ARG 2 231 " model vdw 2.328 3.120 nonbonded pdb=" O SER 3 255 " pdb=" OG SER 3 258 " model vdw 2.350 3.040 ... (remaining 81150 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=0.08 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 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: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.610 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 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 0.087 10880 Z= 0.220 Angle : 0.561 7.501 14870 Z= 0.276 Chirality : 0.186 5.357 1725 Planarity : 0.004 0.098 1969 Dihedral : 14.870 172.733 3664 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.11 % Allowed : 0.43 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.22), residues: 1500 helix: 2.85 (0.20), residues: 635 sheet: 0.13 (0.49), residues: 132 loop : -1.09 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 554 HIS 0.005 0.000 HIS 2 390 PHE 0.010 0.001 PHE 2 250 TYR 0.010 0.001 TYR 3 478 ARG 0.010 0.000 ARG 2 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: 2 250 PHE cc_start: 0.6027 (m-10) cc_final: 0.5815 (m-10) REVERT: 2 410 MET cc_start: 0.6932 (ppp) cc_final: 0.6662 (ppp) REVERT: 3 422 MET cc_start: 0.5571 (ttp) cc_final: 0.5050 (ttp) REVERT: 3 537 TYR cc_start: 0.6835 (p90) cc_final: 0.6511 (p90) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.2735 time to fit residues: 46.2665 Evaluate side-chains 90 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 39 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 118 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 88 optimal weight: 0.0770 chunk 137 optimal weight: 4.9990 overall best weight: 1.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 162 GLN 2 425 ASN 2 655 ASN 3 67 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 405 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10880 Z= 0.336 Angle : 0.605 10.636 14870 Z= 0.311 Chirality : 0.044 0.165 1725 Planarity : 0.004 0.065 1969 Dihedral : 5.168 39.858 1706 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.08 % Allowed : 8.17 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.22), residues: 1500 helix: 2.55 (0.20), residues: 652 sheet: -0.37 (0.44), residues: 140 loop : -1.13 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 3 303 HIS 0.004 0.001 HIS 2 87 PHE 0.021 0.002 PHE 2 327 TYR 0.018 0.002 TYR 3 256 ARG 0.015 0.001 ARG 2 354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 1.222 Fit side-chains REVERT: 2 238 SER cc_start: 0.8094 (t) cc_final: 0.7720 (p) REVERT: 2 245 MET cc_start: 0.4635 (OUTLIER) cc_final: 0.3735 (tmm) REVERT: 2 250 PHE cc_start: 0.6143 (m-10) cc_final: 0.5817 (m-10) REVERT: 2 410 MET cc_start: 0.6966 (ppp) cc_final: 0.6489 (ppp) REVERT: 3 49 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7108 (mt-10) outliers start: 10 outliers final: 7 residues processed: 107 average time/residue: 0.2587 time to fit residues: 39.2437 Evaluate side-chains 96 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 158 PHE Chi-restraints excluded: chain 2 residue 195 MET Chi-restraints excluded: chain 2 residue 198 ILE Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 292 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 110 optimal weight: 0.2980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10880 Z= 0.304 Angle : 0.568 10.460 14870 Z= 0.291 Chirality : 0.043 0.183 1725 Planarity : 0.004 0.057 1969 Dihedral : 4.906 31.133 1706 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.72 % Allowed : 11.08 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1500 helix: 2.49 (0.20), residues: 664 sheet: -0.96 (0.41), residues: 138 loop : -1.18 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 3 303 HIS 0.005 0.001 HIS 2 390 PHE 0.020 0.002 PHE 2 327 TYR 0.015 0.002 TYR 2 216 ARG 0.007 0.001 ARG 3 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.200 Fit side-chains REVERT: 2 245 MET cc_start: 0.5167 (OUTLIER) cc_final: 0.4480 (tmm) REVERT: 2 410 MET cc_start: 0.6639 (ppp) cc_final: 0.6215 (ppp) REVERT: 3 49 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6993 (mt-10) REVERT: 3 239 ILE cc_start: 0.6802 (OUTLIER) cc_final: 0.6484 (mp) REVERT: 3 432 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7320 (ttmm) outliers start: 16 outliers final: 9 residues processed: 109 average time/residue: 0.2423 time to fit residues: 37.8563 Evaluate side-chains 94 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 198 ILE Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 281 SER Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 315 HIS Chi-restraints excluded: chain 3 residue 432 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 30.0000 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 130 optimal weight: 8.9990 chunk 39 optimal weight: 0.0670 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 162 GLN 2 351 GLN 2 425 ASN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10880 Z= 0.201 Angle : 0.523 8.224 14870 Z= 0.267 Chirality : 0.041 0.155 1725 Planarity : 0.004 0.067 1969 Dihedral : 4.592 27.266 1706 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.97 % Allowed : 13.33 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.22), residues: 1500 helix: 2.62 (0.19), residues: 660 sheet: -1.01 (0.41), residues: 138 loop : -1.23 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 2 337 HIS 0.004 0.001 HIS 2 390 PHE 0.015 0.001 PHE 2 327 TYR 0.021 0.001 TYR 2 216 ARG 0.003 0.000 ARG 2 445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 1.215 Fit side-chains REVERT: 2 180 TYR cc_start: 0.7863 (m-10) cc_final: 0.7608 (m-10) REVERT: 2 245 MET cc_start: 0.5396 (OUTLIER) cc_final: 0.4774 (tmm) REVERT: 2 334 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7354 (mp) REVERT: 2 466 TYR cc_start: 0.7270 (m-10) cc_final: 0.6924 (m-10) REVERT: 3 540 LEU cc_start: 0.4546 (tt) cc_final: 0.4189 (mp) outliers start: 9 outliers final: 3 residues processed: 96 average time/residue: 0.2359 time to fit residues: 32.8880 Evaluate side-chains 88 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 285 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 108 optimal weight: 0.0980 chunk 60 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 131 optimal weight: 50.0000 chunk 36 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 54 ASN ** 2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 351 GLN 2 425 ASN ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 402 HIS 3 731 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 10880 Z= 0.427 Angle : 0.637 11.589 14870 Z= 0.329 Chirality : 0.045 0.183 1725 Planarity : 0.004 0.065 1969 Dihedral : 4.995 36.026 1706 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.26 % Allowed : 13.98 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1500 helix: 2.41 (0.20), residues: 665 sheet: -1.50 (0.40), residues: 142 loop : -1.33 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 3 303 HIS 0.005 0.001 HIS 2 87 PHE 0.020 0.002 PHE 2 327 TYR 0.014 0.002 TYR 2 216 ARG 0.007 0.001 ARG 2 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5485 (OUTLIER) cc_final: 0.4954 (tmm) REVERT: 2 334 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7507 (mp) REVERT: 3 72 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8089 (ttt) REVERT: 3 239 ILE cc_start: 0.6848 (OUTLIER) cc_final: 0.6554 (mp) REVERT: 3 432 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7443 (ttmm) outliers start: 21 outliers final: 12 residues processed: 105 average time/residue: 0.2371 time to fit residues: 36.4854 Evaluate side-chains 101 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 315 HIS Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 432 LYS Chi-restraints excluded: chain 3 residue 531 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 6.9990 chunk 131 optimal weight: 50.0000 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 121 optimal weight: 0.4980 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10880 Z= 0.216 Angle : 0.539 8.533 14870 Z= 0.272 Chirality : 0.041 0.150 1725 Planarity : 0.004 0.073 1969 Dihedral : 4.618 34.782 1706 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.15 % Allowed : 14.52 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1500 helix: 2.57 (0.19), residues: 664 sheet: -1.39 (0.41), residues: 138 loop : -1.29 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 291 HIS 0.004 0.000 HIS 2 390 PHE 0.017 0.001 PHE 3 164 TYR 0.018 0.001 TYR 2 216 ARG 0.004 0.000 ARG 2 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5723 (OUTLIER) cc_final: 0.5139 (tmm) REVERT: 2 334 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7355 (mp) REVERT: 3 239 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6376 (mp) outliers start: 20 outliers final: 12 residues processed: 104 average time/residue: 0.2736 time to fit residues: 42.0510 Evaluate side-chains 98 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 56 HIS Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 492 LEU Chi-restraints excluded: chain 3 residue 531 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 122 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 145 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 20.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 94 HIS ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10880 Z= 0.317 Angle : 0.594 9.790 14870 Z= 0.300 Chirality : 0.043 0.169 1725 Planarity : 0.004 0.075 1969 Dihedral : 4.777 38.292 1706 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.04 % Allowed : 15.81 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.22), residues: 1500 helix: 2.48 (0.19), residues: 669 sheet: -1.38 (0.42), residues: 131 loop : -1.40 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 529 HIS 0.004 0.001 HIS 2 390 PHE 0.018 0.002 PHE 2 327 TYR 0.012 0.002 TYR 3 256 ARG 0.005 0.000 ARG 2 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5417 (OUTLIER) cc_final: 0.4914 (tmm) REVERT: 2 334 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7387 (mp) REVERT: 3 72 MET cc_start: 0.8323 (ttt) cc_final: 0.8073 (ttt) REVERT: 3 186 TYR cc_start: 0.8251 (m-10) cc_final: 0.7876 (m-10) REVERT: 3 239 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6353 (mp) outliers start: 19 outliers final: 15 residues processed: 97 average time/residue: 0.2148 time to fit residues: 30.9561 Evaluate side-chains 100 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 56 HIS Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 315 HIS Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 492 LEU Chi-restraints excluded: chain 3 residue 531 CYS Chi-restraints excluded: chain 3 residue 565 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 28 optimal weight: 0.0000 chunk 92 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 71 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10880 Z= 0.174 Angle : 0.526 7.226 14870 Z= 0.263 Chirality : 0.041 0.144 1725 Planarity : 0.003 0.076 1969 Dihedral : 4.487 35.745 1706 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.72 % Allowed : 16.34 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1500 helix: 2.65 (0.19), residues: 668 sheet: -1.35 (0.42), residues: 131 loop : -1.36 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 2 349 HIS 0.003 0.000 HIS 2 390 PHE 0.017 0.001 PHE 3 164 TYR 0.019 0.001 TYR 2 216 ARG 0.004 0.000 ARG 2 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5510 (OUTLIER) cc_final: 0.4911 (tmm) REVERT: 2 334 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7324 (mp) REVERT: 3 72 MET cc_start: 0.8201 (ttt) cc_final: 0.7915 (ttt) REVERT: 3 186 TYR cc_start: 0.8139 (m-10) cc_final: 0.7752 (m-10) REVERT: 3 239 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6445 (mp) outliers start: 16 outliers final: 11 residues processed: 95 average time/residue: 0.2316 time to fit residues: 32.2412 Evaluate side-chains 94 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 56 HIS Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 492 LEU Chi-restraints excluded: chain 3 residue 531 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 0.9980 chunk 127 optimal weight: 30.0000 chunk 135 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 0.0970 chunk 128 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10880 Z= 0.259 Angle : 0.562 8.204 14870 Z= 0.283 Chirality : 0.042 0.165 1725 Planarity : 0.004 0.077 1969 Dihedral : 4.555 37.165 1706 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.15 % Allowed : 16.02 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1500 helix: 2.63 (0.19), residues: 670 sheet: -1.38 (0.43), residues: 131 loop : -1.37 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 3 554 HIS 0.003 0.001 HIS 2 390 PHE 0.017 0.001 PHE 2 327 TYR 0.012 0.001 TYR 3 256 ARG 0.006 0.000 ARG 2 467 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5491 (OUTLIER) cc_final: 0.4940 (tmm) REVERT: 2 334 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7355 (mp) REVERT: 3 72 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8077 (ttt) REVERT: 3 186 TYR cc_start: 0.8196 (m-10) cc_final: 0.7744 (m-10) REVERT: 3 239 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6503 (mp) outliers start: 20 outliers final: 15 residues processed: 100 average time/residue: 0.2392 time to fit residues: 35.4020 Evaluate side-chains 101 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 331 ARG Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 492 LEU Chi-restraints excluded: chain 3 residue 531 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 150 optimal weight: 40.0000 chunk 138 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 95 optimal weight: 0.5980 chunk 127 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 259 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10880 Z= 0.193 Angle : 0.536 8.030 14870 Z= 0.269 Chirality : 0.041 0.150 1725 Planarity : 0.004 0.076 1969 Dihedral : 4.448 35.169 1706 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.83 % Allowed : 16.45 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1500 helix: 2.72 (0.19), residues: 666 sheet: -1.34 (0.43), residues: 131 loop : -1.34 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 3 355 HIS 0.003 0.000 HIS 2 390 PHE 0.016 0.001 PHE 3 164 TYR 0.010 0.001 TYR 3 256 ARG 0.004 0.000 ARG 2 354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5480 (OUTLIER) cc_final: 0.4898 (tmm) REVERT: 2 334 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7323 (mp) REVERT: 3 186 TYR cc_start: 0.8144 (m-10) cc_final: 0.7750 (m-10) REVERT: 3 239 ILE cc_start: 0.6805 (OUTLIER) cc_final: 0.6480 (mp) outliers start: 17 outliers final: 11 residues processed: 96 average time/residue: 0.2308 time to fit residues: 32.9840 Evaluate side-chains 95 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 492 LEU Chi-restraints excluded: chain 3 residue 531 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 123 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 105 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.188186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124356 restraints weight = 17106.144| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.71 r_work: 0.3466 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10880 Z= 0.224 Angle : 0.548 7.132 14870 Z= 0.275 Chirality : 0.041 0.157 1725 Planarity : 0.004 0.074 1969 Dihedral : 4.424 34.435 1706 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.72 % Allowed : 16.77 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1500 helix: 2.74 (0.19), residues: 666 sheet: -1.37 (0.43), residues: 131 loop : -1.35 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 355 HIS 0.003 0.001 HIS 2 390 PHE 0.015 0.001 PHE 3 164 TYR 0.011 0.001 TYR 3 256 ARG 0.003 0.000 ARG 2 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2288.40 seconds wall clock time: 48 minutes 58.78 seconds (2938.78 seconds total)