Starting phenix.real_space_refine on Thu Sep 18 11:00:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zku_60209/09_2025/8zku_60209.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zku_60209/09_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_60209/09_2025/8zku_60209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zku_60209/09_2025/8zku_60209.map" model { file = "/net/cci-nas-00/data/ceres_data/8zku_60209/09_2025/8zku_60209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zku_60209/09_2025/8zku_60209.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 10, 'PHE:plan': 6, 'TYR:plan': 2, 'GLU:plan': 3, 'TRP:plan': 5, 'HIS:plan': 7, 'ASP:plan': 7, 'ASN:plan1': 4, 'GLN:plan1': 2} 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: {'ARG:plan': 20, 'GLU:plan': 19, 'TYR:plan': 19, 'PHE:plan': 31, 'ASN:plan1': 21, 'GLN:plan1': 12, 'ASP:plan': 15, 'TRP:plan': 9, 'HIS:plan': 4} 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: 3.37, per 1000 atoms: 0.21 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: 1.06 Conformation dependent library (CDL) restraints added in 692.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.33 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: 2.46 Time building geometry restraints manager: 1.52 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: 0.880 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.430 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.220 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG A3972 TYR 0.013 0.001 TYR C 239 PHE 0.023 0.001 PHE A3275 TRP 0.031 0.001 TRP C 507 HIS 0.010 0.001 HIS A3729 Details of bonding type rmsd covalent geometry : bond 0.00405 (16534) covalent geometry : angle 0.61803 (22526) SS BOND : bond 0.49686 ( 3) SS BOND : angle 13.10889 ( 6) hydrogen bonds : bond 0.16509 ( 875) hydrogen bonds : angle 6.02902 ( 2547) link_NAG-ASN : bond 0.00349 ( 6) link_NAG-ASN : angle 2.31488 ( 18) *********************** 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 : 0.378 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: 0.1014 time to fit residues: 32.6816 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 : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 0.0980 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 50.0000 chunk 212 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3729 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.181904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.124113 restraints weight = 22453.533| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.83 r_work: 0.3280 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0993 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= 0.112 Angle : 0.557 10.886 22550 Z= 0.280 Chirality : 0.040 0.241 2629 Planarity : 0.003 0.033 2856 Dihedral : 6.903 94.431 2465 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.82 % Allowed : 6.54 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.19), residues: 2147 helix: 1.55 (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 ARG 0.007 0.000 ARG A3621 TYR 0.010 0.001 TYR B 247 PHE 0.017 0.001 PHE A3344 TRP 0.014 0.001 TRP B 414 HIS 0.021 0.001 HIS A3729 Details of bonding type rmsd covalent geometry : bond 0.00234 (16534) covalent geometry : angle 0.55421 (22526) SS BOND : bond 0.00317 ( 3) SS BOND : angle 1.32017 ( 6) hydrogen bonds : bond 0.04189 ( 875) hydrogen bonds : angle 4.20528 ( 2547) link_NAG-ASN : bond 0.00346 ( 6) link_NAG-ASN : angle 1.96557 ( 18) *********************** 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: 12 poor density : 183 time to evaluate : 0.486 Fit side-chains REVERT: A 3607 LYS cc_start: 0.8413 (ttpp) cc_final: 0.7904 (tttm) REVERT: A 3663 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7958 (ttmm) REVERT: A 3678 MET cc_start: 0.8412 (mmt) cc_final: 0.8198 (mmt) REVERT: B 231 LEU cc_start: 0.9130 (tp) cc_final: 0.8788 (tp) REVERT: C 241 MET cc_start: 0.8515 (ptm) cc_final: 0.8304 (ptt) REVERT: C 537 GLN cc_start: 0.7778 (pp30) cc_final: 0.7504 (pp30) outliers start: 12 outliers final: 7 residues processed: 189 average time/residue: 0.0973 time to fit residues: 29.2205 Evaluate side-chains 176 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 63 optimal weight: 0.8980 chunk 190 optimal weight: 20.0000 chunk 171 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 188 optimal weight: 30.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3559 HIS ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.179676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124309 restraints weight = 22607.740| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.90 r_work: 0.3264 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1137 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= 0.146 Angle : 0.558 10.778 22550 Z= 0.284 Chirality : 0.041 0.241 2629 Planarity : 0.003 0.043 2856 Dihedral : 6.156 87.371 2465 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.57 % Favored : 93.39 % Rotamer: Outliers : 1.57 % Allowed : 9.82 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.19), residues: 2147 helix: 1.65 (0.16), residues: 1120 sheet: -0.71 (0.40), residues: 191 loop : -2.77 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3621 TYR 0.012 0.001 TYR C 486 PHE 0.014 0.001 PHE B 670 TRP 0.011 0.001 TRP B 414 HIS 0.005 0.001 HIS A3729 Details of bonding type rmsd covalent geometry : bond 0.00341 (16534) covalent geometry : angle 0.55413 (22526) SS BOND : bond 0.00115 ( 3) SS BOND : angle 1.08500 ( 6) hydrogen bonds : bond 0.04278 ( 875) hydrogen bonds : angle 4.01835 ( 2547) link_NAG-ASN : bond 0.00275 ( 6) link_NAG-ASN : angle 2.42377 ( 18) *********************** 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 198 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3607 LYS cc_start: 0.8414 (ttpp) cc_final: 0.8106 (tttp) REVERT: A 3663 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7876 (ttmm) REVERT: B 231 LEU cc_start: 0.9116 (tp) cc_final: 0.8765 (tp) REVERT: C 622 GLN cc_start: 0.8647 (mt0) cc_final: 0.8329 (mt0) REVERT: C 686 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8120 (tt0) REVERT: D 603 MET cc_start: 0.8453 (ppp) cc_final: 0.8219 (ppp) outliers start: 23 outliers final: 20 residues processed: 187 average time/residue: 0.1108 time to fit residues: 32.4913 Evaluate side-chains 186 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain D residue 591 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 94 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 185 optimal weight: 50.0000 chunk 39 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 195 optimal weight: 50.0000 chunk 79 optimal weight: 0.0570 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.180504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125295 restraints weight = 22493.876| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.80 r_work: 0.3278 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1326 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= 0.128 Angle : 0.544 10.831 22550 Z= 0.274 Chirality : 0.040 0.259 2629 Planarity : 0.003 0.043 2856 Dihedral : 5.695 80.104 2465 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.75 % Favored : 93.20 % Rotamer: Outliers : 2.18 % Allowed : 11.04 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.19), residues: 2147 helix: 1.72 (0.16), residues: 1126 sheet: -0.71 (0.39), residues: 191 loop : -2.72 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3621 TYR 0.010 0.001 TYR B 348 PHE 0.011 0.001 PHE B 670 TRP 0.010 0.001 TRP B 414 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00295 (16534) covalent geometry : angle 0.53880 (22526) SS BOND : bond 0.00148 ( 3) SS BOND : angle 0.87899 ( 6) hydrogen bonds : bond 0.03937 ( 875) hydrogen bonds : angle 3.86606 ( 2547) link_NAG-ASN : bond 0.00278 ( 6) link_NAG-ASN : angle 2.58335 ( 18) *********************** 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 210 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 3268 ASP cc_start: 0.8776 (t0) cc_final: 0.8544 (t0) REVERT: A 3346 MET cc_start: 0.8473 (ptt) cc_final: 0.8226 (ptt) REVERT: A 3607 LYS cc_start: 0.8392 (ttpp) cc_final: 0.8042 (tttp) REVERT: B 231 LEU cc_start: 0.9114 (tp) cc_final: 0.8758 (tp) REVERT: C 622 GLN cc_start: 0.8603 (mt0) cc_final: 0.8255 (mt0) REVERT: C 686 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7994 (tt0) REVERT: D 589 THR cc_start: 0.6971 (m) cc_final: 0.6763 (m) REVERT: D 590 MET cc_start: 0.7862 (ppp) cc_final: 0.7527 (ppp) REVERT: D 603 MET cc_start: 0.8549 (ppp) cc_final: 0.8257 (ppp) outliers start: 32 outliers final: 23 residues processed: 195 average time/residue: 0.1033 time to fit residues: 32.2137 Evaluate side-chains 185 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 3340 ILE 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 3820 VAL 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 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 C residue 413 VAL Chi-restraints excluded: chain D residue 625 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 127 optimal weight: 0.4980 chunk 160 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 199 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 191 optimal weight: 0.9980 chunk 182 optimal weight: 50.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 ASN D 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.182544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122963 restraints weight = 22483.883| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.70 r_work: 0.3292 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1539 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= 0.102 Angle : 0.524 11.591 22550 Z= 0.261 Chirality : 0.039 0.270 2629 Planarity : 0.003 0.041 2856 Dihedral : 5.187 64.936 2465 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.77 % Allowed : 12.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.19), residues: 2147 helix: 1.88 (0.16), residues: 1127 sheet: -0.36 (0.41), residues: 178 loop : -2.72 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3972 TYR 0.014 0.001 TYR C 486 PHE 0.009 0.001 PHE A4008 TRP 0.007 0.001 TRP B 414 HIS 0.006 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00221 (16534) covalent geometry : angle 0.51768 (22526) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.78987 ( 6) hydrogen bonds : bond 0.03464 ( 875) hydrogen bonds : angle 3.72365 ( 2547) link_NAG-ASN : bond 0.00249 ( 6) link_NAG-ASN : angle 2.82957 ( 18) *********************** 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 191 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 3268 ASP cc_start: 0.8987 (t0) cc_final: 0.8715 (t0) REVERT: A 3607 LYS cc_start: 0.8338 (ttpp) cc_final: 0.7978 (tttp) REVERT: A 3611 GLU cc_start: 0.8502 (tp30) cc_final: 0.8197 (tp30) REVERT: B 231 LEU cc_start: 0.9178 (tp) cc_final: 0.8824 (tp) REVERT: B 338 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7485 (mtp85) REVERT: D 603 MET cc_start: 0.8686 (ppp) cc_final: 0.8388 (ppp) REVERT: D 682 ASP cc_start: 0.8751 (t0) cc_final: 0.8531 (t0) REVERT: D 695 LYS cc_start: 0.7736 (tptm) cc_final: 0.7466 (tppt) outliers start: 26 outliers final: 23 residues processed: 179 average time/residue: 0.1053 time to fit residues: 30.2536 Evaluate side-chains 182 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 413 VAL Chi-restraints excluded: chain D residue 585 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 105 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 144 optimal weight: 0.4980 chunk 192 optimal weight: 9.9990 chunk 185 optimal weight: 50.0000 chunk 106 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.4379 r_free = 0.4379 target = 0.191607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132422 restraints weight = 22689.563| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.28 r_work: 0.3540 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1585 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= 0.120 Angle : 0.536 10.834 22550 Z= 0.267 Chirality : 0.040 0.280 2629 Planarity : 0.003 0.040 2856 Dihedral : 4.976 59.207 2465 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.32 % Allowed : 13.36 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.19), residues: 2147 helix: 1.90 (0.16), residues: 1128 sheet: -0.55 (0.40), residues: 188 loop : -2.71 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A3621 TYR 0.009 0.001 TYR B 348 PHE 0.011 0.001 PHE D 604 TRP 0.007 0.001 TRP B 414 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00275 (16534) covalent geometry : angle 0.52767 (22526) SS BOND : bond 0.00104 ( 3) SS BOND : angle 0.85653 ( 6) hydrogen bonds : bond 0.03635 ( 875) hydrogen bonds : angle 3.69795 ( 2547) link_NAG-ASN : bond 0.00178 ( 6) link_NAG-ASN : angle 3.37188 ( 18) *********************** 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 198 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3268 ASP cc_start: 0.9002 (t0) cc_final: 0.8757 (t0) REVERT: A 3275 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.7112 (t80) REVERT: A 3607 LYS cc_start: 0.8379 (ttpp) cc_final: 0.7994 (tttp) REVERT: A 3611 GLU cc_start: 0.8563 (tp30) cc_final: 0.8215 (tp30) REVERT: B 231 LEU cc_start: 0.9189 (tp) cc_final: 0.8838 (tp) REVERT: B 338 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7512 (mtp85) REVERT: C 239 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.5409 (t80) REVERT: C 253 MET cc_start: 0.8496 (tpp) cc_final: 0.8267 (mmt) REVERT: C 622 GLN cc_start: 0.8862 (mt0) cc_final: 0.8455 (mt0) REVERT: D 603 MET cc_start: 0.8761 (ppp) cc_final: 0.8467 (ppp) REVERT: D 698 MET cc_start: 0.5800 (ppp) cc_final: 0.5159 (mmm) outliers start: 34 outliers final: 27 residues processed: 184 average time/residue: 0.0994 time to fit residues: 29.6606 Evaluate side-chains 190 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 3340 ILE 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 3615 PHE 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 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 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 239 TYR 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 413 VAL Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 676 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 182 optimal weight: 50.0000 chunk 23 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 192 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 205 optimal weight: 0.0030 chunk 213 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.9592 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.192508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.133470 restraints weight = 22588.108| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.29 r_work: 0.3560 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1702 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 : 0.514 10.915 22550 Z= 0.258 Chirality : 0.039 0.222 2629 Planarity : 0.003 0.039 2856 Dihedral : 4.456 57.625 2465 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.11 % Allowed : 14.04 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.19), residues: 2147 helix: 2.03 (0.16), residues: 1122 sheet: -0.34 (0.41), residues: 180 loop : -2.72 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 338 TYR 0.008 0.001 TYR B 247 PHE 0.010 0.001 PHE D 604 TRP 0.007 0.001 TRP A3922 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00238 (16534) covalent geometry : angle 0.50727 (22526) SS BOND : bond 0.00134 ( 3) SS BOND : angle 0.81050 ( 6) hydrogen bonds : bond 0.03441 ( 875) hydrogen bonds : angle 3.62468 ( 2547) link_NAG-ASN : bond 0.00505 ( 6) link_NAG-ASN : angle 2.85712 ( 18) *********************** 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 201 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3607 LYS cc_start: 0.8388 (ttpp) cc_final: 0.7961 (tttp) REVERT: A 3611 GLU cc_start: 0.8630 (tp30) cc_final: 0.8352 (tp30) REVERT: A 3615 PHE cc_start: 0.7673 (t80) cc_final: 0.7453 (t80) REVERT: B 231 LEU cc_start: 0.9186 (tp) cc_final: 0.8832 (tp) REVERT: B 338 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7454 (mtp85) REVERT: C 239 TYR cc_start: 0.6342 (OUTLIER) cc_final: 0.5406 (t80) REVERT: C 253 MET cc_start: 0.8470 (tpp) cc_final: 0.8255 (mmt) REVERT: D 603 MET cc_start: 0.8709 (ppp) cc_final: 0.8413 (ppp) REVERT: D 698 MET cc_start: 0.5671 (ppp) cc_final: 0.5389 (mmp) outliers start: 31 outliers final: 26 residues processed: 189 average time/residue: 0.1017 time to fit residues: 30.4556 Evaluate side-chains 190 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 225 VAL Chi-restraints excluded: chain B residue 226 THR 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 239 TYR 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 413 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 676 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 191 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 175 optimal weight: 30.0000 chunk 203 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 0.0770 overall best weight: 1.8144 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.180371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120743 restraints weight = 22454.276| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.76 r_work: 0.3249 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16543 Z= 0.148 Angle : 0.550 10.712 22550 Z= 0.277 Chirality : 0.041 0.232 2629 Planarity : 0.003 0.049 2856 Dihedral : 4.552 58.689 2465 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.11 % Rotamer: Outliers : 2.52 % Allowed : 14.11 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.19), residues: 2147 helix: 1.92 (0.16), residues: 1132 sheet: -0.43 (0.40), residues: 184 loop : -2.66 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3972 TYR 0.011 0.001 TYR B 348 PHE 0.013 0.001 PHE B 670 TRP 0.007 0.001 TRP B 414 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00352 (16534) covalent geometry : angle 0.54340 (22526) SS BOND : bond 0.00123 ( 3) SS BOND : angle 0.95035 ( 6) hydrogen bonds : bond 0.03984 ( 875) hydrogen bonds : angle 3.69944 ( 2547) link_NAG-ASN : bond 0.00282 ( 6) link_NAG-ASN : angle 3.01831 ( 18) *********************** 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 206 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 3607 LYS cc_start: 0.8412 (ttpp) cc_final: 0.8003 (tttp) REVERT: A 3611 GLU cc_start: 0.8608 (tp30) cc_final: 0.8360 (tp30) REVERT: B 231 LEU cc_start: 0.9153 (tp) cc_final: 0.8803 (tp) REVERT: B 338 ARG cc_start: 0.8054 (ttm-80) cc_final: 0.7460 (mtp85) REVERT: B 477 GLU cc_start: 0.4619 (mm-30) cc_final: 0.3444 (mm-30) REVERT: C 253 MET cc_start: 0.8568 (tpp) cc_final: 0.8337 (mmt) REVERT: C 622 GLN cc_start: 0.8967 (mt0) cc_final: 0.8558 (mt0) REVERT: D 603 MET cc_start: 0.8778 (ppp) cc_final: 0.8429 (ppp) outliers start: 37 outliers final: 28 residues processed: 194 average time/residue: 0.1098 time to fit residues: 33.8078 Evaluate side-chains 192 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 3606 LEU Chi-restraints excluded: chain A residue 3723 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 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 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 413 VAL Chi-restraints excluded: chain C residue 442 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 72 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 172 optimal weight: 40.0000 chunk 106 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.181650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124741 restraints weight = 22304.466| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.70 r_work: 0.3292 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1774 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= 0.114 Angle : 0.530 10.839 22550 Z= 0.266 Chirality : 0.040 0.234 2629 Planarity : 0.003 0.040 2856 Dihedral : 4.469 56.109 2465 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.11 % Allowed : 14.59 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.19), residues: 2147 helix: 1.99 (0.16), residues: 1131 sheet: -0.38 (0.40), residues: 185 loop : -2.62 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3972 TYR 0.014 0.001 TYR C 486 PHE 0.011 0.001 PHE D 604 TRP 0.007 0.001 TRP A3922 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00259 (16534) covalent geometry : angle 0.52232 (22526) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.85741 ( 6) hydrogen bonds : bond 0.03602 ( 875) hydrogen bonds : angle 3.64156 ( 2547) link_NAG-ASN : bond 0.00308 ( 6) link_NAG-ASN : angle 3.14699 ( 18) *********************** 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 196 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 3607 LYS cc_start: 0.8511 (ttpp) cc_final: 0.8088 (tttp) REVERT: A 3611 GLU cc_start: 0.8561 (tp30) cc_final: 0.8341 (tp30) REVERT: A 3615 PHE cc_start: 0.7905 (t80) cc_final: 0.7577 (t80) REVERT: B 231 LEU cc_start: 0.9157 (tp) cc_final: 0.8799 (tp) REVERT: B 338 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7553 (mtt-85) REVERT: C 253 MET cc_start: 0.8571 (tpp) cc_final: 0.8355 (mmt) REVERT: D 603 MET cc_start: 0.8763 (ppp) cc_final: 0.8434 (ppp) REVERT: D 682 ASP cc_start: 0.8678 (t0) cc_final: 0.8415 (t0) outliers start: 31 outliers final: 29 residues processed: 184 average time/residue: 0.0954 time to fit residues: 28.2678 Evaluate side-chains 191 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 3606 LEU Chi-restraints excluded: chain A residue 3723 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 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 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 413 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 690 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 206 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 11 optimal weight: 50.0000 chunk 1 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.179893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122307 restraints weight = 22361.491| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.69 r_work: 0.3258 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16543 Z= 0.148 Angle : 0.555 10.767 22550 Z= 0.280 Chirality : 0.041 0.234 2629 Planarity : 0.003 0.048 2856 Dihedral : 4.575 57.043 2465 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.94 % Favored : 93.01 % Rotamer: Outliers : 1.98 % Allowed : 15.00 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.19), residues: 2147 helix: 1.91 (0.16), residues: 1133 sheet: -0.37 (0.41), residues: 183 loop : -2.65 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3972 TYR 0.012 0.001 TYR B 348 PHE 0.013 0.001 PHE B 670 TRP 0.010 0.001 TRP B 414 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00351 (16534) covalent geometry : angle 0.54796 (22526) SS BOND : bond 0.00148 ( 3) SS BOND : angle 0.95462 ( 6) hydrogen bonds : bond 0.04005 ( 875) hydrogen bonds : angle 3.69011 ( 2547) link_NAG-ASN : bond 0.00305 ( 6) link_NAG-ASN : angle 3.07206 ( 18) ********************** 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 196 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 3607 LYS cc_start: 0.8415 (ttpp) cc_final: 0.8001 (tttp) REVERT: A 3611 GLU cc_start: 0.8687 (tp30) cc_final: 0.8451 (tp30) REVERT: A 3615 PHE cc_start: 0.7850 (t80) cc_final: 0.7565 (t80) REVERT: B 231 LEU cc_start: 0.9138 (tp) cc_final: 0.8795 (tp) REVERT: B 338 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7484 (mtp85) REVERT: B 477 GLU cc_start: 0.4775 (mm-30) cc_final: 0.3571 (mm-30) REVERT: B 543 ASN cc_start: 0.8301 (t0) cc_final: 0.8087 (t0) REVERT: C 223 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: C 253 MET cc_start: 0.8567 (tpp) cc_final: 0.8339 (mmt) REVERT: C 622 GLN cc_start: 0.8956 (mt0) cc_final: 0.8555 (mt0) REVERT: D 603 MET cc_start: 0.8775 (ppp) cc_final: 0.8424 (ppp) outliers start: 29 outliers final: 27 residues processed: 184 average time/residue: 0.0963 time to fit residues: 28.9014 Evaluate side-chains 192 residues out of total 1897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 3739 GLN Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3820 VAL Chi-restraints excluded: chain A residue 3839 LEU 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 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 340 GLU Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 198 optimal weight: 40.0000 chunk 182 optimal weight: 30.0000 chunk 124 optimal weight: 0.8980 chunk 179 optimal weight: 0.0980 chunk 162 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.179763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119910 restraints weight = 22369.151| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.52 r_work: 0.3277 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16543 Z= 0.147 Angle : 0.547 10.826 22550 Z= 0.277 Chirality : 0.041 0.232 2629 Planarity : 0.003 0.047 2856 Dihedral : 4.583 59.881 2465 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.71 % Favored : 93.25 % Rotamer: Outliers : 2.18 % Allowed : 15.00 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.19), residues: 2147 helix: 1.92 (0.16), residues: 1132 sheet: -0.34 (0.41), residues: 183 loop : -2.62 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3972 TYR 0.016 0.001 TYR C 486 PHE 0.012 0.001 PHE D 604 TRP 0.014 0.001 TRP C 507 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00347 (16534) covalent geometry : angle 0.54113 (22526) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.99015 ( 6) hydrogen bonds : bond 0.03980 ( 875) hydrogen bonds : angle 3.68793 ( 2547) link_NAG-ASN : bond 0.00297 ( 6) link_NAG-ASN : angle 2.95368 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4358.32 seconds wall clock time: 74 minutes 53.36 seconds (4493.36 seconds total)