Starting phenix.real_space_refine on Sat Jun 14 13:47:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zku_60209/06_2025/8zku_60209.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zku_60209/06_2025/8zku_60209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zku_60209/06_2025/8zku_60209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zku_60209/06_2025/8zku_60209.map" model { file = "/net/cci-nas-00/data/ceres_data/8zku_60209/06_2025/8zku_60209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zku_60209/06_2025/8zku_60209.cif" } resolution = 3.34 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= 0.016 sd= 0.107 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 67 5.16 5 C 10478 2.51 5 N 2752 2.21 5 O 2877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16174 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5555 Classifications: {'peptide': 748} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 31, 'TRANS': 716} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 383 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 7, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 233 Chain: "B" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3932 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3860 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 457} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 2743 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 332} Link IDs: {'PTRANS': 11, 'TRANS': 467} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1286 Unresolved non-hydrogen angles: 1674 Unresolved non-hydrogen dihedrals: 1098 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 19, 'ASN:plan1': 21, 'TRP:plan': 9, 'ASP:plan': 15, 'PHE:plan': 31, 'GLU:plan': 19, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 752 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.43, per 1000 atoms: 0.64 Number of scatterers: 16174 At special positions: 0 Unit cell: (126.092, 168.485, 132.614, 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 67 16.00 O 2877 8.00 N 2752 7.00 C 10478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A3770 " - pdb=" SG CYS A3811 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=1.17 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " 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 B1001 " - " ASN B 375 " " NAG B1002 " - " ASN B 362 " " NAG B1003 " - " ASN B 328 " " NAG C1001 " - " ASN C 375 " " NAG C1002 " - " ASN C 362 " " NAG C1003 " - " ASN C 328 " Time building additional restraints: 4.29 Conformation dependent library (CDL) restraints added in 2.2 seconds 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4118 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 6 sheets defined 55.7% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 3074 through 3106 removed outlier: 3.982A pdb=" N MET A3078 " --> pdb=" O ASN A3074 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A3088 " --> pdb=" O CYS A3084 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A3091 " --> pdb=" O THR A3087 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU A3101 " --> pdb=" O LYS A3097 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A3102 " --> pdb=" O LEU A3098 " (cutoff:3.500A) Processing helix chain 'A' and resid 3244 through 3257 removed outlier: 3.744A pdb=" N LEU A3248 " --> pdb=" O ARG A3244 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A3250 " --> pdb=" O ARG A3246 " (cutoff:3.500A) Processing helix chain 'A' and resid 3262 through 3266 removed outlier: 3.577A pdb=" N SER A3265 " --> pdb=" O ILE A3262 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE A3266 " --> pdb=" O TRP A3263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3262 through 3266' Processing helix chain 'A' and resid 3279 through 3299 Processing helix chain 'A' and resid 3322 through 3345 removed outlier: 3.594A pdb=" N VAL A3333 " --> pdb=" O SER A3329 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR A3334 " --> pdb=" O SER A3330 " (cutoff:3.500A) Proline residue: A3335 - end of helix removed outlier: 4.109A pdb=" N ALA A3339 " --> pdb=" O PRO A3335 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A3340 " --> pdb=" O VAL A3336 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A3343 " --> pdb=" O ALA A3339 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A3345 " --> pdb=" O LEU A3341 " (cutoff:3.500A) Processing helix chain 'A' and resid 3553 through 3577 removed outlier: 4.138A pdb=" N LEU A3557 " --> pdb=" O TRP A3553 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS A3559 " --> pdb=" O ALA A3555 " (cutoff:3.500A) Processing helix chain 'A' and resid 3578 through 3580 No H-bonds generated for 'chain 'A' and resid 3578 through 3580' Processing helix chain 'A' and resid 3581 through 3599 removed outlier: 3.745A pdb=" N SER A3585 " --> pdb=" O PRO A3581 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL A3586 " --> pdb=" O PRO A3582 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA A3587 " --> pdb=" O GLY A3583 " (cutoff:3.500A) Processing helix chain 'A' and resid 3603 through 3618 Processing helix chain 'A' and resid 3656 through 3690 removed outlier: 3.901A pdb=" N LEU A3675 " --> pdb=" O LEU A3671 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A3676 " --> pdb=" O ARG A3672 " (cutoff:3.500A) Processing helix chain 'A' and resid 3693 through 3709 removed outlier: 4.509A pdb=" N HIS A3697 " --> pdb=" O SER A3693 " (cutoff:3.500A) Processing helix chain 'A' and resid 3710 through 3716 Processing helix chain 'A' and resid 3719 through 3721 No H-bonds generated for 'chain 'A' and resid 3719 through 3721' Processing helix chain 'A' and resid 3722 through 3730 Processing helix chain 'A' and resid 3730 through 3736 Processing helix chain 'A' and resid 3826 through 3839 Processing helix chain 'A' and resid 3892 through 3896 removed outlier: 3.732A pdb=" N GLY A3896 " --> pdb=" O LEU A3893 " (cutoff:3.500A) Processing helix chain 'A' and resid 3898 through 3903 Processing helix chain 'A' and resid 3906 through 3926 removed outlier: 4.602A pdb=" N THR A3921 " --> pdb=" O ALA A3917 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP A3922 " --> pdb=" O GLU A3918 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS A3923 " --> pdb=" O ALA A3919 " (cutoff:3.500A) Processing helix chain 'A' and resid 3932 through 3935 Processing helix chain 'A' and resid 3936 through 3970 removed outlier: 3.875A pdb=" N LEU A3941 " --> pdb=" O ALA A3937 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A3943 " --> pdb=" O TRP A3939 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A3952 " --> pdb=" O THR A3948 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A3953 " --> pdb=" O ALA A3949 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A3969 " --> pdb=" O ARG A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3971 through 3973 No H-bonds generated for 'chain 'A' and resid 3971 through 3973' Processing helix chain 'A' and resid 3977 through 4005 removed outlier: 3.680A pdb=" N ARG A3988 " --> pdb=" O SER A3984 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A3992 " --> pdb=" O ARG A3988 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A3993 " --> pdb=" O GLY A3989 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A3995 " --> pdb=" O ALA A3991 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A3996 " --> pdb=" O ALA A3992 " (cutoff:3.500A) Processing helix chain 'A' and resid 4013 through 4037 removed outlier: 4.021A pdb=" N LYS A4017 " --> pdb=" O SER A4013 " (cutoff:3.500A) Proline residue: A4024 - end of helix Processing helix chain 'A' and resid 4100 through 4119 removed outlier: 3.984A pdb=" N VAL A4104 " --> pdb=" O ARG A4100 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A4119 " --> pdb=" O GLY A4115 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.814A pdb=" N VAL B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 221' Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.601A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 275 through 284 removed outlier: 3.572A pdb=" N PHE B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP B 280 " --> pdb=" O MET B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.831A pdb=" N GLU B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 removed outlier: 4.103A pdb=" N ALA B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 493 Processing helix chain 'B' and resid 510 through 531 removed outlier: 3.528A pdb=" N ASN B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 541 removed outlier: 3.847A pdb=" N LEU B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 572 removed outlier: 3.634A pdb=" N ILE B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.702A pdb=" N ILE B 577 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 593 removed outlier: 3.938A pdb=" N LEU B 586 " --> pdb=" O THR B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 620 removed outlier: 3.650A pdb=" N ILE B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 648 through 653 removed outlier: 3.699A pdb=" N ALA B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 removed outlier: 4.166A pdb=" N ILE B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 696 removed outlier: 4.342A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 241 Processing helix chain 'C' and resid 244 through 258 removed outlier: 3.796A pdb=" N TYR C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.638A pdb=" N LEU C 273 " --> pdb=" O PHE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.973A pdb=" N GLU C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 375 removed outlier: 3.655A pdb=" N ASN C 375 " --> pdb=" O LYS C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 412 removed outlier: 4.019A pdb=" N ALA C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 498 Processing helix chain 'C' and resid 509 through 531 removed outlier: 3.856A pdb=" N ASN C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 537 removed outlier: 3.751A pdb=" N GLN C 537 " --> pdb=" O GLU C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 572 removed outlier: 3.954A pdb=" N ILE C 556 " --> pdb=" O ALA C 552 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN C 559 " --> pdb=" O GLN C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.802A pdb=" N ILE C 577 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN C 578 " --> pdb=" O LYS C 575 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE C 579 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 620 removed outlier: 5.045A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 602 " --> pdb=" O PHE C 598 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 642 removed outlier: 3.550A pdb=" N LEU C 641 " --> pdb=" O PHE C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.565A pdb=" N GLU C 650 " --> pdb=" O PHE C 646 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 670 Processing helix chain 'C' and resid 672 through 696 removed outlier: 4.239A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 223 removed outlier: 3.780A pdb=" N GLU D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 242 removed outlier: 4.241A pdb=" N TYR D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 257 Processing helix chain 'D' and resid 275 through 291 Processing helix chain 'D' and resid 363 through 367 removed outlier: 3.698A pdb=" N ILE D 367 " --> pdb=" O THR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 412 removed outlier: 3.872A pdb=" N ASN D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 475 Processing helix chain 'D' and resid 476 through 498 removed outlier: 3.899A pdb=" N PHE D 480 " --> pdb=" O CYS D 476 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU D 493 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 533 removed outlier: 3.820A pdb=" N GLU D 533 " --> pdb=" O THR D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 579 removed outlier: 4.217A pdb=" N TRP D 554 " --> pdb=" O HIS D 550 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLN D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE D 556 " --> pdb=" O ALA D 552 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN D 560 " --> pdb=" O ILE D 556 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D 563 " --> pdb=" O ASN D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 593 through 619 removed outlier: 4.507A pdb=" N LEU D 597 " --> pdb=" O CYS D 593 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 601 " --> pdb=" O LEU D 597 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET D 603 " --> pdb=" O GLY D 599 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D 606 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 641 Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.577A pdb=" N GLU D 650 " --> pdb=" O PHE D 646 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 651 " --> pdb=" O ALA D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 removed outlier: 3.573A pdb=" N TYR D 660 " --> pdb=" O LEU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 698 removed outlier: 4.139A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3135 through 3140 Processing sheet with id=AA2, first strand: chain 'A' and resid 3748 through 3749 removed outlier: 3.706A pdb=" N ARG A3748 " --> pdb=" O GLU A3853 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A3853 " --> pdb=" O ARG A3748 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3748 through 3749 removed outlier: 3.706A pdb=" N ARG A3748 " --> pdb=" O GLU A3853 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A3853 " --> pdb=" O ARG A3748 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.784A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 391 through 394 removed outlier: 7.106A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 421 through 427 removed outlier: 3.775A pdb=" N PHE D 426 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL D 439 " --> pdb=" O PHE D 426 " (cutoff:3.500A) 877 hydrogen bonds defined for protein. 2547 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: 4.55 Time building geometry restraints manager: 5.07 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: 5218 1.34 - 1.46: 4020 1.46 - 1.58: 7193 1.58 - 1.70: 0 1.70 - 1.81: 103 Bond restraints: 16534 Sorted by residual: bond pdb=" C1 NAG C1001 " pdb=" O5 NAG C1001 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1 NAG B1003 " pdb=" O5 NAG B1003 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" C5 NAG C1001 " pdb=" O5 NAG C1001 " ideal model delta sigma weight residual 1.413 1.441 -0.028 2.00e-02 2.50e+03 1.99e+00 bond pdb=" C1 NAG C1003 " pdb=" O5 NAG C1003 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.89e+00 ... (remaining 16529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 22238 2.19 - 4.38: 245 4.38 - 6.57: 35 6.57 - 8.76: 6 8.76 - 10.94: 2 Bond angle restraints: 22526 Sorted by residual: angle pdb=" N VAL C 466 " pdb=" CA VAL C 466 " pdb=" C VAL C 466 " ideal model delta sigma weight residual 113.71 109.91 3.80 9.50e-01 1.11e+00 1.60e+01 angle pdb=" N ARG B 464 " pdb=" CA ARG B 464 " pdb=" C ARG B 464 " ideal model delta sigma weight residual 111.11 115.19 -4.08 1.20e+00 6.94e-01 1.15e+01 angle pdb=" C GLU A3853 " pdb=" N LEU A3854 " pdb=" CA LEU A3854 " ideal model delta sigma weight residual 121.54 115.08 6.46 1.91e+00 2.74e-01 1.14e+01 angle pdb=" N VAL A3767 " pdb=" CA VAL A3767 " pdb=" C VAL A3767 " ideal model delta sigma weight residual 113.07 108.76 4.31 1.36e+00 5.41e-01 1.01e+01 angle pdb=" N THR A3975 " pdb=" CA THR A3975 " pdb=" CB THR A3975 " ideal model delta sigma weight residual 114.17 110.61 3.56 1.14e+00 7.69e-01 9.76e+00 ... (remaining 22521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.31: 9132 23.31 - 46.62: 482 46.62 - 69.92: 54 69.92 - 93.23: 14 93.23 - 116.54: 5 Dihedral angle restraints: 9687 sinusoidal: 3337 harmonic: 6350 Sorted by residual: dihedral pdb=" CB CYS A3770 " pdb=" SG CYS A3770 " pdb=" SG CYS A3811 " pdb=" CB CYS A3811 " ideal model delta sinusoidal sigma weight residual -86.00 0.30 -86.30 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 344 " pdb=" CB CYS B 344 " ideal model delta sinusoidal sigma weight residual 93.00 161.81 -68.81 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CA CYS C 331 " pdb=" C CYS C 331 " pdb=" N SER C 332 " pdb=" CA SER C 332 " ideal model delta harmonic sigma weight residual 180.00 153.11 26.89 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 9684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2028 0.048 - 0.096: 524 0.096 - 0.145: 73 0.145 - 0.193: 3 0.193 - 0.241: 1 Chirality restraints: 2629 Sorted by residual: chirality pdb=" C1 NAG C1001 " pdb=" ND2 ASN C 375 " pdb=" C2 NAG C1001 " pdb=" O5 NAG C1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C2 NAG C1001 " pdb=" C1 NAG C1001 " pdb=" C3 NAG C1001 " pdb=" N2 NAG C1001 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA THR A3276 " pdb=" N THR A3276 " pdb=" C THR A3276 " pdb=" CB THR A3276 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 2626 not shown) Planarity restraints: 2862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 624 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C ASP C 624 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP C 624 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP C 625 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 507 " 0.014 2.00e-02 2.50e+03 1.16e-02 3.38e+00 pdb=" CG TRP C 507 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP C 507 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 507 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 507 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 507 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 507 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 507 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 507 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 507 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO C 658 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " -0.025 5.00e-02 4.00e+02 ... (remaining 2859 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2807 2.76 - 3.30: 15320 3.30 - 3.83: 25398 3.83 - 4.37: 27085 4.37 - 4.90: 49279 Nonbonded interactions: 119889 Sorted by model distance: nonbonded pdb=" OH TYR C 247 " pdb=" OD1 ASP D 624 " model vdw 2.228 3.040 nonbonded pdb=" NH1 ARG A3621 " pdb=" O HIS A3623 " model vdw 2.233 3.120 nonbonded pdb=" OH TYR B 386 " pdb=" OE1 GLU B 444 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR C 227 " pdb=" O VAL C 569 " model vdw 2.269 3.040 nonbonded pdb=" NH1 ARG C 592 " pdb=" OE2 GLU C 686 " model vdw 2.280 3.120 ... (remaining 119884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 217 through 239 and (name N or name CA or name C or name \ O or name CB )) or resid 240 or (resid 241 through 284 and (name N or name CA or \ name C or name O or name CB )) or resid 285 or (resid 286 through 289 and (name \ N or name CA or name C or name O or name CB )) or resid 290 or (resid 291 throu \ gh 294 and (name N or name CA or name C or name O or name CB )) or (resid 314 th \ rough 316 and (name N or name CA or name C or name O or name CB )) or resid 317 \ or (resid 318 through 328 and (name N or name CA or name C or name O or name CB \ )) or resid 329 or (resid 330 through 358 and (name N or name CA or name C or na \ me O or name CB )) or resid 359 or (resid 360 through 362 and (name N or name CA \ or name C or name O or name CB )) or resid 363 or (resid 364 through 375 and (n \ ame N or name CA or name C or name O or name CB )) or resid 376 or (resid 377 th \ rough 380 and (name N or name CA or name C or name O or name CB )) or resid 381 \ or (resid 382 through 387 and (name N or name CA or name C or name O or name CB \ )) or (resid 388 through 417 and (name N or name CA or name C or name O or name \ CB )) or resid 418 or (resid 419 through 448 and (name N or name CA or name C or \ name O or name CB )) or resid 449 through 450 or (resid 451 through 522 and (na \ me N or name CA or name C or name O or name CB )) or resid 523 or (resid 524 thr \ ough 581 and (name N or name CA or name C or name O or name CB )) or resid 582 t \ hrough 698)) selection = (chain 'C' and ((resid 217 through 239 and (name N or name CA or name C or name \ O or name CB )) or resid 240 or (resid 241 through 284 and (name N or name CA or \ name C or name O or name CB )) or resid 285 or (resid 286 through 289 and (name \ N or name CA or name C or name O or name CB )) or resid 290 or (resid 291 throu \ gh 294 and (name N or name CA or name C or name O or name CB )) or (resid 314 th \ rough 316 and (name N or name CA or name C or name O or name CB )) or resid 317 \ or (resid 318 through 328 and (name N or name CA or name C or name O or name CB \ )) or resid 329 or (resid 330 through 358 and (name N or name CA or name C or na \ me O or name CB )) or resid 359 or (resid 360 through 362 and (name N or name CA \ or name C or name O or name CB )) or resid 363 or (resid 364 through 375 and (n \ ame N or name CA or name C or name O or name CB )) or resid 376 or (resid 377 th \ rough 380 and (name N or name CA or name C or name O or name CB )) or resid 381 \ or (resid 382 through 387 and (name N or name CA or name C or name O or name CB \ )) or (resid 388 through 417 and (name N or name CA or name C or name O or name \ CB )) or resid 418 or (resid 419 through 448 and (name N or name CA or name C or \ name O or name CB )) or resid 449 through 450 or (resid 451 through 522 and (na \ me N or name CA or name C or name O or name CB )) or resid 523 or (resid 524 thr \ ough 581 and (name N or name CA or name C or name O or name CB )) or resid 582 t \ hrough 698)) selection = (chain 'D' and (resid 217 through 294 or resid 314 through 698)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.880 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.008 0.861 16543 Z= 0.380 Angle : 0.657 31.427 22550 Z= 0.348 Chirality : 0.042 0.241 2629 Planarity : 0.003 0.044 2856 Dihedral : 14.280 116.540 5560 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.19), residues: 2147 helix: 1.17 (0.16), residues: 1103 sheet: -0.52 (0.41), residues: 189 loop : -2.73 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 507 HIS 0.010 0.001 HIS A3729 PHE 0.023 0.001 PHE A3275 TYR 0.013 0.001 TYR C 239 ARG 0.006 0.000 ARG A3972 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 6) link_NAG-ASN : angle 2.31488 ( 18) hydrogen bonds : bond 0.16509 ( 875) hydrogen bonds : angle 6.02902 ( 2547) SS BOND : bond 0.49686 ( 3) SS BOND : angle 13.10889 ( 6) covalent geometry : bond 0.00405 (16534) covalent geometry : angle 0.61803 (22526) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3607 LYS cc_start: 0.8478 (ttpp) cc_final: 0.7961 (tttm) REVERT: A 3678 MET cc_start: 0.8101 (mmt) cc_final: 0.7699 (mmt) REVERT: A 3972 ARG cc_start: 0.6719 (mtm-85) cc_final: 0.6480 (mtt90) REVERT: C 241 MET cc_start: 0.8505 (ptm) cc_final: 0.8283 (ptt) REVERT: C 622 GLN cc_start: 0.8058 (mt0) cc_final: 0.7833 (mt0) REVERT: D 585 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7866 (tm-30) REVERT: D 589 THR cc_start: 0.6632 (m) cc_final: 0.6357 (m) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2541 time to fit residues: 81.4405 Evaluate side-chains 174 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 8.9990 chunk 162 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 86 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 194 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.181773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124759 restraints weight = 22300.642| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.92 r_work: 0.3260 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 16543 Z= 0.113 Angle : 0.559 10.885 22550 Z= 0.282 Chirality : 0.040 0.225 2629 Planarity : 0.003 0.033 2856 Dihedral : 6.896 94.137 2465 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.80 % Favored : 93.15 % Rotamer: Outliers : 0.89 % Allowed : 6.41 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 2147 helix: 1.54 (0.16), residues: 1125 sheet: -0.63 (0.41), residues: 189 loop : -2.73 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 414 HIS 0.020 0.001 HIS A3729 PHE 0.017 0.001 PHE A3344 TYR 0.010 0.001 TYR B 247 ARG 0.008 0.000 ARG A3621 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 6) link_NAG-ASN : angle 1.97182 ( 18) hydrogen bonds : bond 0.04199 ( 875) hydrogen bonds : angle 4.20886 ( 2547) SS BOND : bond 0.00281 ( 3) SS BOND : angle 1.28838 ( 6) covalent geometry : bond 0.00238 (16534) covalent geometry : angle 0.55610 (22526) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 1.823 Fit side-chains REVERT: A 3607 LYS cc_start: 0.8360 (ttpp) cc_final: 0.7870 (tttm) REVERT: A 3663 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7904 (ttmm) REVERT: A 3678 MET cc_start: 0.8453 (mmt) cc_final: 0.8228 (mmt) REVERT: B 231 LEU cc_start: 0.9093 (tp) cc_final: 0.8760 (tp) REVERT: C 223 GLU cc_start: 0.7271 (mp0) cc_final: 0.7049 (mp0) REVERT: C 537 GLN cc_start: 0.7756 (pp30) cc_final: 0.7489 (pp30) outliers start: 13 outliers final: 8 residues processed: 189 average time/residue: 0.2564 time to fit residues: 76.0640 Evaluate side-chains 176 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3104 SER Chi-restraints excluded: chain A residue 3340 ILE Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 602 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 133 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 167 optimal weight: 50.0000 chunk 182 optimal weight: 50.0000 chunk 175 optimal weight: 0.0060 chunk 46 optimal weight: 20.0000 chunk 146 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3559 HIS A3729 HIS B 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.180380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124135 restraints weight = 22307.412| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.81 r_work: 0.3238 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16543 Z= 0.130 Angle : 0.541 10.782 22550 Z= 0.275 Chirality : 0.041 0.243 2629 Planarity : 0.003 0.039 2856 Dihedral : 6.072 87.040 2465 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.47 % Favored : 93.48 % Rotamer: Outliers : 1.43 % Allowed : 9.88 % Favored : 88.68 % 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: -0.24 (0.19), residues: 2147 helix: 1.68 (0.16), residues: 1120 sheet: -0.68 (0.40), residues: 191 loop : -2.76 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 414 HIS 0.017 0.001 HIS A3729 PHE 0.012 0.001 PHE B 670 TYR 0.012 0.001 TYR C 486 ARG 0.006 0.000 ARG A3621 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 6) link_NAG-ASN : angle 2.35072 ( 18) hydrogen bonds : bond 0.04113 ( 875) hydrogen bonds : angle 3.95640 ( 2547) SS BOND : bond 0.00163 ( 3) SS BOND : angle 1.02166 ( 6) covalent geometry : bond 0.00297 (16534) covalent geometry : angle 0.53729 (22526) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 1.877 Fit side-chains revert: symmetry clash REVERT: A 3607 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8110 (tttp) REVERT: A 3663 LYS cc_start: 0.8192 (ttmm) cc_final: 0.7916 (ttmm) REVERT: B 231 LEU cc_start: 0.9128 (tp) cc_final: 0.8776 (tp) REVERT: C 223 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: C 537 GLN cc_start: 0.7903 (pp30) cc_final: 0.7486 (pp30) REVERT: C 622 GLN cc_start: 0.8674 (mt0) cc_final: 0.8315 (mt0) REVERT: C 686 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8206 (tt0) REVERT: D 603 MET cc_start: 0.8504 (ppp) cc_final: 0.8278 (ppp) outliers start: 21 outliers final: 17 residues processed: 184 average time/residue: 0.2522 time to fit residues: 74.6797 Evaluate side-chains 181 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3089 MET Chi-restraints excluded: chain A residue 3340 ILE Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3820 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 344 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 141 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 40.0000 chunk 36 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.176526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114988 restraints weight = 22413.027| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.19 r_work: 0.3225 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16543 Z= 0.245 Angle : 0.630 10.871 22550 Z= 0.322 Chirality : 0.044 0.245 2629 Planarity : 0.004 0.068 2856 Dihedral : 5.925 79.238 2465 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.87 % Favored : 92.08 % Rotamer: Outliers : 2.18 % Allowed : 11.72 % Favored : 86.09 % 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: -0.46 (0.19), residues: 2147 helix: 1.44 (0.16), residues: 1130 sheet: -0.83 (0.39), residues: 193 loop : -2.82 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 414 HIS 0.019 0.002 HIS A3729 PHE 0.023 0.002 PHE B 670 TYR 0.015 0.002 TYR B 348 ARG 0.005 0.000 ARG A3621 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 6) link_NAG-ASN : angle 2.88564 ( 18) hydrogen bonds : bond 0.05087 ( 875) hydrogen bonds : angle 4.11173 ( 2547) SS BOND : bond 0.00167 ( 3) SS BOND : angle 1.24741 ( 6) covalent geometry : bond 0.00597 (16534) covalent geometry : angle 0.62485 (22526) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 1.863 Fit side-chains REVERT: A 3268 ASP cc_start: 0.8897 (t0) cc_final: 0.8670 (t0) REVERT: A 3346 MET cc_start: 0.8515 (ptt) cc_final: 0.8270 (ptt) REVERT: A 3607 LYS cc_start: 0.8460 (ttpp) cc_final: 0.8099 (tttp) REVERT: A 3611 GLU cc_start: 0.8450 (tp30) cc_final: 0.8103 (tp30) REVERT: B 338 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7562 (mtp85) REVERT: B 477 GLU cc_start: 0.4714 (mm-30) cc_final: 0.3452 (mm-30) REVERT: C 223 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: D 585 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8228 (tm-30) REVERT: D 589 THR cc_start: 0.7057 (m) cc_final: 0.6835 (m) REVERT: D 603 MET cc_start: 0.8801 (ppp) cc_final: 0.8491 (ppp) outliers start: 32 outliers final: 25 residues processed: 191 average time/residue: 0.2397 time to fit residues: 72.7173 Evaluate side-chains 187 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3073 VAL Chi-restraints excluded: chain A residue 3089 MET Chi-restraints excluded: chain A residue 3104 SER Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3584 VAL Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 3739 GLN Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3820 VAL Chi-restraints excluded: chain A residue 3854 LEU Chi-restraints excluded: chain A residue 3868 THR Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 690 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 119 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 195 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3729 HIS ** 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 = 0.4172 r_free = 0.4172 target = 0.178508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.118548 restraints weight = 22567.618| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.70 r_work: 0.3220 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16543 Z= 0.158 Angle : 0.567 11.644 22550 Z= 0.287 Chirality : 0.041 0.262 2629 Planarity : 0.003 0.048 2856 Dihedral : 5.500 64.918 2465 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.94 % Favored : 93.01 % Rotamer: Outliers : 2.45 % Allowed : 12.27 % Favored : 85.28 % 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: -0.31 (0.19), residues: 2147 helix: 1.55 (0.16), residues: 1138 sheet: -0.74 (0.39), residues: 191 loop : -2.76 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 414 HIS 0.011 0.001 HIS A3729 PHE 0.014 0.001 PHE B 670 TYR 0.011 0.001 TYR B 348 ARG 0.005 0.000 ARG A3621 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 6) link_NAG-ASN : angle 2.98762 ( 18) hydrogen bonds : bond 0.04333 ( 875) hydrogen bonds : angle 3.92700 ( 2547) SS BOND : bond 0.00161 ( 3) SS BOND : angle 1.05031 ( 6) covalent geometry : bond 0.00375 (16534) covalent geometry : angle 0.56071 (22526) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 1.766 Fit side-chains REVERT: A 3268 ASP cc_start: 0.8926 (t0) cc_final: 0.8653 (t0) REVERT: A 3275 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.7031 (t80) REVERT: A 3607 LYS cc_start: 0.8333 (ttpp) cc_final: 0.7986 (tttp) REVERT: A 3611 GLU cc_start: 0.8484 (tp30) cc_final: 0.8213 (tp30) REVERT: B 338 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7543 (mtp85) REVERT: B 477 GLU cc_start: 0.4687 (mm-30) cc_final: 0.3396 (mm-30) REVERT: C 340 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7494 (mt-10) REVERT: D 589 THR cc_start: 0.6972 (m) cc_final: 0.6730 (m) REVERT: D 603 MET cc_start: 0.8807 (ppp) cc_final: 0.8437 (ppp) outliers start: 36 outliers final: 29 residues processed: 187 average time/residue: 0.2348 time to fit residues: 69.5693 Evaluate side-chains 191 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3104 SER Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3584 VAL Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3820 VAL Chi-restraints excluded: chain A residue 3854 LEU Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain A residue 4031 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 690 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 209 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 155 optimal weight: 0.0000 chunk 90 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 78 optimal weight: 0.4980 chunk 4 optimal weight: 20.0000 chunk 145 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.181761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125486 restraints weight = 22369.717| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.64 r_work: 0.3290 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 16543 Z= 0.103 Angle : 0.521 10.759 22550 Z= 0.262 Chirality : 0.039 0.298 2629 Planarity : 0.003 0.043 2856 Dihedral : 4.889 59.248 2465 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.11 % Allowed : 13.77 % Favored : 84.12 % 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: -0.03 (0.19), residues: 2147 helix: 1.82 (0.16), residues: 1130 sheet: -0.54 (0.40), residues: 189 loop : -2.68 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 380 HIS 0.011 0.001 HIS A3729 PHE 0.011 0.001 PHE A3600 TYR 0.009 0.001 TYR B 247 ARG 0.012 0.000 ARG A3621 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 6) link_NAG-ASN : angle 3.48467 ( 18) hydrogen bonds : bond 0.03506 ( 875) hydrogen bonds : angle 3.72240 ( 2547) SS BOND : bond 0.00153 ( 3) SS BOND : angle 0.86214 ( 6) covalent geometry : bond 0.00220 (16534) covalent geometry : angle 0.51194 (22526) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.891 Fit side-chains revert: symmetry clash REVERT: A 3268 ASP cc_start: 0.8981 (t0) cc_final: 0.8730 (t0) REVERT: A 3275 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.7113 (t80) REVERT: A 3607 LYS cc_start: 0.8383 (ttpp) cc_final: 0.8003 (tttp) REVERT: A 3611 GLU cc_start: 0.8477 (tp30) cc_final: 0.8205 (tp30) REVERT: B 231 LEU cc_start: 0.9171 (tp) cc_final: 0.8811 (tp) REVERT: B 338 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7499 (mtp85) REVERT: B 477 GLU cc_start: 0.5094 (mm-30) cc_final: 0.3926 (tp30) REVERT: C 223 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: C 253 MET cc_start: 0.8535 (tpp) cc_final: 0.8311 (mmt) REVERT: C 340 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7327 (mt-10) REVERT: D 585 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7992 (tm-30) REVERT: D 589 THR cc_start: 0.7065 (m) cc_final: 0.6679 (m) REVERT: D 603 MET cc_start: 0.8746 (ppp) cc_final: 0.8389 (ppp) REVERT: D 695 LYS cc_start: 0.7793 (tptm) cc_final: 0.7542 (tppt) outliers start: 31 outliers final: 20 residues processed: 186 average time/residue: 0.2563 time to fit residues: 75.7859 Evaluate side-chains 182 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3073 VAL Chi-restraints excluded: chain A residue 3104 SER Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3340 ILE Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3820 VAL Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 344 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 79 optimal weight: 0.0060 chunk 195 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 186 optimal weight: 40.0000 chunk 157 optimal weight: 0.4980 chunk 126 optimal weight: 5.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.182526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126005 restraints weight = 22305.126| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.79 r_work: 0.3275 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16543 Z= 0.099 Angle : 0.507 10.785 22550 Z= 0.255 Chirality : 0.039 0.225 2629 Planarity : 0.003 0.046 2856 Dihedral : 4.453 57.561 2465 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.04 % Allowed : 14.38 % Favored : 83.57 % 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: 0.13 (0.19), residues: 2147 helix: 1.95 (0.16), residues: 1130 sheet: -0.22 (0.41), residues: 184 loop : -2.67 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3724 HIS 0.010 0.001 HIS A3729 PHE 0.011 0.001 PHE A3600 TYR 0.009 0.001 TYR B 247 ARG 0.004 0.000 ARG A3621 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 6) link_NAG-ASN : angle 2.92719 ( 18) hydrogen bonds : bond 0.03329 ( 875) hydrogen bonds : angle 3.62555 ( 2547) SS BOND : bond 0.00150 ( 3) SS BOND : angle 0.79322 ( 6) covalent geometry : bond 0.00213 (16534) covalent geometry : angle 0.50055 (22526) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.764 Fit side-chains revert: symmetry clash REVERT: A 3268 ASP cc_start: 0.8858 (t0) cc_final: 0.8640 (t0) REVERT: A 3607 LYS cc_start: 0.8337 (ttpp) cc_final: 0.7954 (tttp) REVERT: A 3611 GLU cc_start: 0.8504 (tp30) cc_final: 0.8253 (tp30) REVERT: B 231 LEU cc_start: 0.9060 (tp) cc_final: 0.8694 (tp) REVERT: B 338 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7462 (mtp85) REVERT: B 477 GLU cc_start: 0.4747 (mm-30) cc_final: 0.3708 (tp30) REVERT: C 223 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: C 253 MET cc_start: 0.8354 (tpp) cc_final: 0.8118 (mmt) REVERT: C 340 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7411 (mt-10) REVERT: C 490 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6582 (mp0) REVERT: D 585 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7885 (tm-30) REVERT: D 589 THR cc_start: 0.6764 (m) cc_final: 0.6353 (m) REVERT: D 603 MET cc_start: 0.8537 (ppp) cc_final: 0.8133 (ppp) REVERT: D 698 MET cc_start: 0.5645 (ppp) cc_final: 0.5316 (mmp) outliers start: 30 outliers final: 23 residues processed: 189 average time/residue: 0.2430 time to fit residues: 72.7742 Evaluate side-chains 189 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3073 VAL Chi-restraints excluded: chain A residue 3104 SER Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3340 ILE Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3820 VAL Chi-restraints excluded: chain A residue 3854 LEU Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 586 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 152 optimal weight: 0.0010 chunk 42 optimal weight: 3.9990 chunk 79 optimal weight: 0.0570 chunk 207 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.6506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.183084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126518 restraints weight = 22250.727| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.54 r_work: 0.3306 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16543 Z= 0.098 Angle : 0.512 10.793 22550 Z= 0.255 Chirality : 0.039 0.233 2629 Planarity : 0.003 0.041 2856 Dihedral : 4.382 58.598 2465 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.25 % Allowed : 14.59 % Favored : 83.16 % 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: 0.29 (0.19), residues: 2147 helix: 2.09 (0.16), residues: 1121 sheet: -0.04 (0.42), residues: 175 loop : -2.54 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A3724 HIS 0.011 0.001 HIS A3729 PHE 0.011 0.001 PHE A3600 TYR 0.008 0.001 TYR B 247 ARG 0.006 0.000 ARG A3972 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 6) link_NAG-ASN : angle 2.84880 ( 18) hydrogen bonds : bond 0.03227 ( 875) hydrogen bonds : angle 3.56089 ( 2547) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.76414 ( 6) covalent geometry : bond 0.00211 (16534) covalent geometry : angle 0.50533 (22526) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.689 Fit side-chains revert: symmetry clash REVERT: A 3607 LYS cc_start: 0.8464 (ttpp) cc_final: 0.8025 (tttp) REVERT: A 3611 GLU cc_start: 0.8550 (tp30) cc_final: 0.8321 (tp30) REVERT: B 231 LEU cc_start: 0.9135 (tp) cc_final: 0.8791 (tp) REVERT: B 338 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7403 (mtp85) REVERT: B 477 GLU cc_start: 0.5176 (mm-30) cc_final: 0.4026 (tp30) REVERT: C 223 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: C 253 MET cc_start: 0.8499 (tpp) cc_final: 0.8270 (mmt) REVERT: D 585 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7817 (tm-30) REVERT: D 589 THR cc_start: 0.6803 (m) cc_final: 0.6365 (m) REVERT: D 603 MET cc_start: 0.8674 (ppp) cc_final: 0.8328 (ppp) REVERT: D 682 ASP cc_start: 0.8638 (t0) cc_final: 0.8395 (t0) REVERT: D 698 MET cc_start: 0.5649 (ppp) cc_final: 0.5395 (mmp) outliers start: 33 outliers final: 25 residues processed: 191 average time/residue: 0.2358 time to fit residues: 71.9521 Evaluate side-chains 191 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3073 VAL Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3340 ILE Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3584 VAL Chi-restraints excluded: chain A residue 3617 LEU Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3820 VAL Chi-restraints excluded: chain A residue 3854 LEU Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 586 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 65 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 147 optimal weight: 0.0270 chunk 5 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 6 optimal weight: 50.0000 chunk 47 optimal weight: 20.0000 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.182205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124406 restraints weight = 22388.158| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.83 r_work: 0.3292 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16543 Z= 0.107 Angle : 0.519 10.782 22550 Z= 0.259 Chirality : 0.039 0.234 2629 Planarity : 0.003 0.039 2856 Dihedral : 4.357 58.493 2465 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.98 % Allowed : 15.34 % Favored : 82.69 % 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: 0.31 (0.19), residues: 2147 helix: 2.11 (0.16), residues: 1121 sheet: -0.05 (0.42), residues: 175 loop : -2.55 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 507 HIS 0.011 0.001 HIS A3729 PHE 0.011 0.001 PHE A3600 TYR 0.008 0.001 TYR B 247 ARG 0.006 0.000 ARG A3972 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 6) link_NAG-ASN : angle 2.82115 ( 18) hydrogen bonds : bond 0.03389 ( 875) hydrogen bonds : angle 3.55391 ( 2547) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.81520 ( 6) covalent geometry : bond 0.00241 (16534) covalent geometry : angle 0.51299 (22526) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.863 Fit side-chains REVERT: A 3607 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8033 (tttp) REVERT: A 3611 GLU cc_start: 0.8488 (tp30) cc_final: 0.8284 (tp30) REVERT: B 231 LEU cc_start: 0.9082 (tp) cc_final: 0.8715 (tp) REVERT: B 338 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7434 (mtp85) REVERT: B 477 GLU cc_start: 0.5069 (mm-30) cc_final: 0.4091 (tp30) REVERT: C 223 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: C 253 MET cc_start: 0.8343 (tpp) cc_final: 0.8077 (mmt) REVERT: C 413 VAL cc_start: 0.8179 (t) cc_final: 0.7791 (p) REVERT: D 585 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7757 (tm-30) REVERT: D 589 THR cc_start: 0.6789 (m) cc_final: 0.6365 (m) REVERT: D 603 MET cc_start: 0.8500 (ppp) cc_final: 0.8128 (ppp) outliers start: 29 outliers final: 25 residues processed: 187 average time/residue: 0.2492 time to fit residues: 75.0622 Evaluate side-chains 191 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3073 VAL Chi-restraints excluded: chain A residue 3104 SER Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3340 ILE Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3584 VAL Chi-restraints excluded: chain A residue 3617 LEU Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3820 VAL Chi-restraints excluded: chain A residue 3854 LEU Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 586 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 188 optimal weight: 50.0000 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 211 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.181317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123844 restraints weight = 22536.523| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.80 r_work: 0.3271 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16543 Z= 0.121 Angle : 0.536 10.797 22550 Z= 0.268 Chirality : 0.040 0.234 2629 Planarity : 0.003 0.039 2856 Dihedral : 4.389 56.371 2465 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.84 % Allowed : 15.81 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.19), residues: 2147 helix: 2.09 (0.16), residues: 1125 sheet: -0.06 (0.42), residues: 175 loop : -2.59 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3724 HIS 0.011 0.001 HIS A3729 PHE 0.011 0.001 PHE D 604 TYR 0.014 0.001 TYR C 486 ARG 0.007 0.000 ARG A3972 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 6) link_NAG-ASN : angle 3.33898 ( 18) hydrogen bonds : bond 0.03563 ( 875) hydrogen bonds : angle 3.57658 ( 2547) SS BOND : bond 0.00141 ( 3) SS BOND : angle 0.86463 ( 6) covalent geometry : bond 0.00280 (16534) covalent geometry : angle 0.52803 (22526) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.676 Fit side-chains REVERT: A 3607 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8011 (tttp) REVERT: A 3611 GLU cc_start: 0.8519 (tp30) cc_final: 0.8304 (tp30) REVERT: B 231 LEU cc_start: 0.9062 (tp) cc_final: 0.8704 (tp) REVERT: B 338 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7444 (mtp85) REVERT: B 477 GLU cc_start: 0.4817 (mm-30) cc_final: 0.3574 (mm-30) REVERT: C 223 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: C 253 MET cc_start: 0.8356 (tpp) cc_final: 0.8092 (mmt) REVERT: C 413 VAL cc_start: 0.8250 (t) cc_final: 0.7844 (p) REVERT: D 585 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7746 (tm-30) REVERT: D 589 THR cc_start: 0.6880 (m) cc_final: 0.6435 (m) REVERT: D 590 MET cc_start: 0.7511 (ppp) cc_final: 0.7269 (ppp) REVERT: D 603 MET cc_start: 0.8503 (ppp) cc_final: 0.8108 (ppp) outliers start: 27 outliers final: 24 residues processed: 185 average time/residue: 0.2453 time to fit residues: 72.9896 Evaluate side-chains 188 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3073 VAL Chi-restraints excluded: chain A residue 3104 SER Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3340 ILE Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3584 VAL Chi-restraints excluded: chain A residue 3617 LEU Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3820 VAL Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 586 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 183 optimal weight: 30.0000 chunk 32 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 136 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.183394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126182 restraints weight = 22233.216| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.83 r_work: 0.3318 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16543 Z= 0.098 Angle : 0.520 10.857 22550 Z= 0.260 Chirality : 0.039 0.232 2629 Planarity : 0.003 0.043 2856 Dihedral : 4.337 59.315 2465 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.77 % Allowed : 15.95 % Favored : 82.28 % 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: 0.44 (0.19), residues: 2147 helix: 2.26 (0.16), residues: 1116 sheet: 0.03 (0.42), residues: 175 loop : -2.52 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 507 HIS 0.010 0.001 HIS A3729 PHE 0.010 0.001 PHE A3600 TYR 0.009 0.001 TYR B 247 ARG 0.006 0.000 ARG A3972 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 6) link_NAG-ASN : angle 2.68548 ( 18) hydrogen bonds : bond 0.03162 ( 875) hydrogen bonds : angle 3.51147 ( 2547) SS BOND : bond 0.00142 ( 3) SS BOND : angle 0.81154 ( 6) covalent geometry : bond 0.00210 (16534) covalent geometry : angle 0.51447 (22526) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9238.78 seconds wall clock time: 159 minutes 4.81 seconds (9544.81 seconds total)