Starting phenix.real_space_refine on Sun Jun 15 13:09:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zkt_60208/06_2025/8zkt_60208.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zkt_60208/06_2025/8zkt_60208.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/8zkt_60208/06_2025/8zkt_60208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zkt_60208/06_2025/8zkt_60208.map" model { file = "/net/cci-nas-00/data/ceres_data/8zkt_60208/06_2025/8zkt_60208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zkt_60208/06_2025/8zkt_60208.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 77 5.16 5 C 11374 2.51 5 N 2868 2.21 5 O 3050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17369 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5586 Classifications: {'peptide': 753} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 29, 'TRANS': 723} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 383 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 7, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 233 Chain: "B" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3924 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 464} 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: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3923 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 464} 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: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3810 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 452} 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: "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 Chain: "D" 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: 9.53, per 1000 atoms: 0.55 Number of scatterers: 17369 At special positions: 0 Unit cell: (123.918, 160.876, 129.353, 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 77 16.00 O 3050 8.00 N 2868 7.00 C 11374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=1.06 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 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 " " NAG D1001 " - " ASN D 375 " " NAG D1002 " - " ASN D 328 " " NAG D1003 " - " ASN D 362 " Time building additional restraints: 3.88 Conformation dependent library (CDL) restraints added in 2.0 seconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4108 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 6 sheets defined 57.2% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 3074 through 3082 removed outlier: 4.253A pdb=" N MET A3078 " --> pdb=" O ASN A3074 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS A3081 " --> pdb=" O VAL A3077 " (cutoff:3.500A) Processing helix chain 'A' and resid 3082 through 3109 removed outlier: 3.906A pdb=" N VAL A3086 " --> pdb=" O ALA A3082 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A3088 " --> pdb=" O CYS A3084 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A3101 " --> pdb=" O LYS A3097 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A3104 " --> pdb=" O GLN A3100 " (cutoff:3.500A) Processing helix chain 'A' and resid 3246 through 3254 removed outlier: 3.682A pdb=" N VAL A3250 " --> pdb=" O ARG A3246 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU A3252 " --> pdb=" O LEU A3248 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A3254 " --> pdb=" O VAL A3250 " (cutoff:3.500A) Processing helix chain 'A' and resid 3262 through 3266 removed outlier: 3.619A pdb=" N SER A3265 " --> pdb=" O ILE A3262 " (cutoff:3.500A) removed outlier: 4.474A 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 3278 through 3299 removed outlier: 3.813A pdb=" N THR A3282 " --> pdb=" O ILE A3278 " (cutoff:3.500A) Processing helix chain 'A' and resid 3322 through 3345 Proline residue: A3335 - end of helix removed outlier: 4.869A pdb=" N ALA A3339 " --> pdb=" O PRO A3335 " (cutoff:3.500A) Processing helix chain 'A' and resid 3557 through 3577 removed outlier: 3.927A pdb=" N LEU A3561 " --> pdb=" O LEU A3557 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A3563 " --> pdb=" O HIS A3559 " (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: 3.659A pdb=" N SER A3585 " --> pdb=" O PRO A3581 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL A3586 " --> pdb=" O PRO A3582 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA A3587 " --> pdb=" O GLY A3583 " (cutoff:3.500A) Processing helix chain 'A' and resid 3603 through 3615 Processing helix chain 'A' and resid 3656 through 3689 removed outlier: 3.767A pdb=" N ARG A3662 " --> pdb=" O LYS A3658 " (cutoff:3.500A) Processing helix chain 'A' and resid 3691 through 3694 Processing helix chain 'A' and resid 3695 through 3709 removed outlier: 4.106A pdb=" N TYR A3699 " --> pdb=" O HIS A3695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A3700 " --> pdb=" O GLY A3696 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3717 Processing helix chain 'A' and resid 3722 through 3730 removed outlier: 4.088A pdb=" N TRP A3726 " --> pdb=" O GLU A3722 " (cutoff:3.500A) Processing helix chain 'A' and resid 3730 through 3737 removed outlier: 3.534A pdb=" N TYR A3734 " --> pdb=" O VAL A3730 " (cutoff:3.500A) Processing helix chain 'A' and resid 3829 through 3840 removed outlier: 3.527A pdb=" N ARG A3833 " --> pdb=" O GLU A3829 " (cutoff:3.500A) Processing helix chain 'A' and resid 3892 through 3896 removed outlier: 3.882A pdb=" N GLY A3896 " --> pdb=" O LEU A3893 " (cutoff:3.500A) Processing helix chain 'A' and resid 3898 through 3926 Processing helix chain 'A' and resid 3932 through 3968 removed outlier: 3.900A pdb=" N TRP A3936 " --> pdb=" O ARG A3932 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A3968 " --> pdb=" O THR A3964 " (cutoff:3.500A) Processing helix chain 'A' and resid 3977 through 4004 removed outlier: 3.683A pdb=" N ARG A3988 " --> pdb=" O SER A3984 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A3993 " --> pdb=" O GLY A3989 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A3995 " --> pdb=" O ALA A3991 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A4003 " --> pdb=" O LEU A3999 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A4004 " --> pdb=" O VAL A4000 " (cutoff:3.500A) Processing helix chain 'A' and resid 4005 through 4009 removed outlier: 3.555A pdb=" N PHE A4008 " --> pdb=" O GLN A4005 " (cutoff:3.500A) Processing helix chain 'A' and resid 4013 through 4022 removed outlier: 4.024A pdb=" N LYS A4017 " --> pdb=" O SER A4013 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A4022 " --> pdb=" O THR A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4022 through 4045 removed outlier: 3.635A pdb=" N LEU A4026 " --> pdb=" O ALA A4022 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4119 removed outlier: 3.795A pdb=" N TRP A4108 " --> pdb=" O VAL A4104 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A4109 " --> pdb=" O ILE A4105 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A4117 " --> pdb=" O LEU A4113 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 240 removed outlier: 3.652A pdb=" N THR B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 259 removed outlier: 4.050A pdb=" N TYR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.775A pdb=" N LEU B 273 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 284 removed outlier: 3.651A pdb=" N TRP B 280 " --> pdb=" O MET B 276 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.534A pdb=" N GLY B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.605A pdb=" N ARG B 338 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP B 339 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.873A pdb=" N GLU B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'B' and resid 398 through 412 removed outlier: 3.582A pdb=" N ALA B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 497 Processing helix chain 'B' and resid 508 through 530 removed outlier: 3.911A pdb=" N VAL B 512 " --> pdb=" O ASN B 508 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 513 " --> pdb=" O CYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 541 removed outlier: 3.624A pdb=" N ASP B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 removed outlier: 3.635A pdb=" N ALA B 552 " --> pdb=" O PHE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 576 Processing helix chain 'B' and resid 580 through 593 removed outlier: 3.842A pdb=" N LEU B 586 " --> pdb=" O THR B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 620 removed outlier: 3.530A pdb=" N ILE B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 641 removed outlier: 3.507A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 653 removed outlier: 4.110A pdb=" N GLU B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 removed outlier: 3.820A pdb=" N ILE B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 699 removed outlier: 3.597A pdb=" N ILE B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 241 removed outlier: 3.795A pdb=" N THR C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 259 removed outlier: 4.150A pdb=" N TYR C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.601A pdb=" N LEU C 273 " --> pdb=" O PHE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.578A pdb=" N PHE C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP C 280 " --> pdb=" O MET C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 293 removed outlier: 3.841A pdb=" N TRP C 293 " --> pdb=" O ASP C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 338 removed outlier: 3.575A pdb=" N LEU C 337 " --> pdb=" O PRO C 334 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 338 " --> pdb=" O GLN C 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 334 through 338' Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.752A pdb=" N GLU C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 496 removed outlier: 3.597A pdb=" N ARG C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 531 removed outlier: 3.676A pdb=" N ASN C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 540 removed outlier: 3.787A pdb=" N GLU C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.690A pdb=" N ASN C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 593 removed outlier: 3.606A pdb=" N SER C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 620 removed outlier: 3.769A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 642 removed outlier: 3.688A pdb=" N ILE C 640 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 641 " --> pdb=" O PHE C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.535A pdb=" N GLU C 650 " --> pdb=" O PHE C 646 " (cutoff:3.500A) removed outlier: 3.868A 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 673 through 697 removed outlier: 4.399A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 678 " --> pdb=" O ASN C 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 240 removed outlier: 3.544A pdb=" N ARG D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 242 No H-bonds generated for 'chain 'D' and resid 241 through 242' Processing helix chain 'D' and resid 243 through 246 removed outlier: 3.791A pdb=" N VAL D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 243 through 246' Processing helix chain 'D' and resid 247 through 257 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 363 through 367 removed outlier: 4.006A pdb=" N TRP D 366 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE D 367 " --> pdb=" O THR D 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 363 through 367' Processing helix chain 'D' and resid 371 through 375 Processing helix chain 'D' and resid 402 through 412 Processing helix chain 'D' and resid 469 through 498 Processing helix chain 'D' and resid 507 through 535 removed outlier: 3.691A pdb=" N ASP D 511 " --> pdb=" O TRP D 507 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL D 512 " --> pdb=" O ASN D 508 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL D 513 " --> pdb=" O CYS D 509 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 534 " --> pdb=" O SER D 530 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU D 535 " --> pdb=" O ASN D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 572 removed outlier: 3.574A pdb=" N TRP D 554 " --> pdb=" O HIS D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 577 Processing helix chain 'D' and resid 583 through 593 removed outlier: 3.964A pdb=" N THR D 588 " --> pdb=" O SER D 584 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR D 589 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS D 593 " --> pdb=" O THR D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 619 removed outlier: 3.557A pdb=" N MET D 603 " --> pdb=" O GLY D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 640 removed outlier: 3.573A pdb=" N PHE D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 653 Processing helix chain 'D' and resid 657 through 670 Processing helix chain 'D' and resid 673 through 696 removed outlier: 4.395A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 679 " --> pdb=" O MET D 675 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3138 through 3141 Processing sheet with id=AA2, first strand: chain 'A' and resid 3852 through 3858 Processing sheet with id=AA3, first strand: chain 'A' and resid 3852 through 3858 Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.607A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.600A 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: 6.829A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 391 through 394 removed outlier: 6.636A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) 903 hydrogen bonds defined for protein. 2613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 4.70 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: 5396 1.34 - 1.46: 4472 1.46 - 1.58: 7822 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 17807 Sorted by residual: bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C1 NAG C1002 " pdb=" O5 NAG C1002 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CA ALA A3812 " pdb=" CB ALA A3812 " ideal model delta sigma weight residual 1.542 1.520 0.022 8.90e-03 1.26e+04 6.13e+00 bond pdb=" CA PHE B 667 " pdb=" C PHE B 667 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.41e-02 5.03e+03 3.54e+00 bond pdb=" N ALA A3805 " pdb=" CA ALA A3805 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.08e+00 ... (remaining 17802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 23832 2.28 - 4.56: 318 4.56 - 6.84: 39 6.84 - 9.12: 4 9.12 - 11.39: 1 Bond angle restraints: 24194 Sorted by residual: angle pdb=" C VAL B 623 " pdb=" N ASP B 624 " pdb=" CA ASP B 624 " ideal model delta sigma weight residual 126.32 134.37 -8.05 1.74e+00 3.30e-01 2.14e+01 angle pdb=" N ARG A3753 " pdb=" CA ARG A3753 " pdb=" C ARG A3753 " ideal model delta sigma weight residual 107.73 114.94 -7.21 1.61e+00 3.86e-01 2.00e+01 angle pdb=" N SER A3807 " pdb=" CA SER A3807 " pdb=" C SER A3807 " ideal model delta sigma weight residual 111.02 116.17 -5.15 1.25e+00 6.40e-01 1.70e+01 angle pdb=" N VAL A4048 " pdb=" CA VAL A4048 " pdb=" C VAL A4048 " ideal model delta sigma weight residual 112.12 108.89 3.23 8.40e-01 1.42e+00 1.48e+01 angle pdb=" N GLU A3756 " pdb=" CA GLU A3756 " pdb=" C GLU A3756 " ideal model delta sigma weight residual 110.24 115.45 -5.21 1.41e+00 5.03e-01 1.37e+01 ... (remaining 24189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.31: 9814 24.31 - 48.61: 552 48.61 - 72.92: 57 72.92 - 97.22: 14 97.22 - 121.53: 6 Dihedral angle restraints: 10443 sinusoidal: 4088 harmonic: 6355 Sorted by residual: dihedral pdb=" CB CYS D 331 " pdb=" SG CYS D 331 " pdb=" SG CYS D 344 " pdb=" CB CYS D 344 " ideal model delta sinusoidal sigma weight residual 93.00 -179.42 -87.58 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " pdb=" SG CYS C 344 " pdb=" CB CYS C 344 " ideal model delta sinusoidal sigma weight residual -86.00 -171.49 85.49 1 1.00e+01 1.00e-02 8.85e+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 93.00 151.88 -58.88 1 1.00e+01 1.00e-02 4.64e+01 ... (remaining 10440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2526 0.074 - 0.149: 221 0.149 - 0.223: 10 0.223 - 0.297: 2 0.297 - 0.372: 2 Chirality restraints: 2761 Sorted by residual: chirality pdb=" CA LEU A3802 " pdb=" N LEU A3802 " pdb=" C LEU A3802 " pdb=" CB LEU A3802 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA ALA A3805 " pdb=" N ALA A3805 " pdb=" C ALA A3805 " pdb=" CB ALA A3805 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C1 NAG D1003 " pdb=" ND2 ASN D 362 " pdb=" C2 NAG D1003 " pdb=" O5 NAG D1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2758 not shown) Planarity restraints: 3017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 359 " -0.054 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO D 360 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 360 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 360 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 623 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.26e+00 pdb=" C VAL B 623 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL B 623 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP B 624 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A3581 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO A3582 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A3582 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A3582 " -0.029 5.00e-02 4.00e+02 ... (remaining 3014 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 53 2.44 - 3.05: 11208 3.05 - 3.67: 24238 3.67 - 4.28: 35418 4.28 - 4.90: 61219 Nonbonded interactions: 132136 Sorted by model distance: nonbonded pdb=" O TYR A3781 " pdb=" O GLY A3793 " model vdw 1.820 3.040 nonbonded pdb=" NH2 ARG A3750 " pdb=" O ASP A3815 " model vdw 2.023 3.120 nonbonded pdb=" CB ARG D 397 " pdb=" OE1 GLN D 542 " model vdw 2.131 3.440 nonbonded pdb=" O LEU A4099 " pdb=" CD1 LEU A4099 " model vdw 2.156 3.460 nonbonded pdb=" O TYR C 292 " pdb=" OG SER C 307 " model vdw 2.176 3.040 ... (remaining 132131 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 294 or resid 314 through 698 or resid 1001 thr \ ough 1003)) selection = (chain 'C' and (resid 217 through 294 or resid 314 through 698 or resid 1001 thr \ ough 1003)) selection = chain 'D' } 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 36.690 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 0.975 17819 Z= 0.416 Angle : 0.711 36.294 24227 Z= 0.399 Chirality : 0.045 0.372 2761 Planarity : 0.005 0.081 3008 Dihedral : 14.667 121.530 6326 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.06 % Favored : 90.43 % Rotamer: Outliers : 0.11 % Allowed : 0.67 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.19), residues: 2142 helix: 1.00 (0.16), residues: 1111 sheet: -1.06 (0.39), residues: 197 loop : -3.19 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A3922 HIS 0.010 0.001 HIS B 498 PHE 0.027 0.002 PHE B 646 TYR 0.026 0.001 TYR A3334 ARG 0.008 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 9) link_NAG-ASN : angle 2.48660 ( 27) hydrogen bonds : bond 0.16080 ( 895) hydrogen bonds : angle 5.62392 ( 2613) SS BOND : bond 0.56315 ( 3) SS BOND : angle 15.38912 ( 6) covalent geometry : bond 0.00426 (17807) covalent geometry : angle 0.66368 (24194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 254 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3248 LEU cc_start: 0.4388 (tp) cc_final: 0.4019 (tp) REVERT: D 491 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7718 (mt-10) outliers start: 2 outliers final: 1 residues processed: 256 average time/residue: 0.3524 time to fit residues: 137.8147 Evaluate side-chains 207 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3813 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 102 optimal weight: 0.0030 chunk 125 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3790 ASN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN C 335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.152338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.105943 restraints weight = 23466.014| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.32 r_work: 0.2900 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 17819 Z= 0.119 Angle : 0.565 10.197 24227 Z= 0.291 Chirality : 0.041 0.336 2761 Planarity : 0.004 0.048 3008 Dihedral : 7.514 110.093 2564 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.98 % Favored : 91.83 % Rotamer: Outliers : 1.40 % Allowed : 7.37 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 2142 helix: 1.47 (0.16), residues: 1128 sheet: -0.97 (0.39), residues: 189 loop : -3.02 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A3298 HIS 0.005 0.001 HIS B 498 PHE 0.021 0.001 PHE C 506 TYR 0.018 0.001 TYR C 292 ARG 0.008 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 9) link_NAG-ASN : angle 2.31824 ( 27) hydrogen bonds : bond 0.04735 ( 895) hydrogen bonds : angle 3.98813 ( 2613) SS BOND : bond 0.00184 ( 3) SS BOND : angle 2.26647 ( 6) covalent geometry : bond 0.00249 (17807) covalent geometry : angle 0.55874 (24194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 1.926 Fit side-chains revert: symmetry clash REVERT: B 499 LYS cc_start: 0.7071 (ptpt) cc_final: 0.6863 (ptpt) REVERT: C 477 GLU cc_start: 0.6136 (tp30) cc_final: 0.5915 (tp30) outliers start: 25 outliers final: 17 residues processed: 234 average time/residue: 0.3208 time to fit residues: 112.5087 Evaluate side-chains 215 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3609 LEU Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 155 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 213 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS B 531 ASN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.149699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104640 restraints weight = 23413.258| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.15 r_work: 0.2873 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 17819 Z= 0.159 Angle : 0.570 10.790 24227 Z= 0.295 Chirality : 0.042 0.324 2761 Planarity : 0.004 0.047 3008 Dihedral : 6.796 110.559 2563 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.26 % Favored : 91.60 % Rotamer: Outliers : 2.23 % Allowed : 10.28 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.19), residues: 2142 helix: 1.46 (0.16), residues: 1143 sheet: -1.04 (0.39), residues: 191 loop : -3.08 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A3298 HIS 0.006 0.001 HIS B 498 PHE 0.015 0.001 PHE A3680 TYR 0.019 0.001 TYR C 292 ARG 0.007 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 9) link_NAG-ASN : angle 2.77208 ( 27) hydrogen bonds : bond 0.05049 ( 895) hydrogen bonds : angle 3.83276 ( 2613) SS BOND : bond 0.00219 ( 3) SS BOND : angle 1.52794 ( 6) covalent geometry : bond 0.00381 (17807) covalent geometry : angle 0.56221 (24194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 1.925 Fit side-chains REVERT: A 4116 GLU cc_start: 0.8573 (tm-30) cc_final: 0.7887 (tm-30) REVERT: C 477 GLU cc_start: 0.6183 (tp30) cc_final: 0.5954 (tp30) REVERT: D 250 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8520 (p) REVERT: D 490 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6687 (mm-30) REVERT: D 491 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7529 (mt-10) outliers start: 40 outliers final: 29 residues processed: 226 average time/residue: 0.3452 time to fit residues: 120.6521 Evaluate side-chains 222 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3091 MET Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3253 LEU Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3985 SER Chi-restraints excluded: chain A residue 4001 LYS Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 358 PHE Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain D residue 694 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 53 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 17 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN ** C 313 ASN ** 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 = 0.3716 r_free = 0.3716 target = 0.151501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.107258 restraints weight = 23395.491| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.25 r_work: 0.2875 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 17819 Z= 0.148 Angle : 0.542 10.087 24227 Z= 0.282 Chirality : 0.041 0.324 2761 Planarity : 0.004 0.048 3008 Dihedral : 6.560 109.693 2563 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.31 % Favored : 91.55 % Rotamer: Outliers : 2.40 % Allowed : 12.23 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 2142 helix: 1.55 (0.16), residues: 1147 sheet: -0.99 (0.38), residues: 195 loop : -3.03 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A3298 HIS 0.006 0.001 HIS B 498 PHE 0.017 0.001 PHE A3342 TYR 0.020 0.001 TYR C 292 ARG 0.010 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 9) link_NAG-ASN : angle 2.38963 ( 27) hydrogen bonds : bond 0.04757 ( 895) hydrogen bonds : angle 3.75236 ( 2613) SS BOND : bond 0.00222 ( 3) SS BOND : angle 0.86207 ( 6) covalent geometry : bond 0.00349 (17807) covalent geometry : angle 0.53604 (24194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 2.280 Fit side-chains REVERT: A 4116 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7785 (tm-30) REVERT: C 540 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: D 250 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8524 (p) REVERT: D 491 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7527 (mt-10) REVERT: D 583 MET cc_start: 0.8845 (tpp) cc_final: 0.8461 (mmm) outliers start: 43 outliers final: 30 residues processed: 229 average time/residue: 0.2975 time to fit residues: 104.3459 Evaluate side-chains 220 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3091 MET Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3253 LEU Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3985 SER Chi-restraints excluded: chain A residue 4001 LYS Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 358 PHE Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 161 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 6 optimal weight: 50.0000 chunk 57 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 105 optimal weight: 0.0670 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** 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 = 0.3724 r_free = 0.3724 target = 0.152337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106652 restraints weight = 23554.393| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.20 r_work: 0.2902 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.002 0.077 17819 Z= 0.111 Angle : 0.516 10.175 24227 Z= 0.268 Chirality : 0.040 0.319 2761 Planarity : 0.004 0.048 3008 Dihedral : 6.312 109.042 2563 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.94 % Favored : 91.92 % Rotamer: Outliers : 2.07 % Allowed : 13.63 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 2142 helix: 1.71 (0.16), residues: 1151 sheet: -0.87 (0.39), residues: 189 loop : -2.97 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A3298 HIS 0.006 0.001 HIS B 498 PHE 0.022 0.001 PHE D 436 TYR 0.019 0.001 TYR D 502 ARG 0.004 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 9) link_NAG-ASN : angle 2.31231 ( 27) hydrogen bonds : bond 0.04162 ( 895) hydrogen bonds : angle 3.61088 ( 2613) SS BOND : bond 0.00248 ( 3) SS BOND : angle 2.25445 ( 6) covalent geometry : bond 0.00243 (17807) covalent geometry : angle 0.50952 (24194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 1.865 Fit side-chains REVERT: A 3806 TRP cc_start: 0.7420 (m100) cc_final: 0.6697 (m100) REVERT: A 3883 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7725 (pt) REVERT: A 4116 GLU cc_start: 0.8527 (tm-30) cc_final: 0.7787 (tm-30) REVERT: B 669 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8882 (m-80) REVERT: B 698 MET cc_start: 0.7408 (mmp) cc_final: 0.7208 (mmp) REVERT: C 477 GLU cc_start: 0.6342 (tp30) cc_final: 0.5928 (tp30) REVERT: C 537 GLN cc_start: 0.8087 (mt0) cc_final: 0.7867 (mt0) REVERT: D 250 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8529 (p) REVERT: D 583 MET cc_start: 0.8848 (tpp) cc_final: 0.8503 (mmm) outliers start: 37 outliers final: 21 residues processed: 220 average time/residue: 0.2764 time to fit residues: 94.4398 Evaluate side-chains 204 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3609 LEU Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 358 PHE Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 119 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 133 optimal weight: 0.0670 chunk 116 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 578 ASN D 323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108354 restraints weight = 23767.918| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.34 r_work: 0.2857 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.098 17819 Z= 0.110 Angle : 0.510 10.143 24227 Z= 0.265 Chirality : 0.040 0.315 2761 Planarity : 0.004 0.049 3008 Dihedral : 6.170 108.313 2563 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.03 % Favored : 91.88 % Rotamer: Outliers : 2.01 % Allowed : 14.58 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 2142 helix: 1.82 (0.16), residues: 1151 sheet: -0.77 (0.39), residues: 189 loop : -2.90 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A3922 HIS 0.006 0.001 HIS B 498 PHE 0.022 0.001 PHE D 436 TYR 0.018 0.001 TYR C 292 ARG 0.005 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 9) link_NAG-ASN : angle 2.23637 ( 27) hydrogen bonds : bond 0.04008 ( 895) hydrogen bonds : angle 3.55232 ( 2613) SS BOND : bond 0.00261 ( 3) SS BOND : angle 1.90354 ( 6) covalent geometry : bond 0.00247 (17807) covalent geometry : angle 0.50391 (24194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 2.000 Fit side-chains REVERT: A 3708 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7143 (mm-30) REVERT: A 3883 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7782 (pt) REVERT: A 4116 GLU cc_start: 0.8555 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 4119 ARG cc_start: 0.6263 (mtt-85) cc_final: 0.5887 (ttt-90) REVERT: B 669 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8789 (m-80) REVERT: C 477 GLU cc_start: 0.6344 (tp30) cc_final: 0.6139 (tp30) REVERT: C 504 ARG cc_start: 0.7584 (tpm170) cc_final: 0.6007 (tpp80) REVERT: D 250 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8592 (p) REVERT: D 583 MET cc_start: 0.8856 (tpp) cc_final: 0.8533 (mmm) outliers start: 36 outliers final: 24 residues processed: 214 average time/residue: 0.3001 time to fit residues: 99.5419 Evaluate side-chains 210 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 4001 LYS Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4117 LEU Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 358 PHE Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 194 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 157 optimal weight: 0.0980 chunk 101 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 55 optimal weight: 0.0370 chunk 24 optimal weight: 5.9990 overall best weight: 2.0264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3982 GLN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.148317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.101950 restraints weight = 23596.240| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.23 r_work: 0.2870 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 17819 Z= 0.156 Angle : 0.544 10.128 24227 Z= 0.283 Chirality : 0.041 0.317 2761 Planarity : 0.004 0.052 3008 Dihedral : 6.227 108.336 2563 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.12 % Favored : 91.83 % Rotamer: Outliers : 2.46 % Allowed : 14.47 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 2142 helix: 1.71 (0.16), residues: 1157 sheet: -0.84 (0.38), residues: 195 loop : -2.93 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A3922 HIS 0.006 0.001 HIS B 498 PHE 0.024 0.001 PHE D 436 TYR 0.020 0.001 TYR B 527 ARG 0.012 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 9) link_NAG-ASN : angle 2.30447 ( 27) hydrogen bonds : bond 0.04617 ( 895) hydrogen bonds : angle 3.62339 ( 2613) SS BOND : bond 0.00242 ( 3) SS BOND : angle 1.64616 ( 6) covalent geometry : bond 0.00372 (17807) covalent geometry : angle 0.53830 (24194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 1.764 Fit side-chains REVERT: A 3708 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7267 (mm-30) REVERT: A 3780 ASP cc_start: 0.6678 (m-30) cc_final: 0.6193 (t0) REVERT: A 3883 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7745 (pt) REVERT: A 4116 GLU cc_start: 0.8575 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 4119 ARG cc_start: 0.6184 (mtt-85) cc_final: 0.5718 (ttt-90) REVERT: B 669 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8848 (m-80) REVERT: C 477 GLU cc_start: 0.6333 (tp30) cc_final: 0.6067 (tp30) REVERT: C 504 ARG cc_start: 0.7552 (tpm170) cc_final: 0.5966 (tpp80) REVERT: D 242 MET cc_start: 0.7309 (mmm) cc_final: 0.6768 (tpt) REVERT: D 250 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8549 (p) REVERT: D 583 MET cc_start: 0.8888 (tpp) cc_final: 0.8541 (mmm) outliers start: 44 outliers final: 36 residues processed: 216 average time/residue: 0.3023 time to fit residues: 100.1165 Evaluate side-chains 221 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3091 MET Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3253 LEU Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3609 LEU Chi-restraints excluded: chain A residue 3727 MET Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 3916 VAL Chi-restraints excluded: chain A residue 3985 SER Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain A residue 4036 LEU Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4117 LEU Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 358 PHE Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 17 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.149015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.100657 restraints weight = 23379.119| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.36 r_work: 0.2995 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 17819 Z= 0.130 Angle : 0.527 10.036 24227 Z= 0.274 Chirality : 0.040 0.318 2761 Planarity : 0.004 0.050 3008 Dihedral : 6.195 108.340 2563 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.17 % Favored : 91.74 % Rotamer: Outliers : 2.46 % Allowed : 15.03 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 2142 helix: 1.77 (0.16), residues: 1156 sheet: -0.81 (0.39), residues: 195 loop : -2.90 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A3806 HIS 0.006 0.001 HIS B 498 PHE 0.023 0.001 PHE D 436 TYR 0.019 0.001 TYR B 527 ARG 0.013 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 9) link_NAG-ASN : angle 2.29264 ( 27) hydrogen bonds : bond 0.04384 ( 895) hydrogen bonds : angle 3.59162 ( 2613) SS BOND : bond 0.00194 ( 3) SS BOND : angle 1.41837 ( 6) covalent geometry : bond 0.00304 (17807) covalent geometry : angle 0.52079 (24194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 1.758 Fit side-chains REVERT: A 3708 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7322 (mm-30) REVERT: A 3780 ASP cc_start: 0.6706 (m-30) cc_final: 0.6235 (t0) REVERT: A 3883 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7818 (pt) REVERT: A 4116 GLU cc_start: 0.8622 (tm-30) cc_final: 0.7850 (tm-30) REVERT: A 4119 ARG cc_start: 0.6203 (mtt-85) cc_final: 0.5763 (ttt-90) REVERT: B 669 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8870 (m-80) REVERT: C 477 GLU cc_start: 0.6488 (tp30) cc_final: 0.6180 (tp30) REVERT: C 504 ARG cc_start: 0.7590 (tpm170) cc_final: 0.6013 (tpp80) REVERT: D 250 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8578 (p) REVERT: D 436 PHE cc_start: 0.7403 (p90) cc_final: 0.7028 (p90) REVERT: D 583 MET cc_start: 0.8944 (tpp) cc_final: 0.8623 (mmm) outliers start: 44 outliers final: 36 residues processed: 220 average time/residue: 0.2791 time to fit residues: 94.8296 Evaluate side-chains 225 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3091 MET Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3609 LEU Chi-restraints excluded: chain A residue 3727 MET Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 3916 VAL Chi-restraints excluded: chain A residue 3985 SER Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain A residue 4036 LEU Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4117 LEU Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 358 PHE Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 45 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 50.0000 chunk 182 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 94 optimal weight: 0.0670 chunk 213 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 GLN ** C 313 ASN ** 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 = 0.3668 r_free = 0.3668 target = 0.147957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101655 restraints weight = 23640.565| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.31 r_work: 0.2990 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 17819 Z= 0.143 Angle : 0.541 9.941 24227 Z= 0.281 Chirality : 0.041 0.320 2761 Planarity : 0.004 0.055 3008 Dihedral : 6.230 108.397 2563 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.40 % Favored : 91.50 % Rotamer: Outliers : 2.35 % Allowed : 15.25 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.19), residues: 2142 helix: 1.76 (0.16), residues: 1151 sheet: -0.85 (0.38), residues: 195 loop : -2.90 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A3922 HIS 0.006 0.001 HIS B 498 PHE 0.023 0.001 PHE D 436 TYR 0.019 0.001 TYR B 527 ARG 0.014 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 9) link_NAG-ASN : angle 2.30768 ( 27) hydrogen bonds : bond 0.04578 ( 895) hydrogen bonds : angle 3.61799 ( 2613) SS BOND : bond 0.00225 ( 3) SS BOND : angle 1.38454 ( 6) covalent geometry : bond 0.00337 (17807) covalent geometry : angle 0.53541 (24194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 1.752 Fit side-chains REVERT: A 3708 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7322 (mm-30) REVERT: A 3780 ASP cc_start: 0.6682 (m-30) cc_final: 0.6223 (t0) REVERT: A 3883 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7804 (pt) REVERT: A 4116 GLU cc_start: 0.8622 (tm-30) cc_final: 0.7875 (tm-30) REVERT: A 4119 ARG cc_start: 0.6216 (mtt-85) cc_final: 0.5771 (ttt-90) REVERT: B 306 ARG cc_start: 0.7751 (mtm180) cc_final: 0.7548 (mtm180) REVERT: B 354 ASP cc_start: 0.8918 (t0) cc_final: 0.8702 (t0) REVERT: B 669 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8882 (m-80) REVERT: C 504 ARG cc_start: 0.7573 (tpm170) cc_final: 0.6010 (tpp80) REVERT: D 242 MET cc_start: 0.7382 (mmm) cc_final: 0.6842 (tpt) REVERT: D 250 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8568 (p) REVERT: D 436 PHE cc_start: 0.7443 (p90) cc_final: 0.7122 (p90) REVERT: D 583 MET cc_start: 0.8959 (tpp) cc_final: 0.8643 (mmm) outliers start: 42 outliers final: 37 residues processed: 225 average time/residue: 0.2922 time to fit residues: 100.7974 Evaluate side-chains 231 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3091 MET Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3609 LEU Chi-restraints excluded: chain A residue 3727 MET Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 3916 VAL Chi-restraints excluded: chain A residue 3985 SER Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain A residue 4036 LEU Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4117 LEU Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 358 PHE Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 11 optimal weight: 40.0000 chunk 60 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.148120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.101938 restraints weight = 23507.042| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.26 r_work: 0.2857 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17819 Z= 0.150 Angle : 0.548 9.939 24227 Z= 0.285 Chirality : 0.041 0.321 2761 Planarity : 0.004 0.056 3008 Dihedral : 6.264 108.675 2563 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.50 % Favored : 91.41 % Rotamer: Outliers : 2.40 % Allowed : 15.14 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.19), residues: 2142 helix: 1.75 (0.16), residues: 1153 sheet: -0.87 (0.38), residues: 195 loop : -2.91 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A3922 HIS 0.007 0.001 HIS B 498 PHE 0.023 0.001 PHE D 436 TYR 0.021 0.001 TYR B 527 ARG 0.014 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 9) link_NAG-ASN : angle 2.32913 ( 27) hydrogen bonds : bond 0.04667 ( 895) hydrogen bonds : angle 3.63494 ( 2613) SS BOND : bond 0.00230 ( 3) SS BOND : angle 1.29883 ( 6) covalent geometry : bond 0.00356 (17807) covalent geometry : angle 0.54225 (24194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 2.336 Fit side-chains REVERT: A 3708 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 3780 ASP cc_start: 0.6660 (m-30) cc_final: 0.6210 (t0) REVERT: A 3883 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7695 (pt) REVERT: A 4116 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 4119 ARG cc_start: 0.6252 (mtt-85) cc_final: 0.5854 (ttt-90) REVERT: B 354 ASP cc_start: 0.8874 (t0) cc_final: 0.8609 (t0) REVERT: B 669 PHE cc_start: 0.9313 (OUTLIER) cc_final: 0.8836 (m-80) REVERT: C 504 ARG cc_start: 0.7545 (tpm170) cc_final: 0.5976 (tpp80) REVERT: D 242 MET cc_start: 0.7400 (mmm) cc_final: 0.6801 (tpt) REVERT: D 250 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8544 (p) REVERT: D 436 PHE cc_start: 0.7378 (p90) cc_final: 0.7155 (p90) REVERT: D 583 MET cc_start: 0.8913 (tpp) cc_final: 0.8601 (mmm) outliers start: 43 outliers final: 37 residues processed: 224 average time/residue: 0.3293 time to fit residues: 113.2450 Evaluate side-chains 231 residues out of total 1890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3091 MET Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3727 MET Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 3916 VAL Chi-restraints excluded: chain A residue 3985 SER Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain A residue 4036 LEU Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4117 LEU Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 358 PHE Chi-restraints excluded: chain D residue 405 GLN Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 26 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 100 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** 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 = 0.3656 r_free = 0.3656 target = 0.147015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100631 restraints weight = 23550.388| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.28 r_work: 0.2848 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 17819 Z= 0.154 Angle : 0.552 9.891 24227 Z= 0.288 Chirality : 0.041 0.324 2761 Planarity : 0.004 0.057 3008 Dihedral : 6.304 108.869 2563 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.31 % Favored : 91.60 % Rotamer: Outliers : 2.18 % Allowed : 15.47 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 2142 helix: 1.75 (0.16), residues: 1150 sheet: -0.86 (0.38), residues: 195 loop : -2.91 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A3922 HIS 0.006 0.001 HIS B 498 PHE 0.023 0.001 PHE D 436 TYR 0.022 0.001 TYR A3614 ARG 0.014 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 9) link_NAG-ASN : angle 2.34932 ( 27) hydrogen bonds : bond 0.04744 ( 895) hydrogen bonds : angle 3.65174 ( 2613) SS BOND : bond 0.00243 ( 3) SS BOND : angle 1.30964 ( 6) covalent geometry : bond 0.00367 (17807) covalent geometry : angle 0.54636 (24194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10511.83 seconds wall clock time: 184 minutes 2.37 seconds (11042.37 seconds total)