Starting phenix.real_space_refine on Thu Feb 5 10:06:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l0m_62719/02_2026/9l0m_62719.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l0m_62719/02_2026/9l0m_62719.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/9l0m_62719/02_2026/9l0m_62719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l0m_62719/02_2026/9l0m_62719.map" model { file = "/net/cci-nas-00/data/ceres_data/9l0m_62719/02_2026/9l0m_62719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l0m_62719/02_2026/9l0m_62719.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 10534 2.51 5 N 2767 2.21 5 O 2888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16256 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5654 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 31, 'TRANS': 729} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 383 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ARG:plan': 10, 'PHE:plan': 6, 'TYR:plan': 2, 'GLU:plan': 3, 'TRP:plan': 5, 'HIS:plan': 7, 'ASP:plan': 7, 'ASN:plan1': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 233 Chain: "B" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3932 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3860 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 10, 'TRANS': 457} Chain breaks: 1 Chain: "D" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 2726 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 329} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1289 Unresolved non-hydrogen angles: 1678 Unresolved non-hydrogen dihedrals: 1105 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'TYR:plan': 21, 'ARG:plan': 20, 'GLU:plan': 19, 'PHE:plan': 31, 'ASN:plan1': 20, 'GLN:plan1': 11, 'ASP:plan': 14, 'TRP:plan': 9, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 756 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.53, per 1000 atoms: 0.22 Number of scatterers: 16256 At special positions: 0 Unit cell: (123.918, 166.311, 125.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 2888 8.00 N 2767 7.00 C 10534 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A3770 " - pdb=" SG CYS A3811 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B1001 " - " ASN B 375 " " NAG B1002 " - " ASN B 362 " " NAG B1003 " - " ASN B 328 " " NAG C1001 " - " ASN C 375 " " NAG C1002 " - " ASN C 362 " " NAG C1003 " - " ASN C 328 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 649.5 milliseconds 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4138 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 6 sheets defined 56.0% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 3074 through 3082 removed outlier: 3.692A pdb=" N MET A3078 " --> pdb=" O ASN A3074 " (cutoff:3.500A) Processing helix chain 'A' and resid 3085 through 3106 removed outlier: 3.688A pdb=" N MET A3091 " --> pdb=" O THR A3087 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A3093 " --> pdb=" O MET A3089 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A3094 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A3101 " --> pdb=" O LYS A3097 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP A3102 " --> pdb=" O LEU A3098 " (cutoff:3.500A) Processing helix chain 'A' and resid 3244 through 3257 removed outlier: 4.168A pdb=" N VAL A3250 " --> pdb=" O ARG A3246 " (cutoff:3.500A) Processing helix chain 'A' and resid 3262 through 3266 removed outlier: 3.548A pdb=" N SER A3265 " --> pdb=" O ILE A3262 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE A3266 " --> pdb=" O TRP A3263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3262 through 3266' Processing helix chain 'A' and resid 3279 through 3299 removed outlier: 3.586A pdb=" N VAL A3285 " --> pdb=" O ALA A3281 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A3299 " --> pdb=" O ASN A3295 " (cutoff:3.500A) Processing helix chain 'A' and resid 3309 through 3313 removed outlier: 3.776A pdb=" N VAL A3312 " --> pdb=" O THR A3309 " (cutoff:3.500A) Processing helix chain 'A' and resid 3323 through 3341 removed outlier: 3.637A pdb=" N TYR A3334 " --> pdb=" O SER A3330 " (cutoff:3.500A) Proline residue: A3335 - end of helix removed outlier: 4.117A pdb=" N ALA A3339 " --> pdb=" O PRO A3335 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A3340 " --> pdb=" O VAL A3336 " (cutoff:3.500A) Processing helix chain 'A' and resid 3342 through 3344 No H-bonds generated for 'chain 'A' and resid 3342 through 3344' Processing helix chain 'A' and resid 3553 through 3578 removed outlier: 3.661A pdb=" N LEU A3557 " --> pdb=" O TRP A3553 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A3567 " --> pdb=" O LEU A3563 " (cutoff:3.500A) Processing helix chain 'A' and resid 3583 through 3597 removed outlier: 4.097A pdb=" N ALA A3587 " --> pdb=" O GLY A3583 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A3589 " --> pdb=" O SER A3585 " (cutoff:3.500A) Processing helix chain 'A' and resid 3603 through 3618 Processing helix chain 'A' and resid 3656 through 3690 removed outlier: 4.013A pdb=" N GLU A3660 " --> pdb=" O LEU A3656 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A3675 " --> pdb=" O LEU A3671 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL A3676 " --> pdb=" O ARG A3672 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A3677 " --> pdb=" O SER A3673 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A3688 " --> pdb=" O THR A3684 " (cutoff:3.500A) Processing helix chain 'A' and resid 3695 through 3707 removed outlier: 3.734A pdb=" N LYS A3706 " --> pdb=" O GLN A3702 " (cutoff:3.500A) Processing helix chain 'A' and resid 3710 through 3716 Processing helix chain 'A' and resid 3722 through 3730 Processing helix chain 'A' and resid 3730 through 3736 Processing helix chain 'A' and resid 3826 through 3840 Processing helix chain 'A' and resid 3892 through 3896 removed outlier: 4.001A pdb=" N GLY A3896 " --> pdb=" O LEU A3893 " (cutoff:3.500A) Processing helix chain 'A' and resid 3898 through 3926 removed outlier: 3.814A pdb=" N SER A3904 " --> pdb=" O PRO A3900 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU A3907 " --> pdb=" O THR A3903 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A3908 " --> pdb=" O SER A3904 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A3912 " --> pdb=" O LEU A3908 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A3915 " --> pdb=" O ALA A3911 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A3918 " --> pdb=" O PHE A3914 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A3921 " --> pdb=" O ALA A3917 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A3924 " --> pdb=" O ARG A3920 " (cutoff:3.500A) Processing helix chain 'A' and resid 3932 through 3936 Processing helix chain 'A' and resid 3938 through 3969 removed outlier: 3.813A pdb=" N ALA A3947 " --> pdb=" O ALA A3943 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A3952 " --> pdb=" O THR A3948 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A3953 " --> pdb=" O ALA A3949 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A3954 " --> pdb=" O LEU A3950 " (cutoff:3.500A) Processing helix chain 'A' and resid 3970 through 3973 removed outlier: 3.664A pdb=" N ARG A3973 " --> pdb=" O ARG A3970 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3970 through 3973' Processing helix chain 'A' and resid 3977 through 4005 removed outlier: 3.733A pdb=" N ALA A3981 " --> pdb=" O PHE A3977 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A3985 " --> pdb=" O ALA A3981 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG A3988 " --> pdb=" O SER A3984 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A3991 " --> pdb=" O ALA A3987 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A3995 " --> pdb=" O ALA A3991 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A3996 " --> pdb=" O ALA A3992 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4012 Processing helix chain 'A' and resid 4013 through 4022 removed outlier: 3.791A pdb=" N LYS A4017 " --> pdb=" O SER A4013 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A4022 " --> pdb=" O THR A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4022 through 4043 removed outlier: 3.785A pdb=" N LEU A4043 " --> pdb=" O ALA A4039 " (cutoff:3.500A) Processing helix chain 'A' and resid 4092 through 4100 Processing helix chain 'A' and resid 4100 through 4119 removed outlier: 3.999A pdb=" N VAL A4104 " --> pdb=" O ARG A4100 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A4109 " --> pdb=" O ILE A4105 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A4119 " --> pdb=" O GLY A4115 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.617A pdb=" N TYR B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 258 removed outlier: 4.288A pdb=" N TYR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 256 " --> pdb=" O MET B 252 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.796A pdb=" N LEU B 273 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 284 removed outlier: 3.593A pdb=" N PHE B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.036A pdb=" N GLU B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 removed outlier: 3.996A pdb=" N ALA B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 493 Processing helix chain 'B' and resid 508 through 530 removed outlier: 3.673A pdb=" N VAL B 513 " --> pdb=" O CYS B 509 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 541 removed outlier: 3.505A pdb=" N LEU B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 removed outlier: 3.624A pdb=" N ILE B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 567 " --> pdb=" O ALA B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.538A pdb=" N ILE B 577 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 620 removed outlier: 3.766A pdb=" N LEU B 586 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 600 " --> pdb=" O ASP B 596 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 641 Processing helix chain 'B' and resid 648 through 653 removed outlier: 3.830A pdb=" N ALA B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 648 through 653' Processing helix chain 'B' and resid 656 through 670 removed outlier: 3.507A pdb=" N TYR B 660 " --> pdb=" O LEU B 656 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 661 " --> pdb=" O GLY B 657 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 698 removed outlier: 3.829A pdb=" N ILE B 680 " --> pdb=" O PHE B 676 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN B 694 " --> pdb=" O ASP B 690 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET B 698 " --> pdb=" O GLN B 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 240 removed outlier: 3.526A pdb=" N GLY C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 259 removed outlier: 3.830A pdb=" N TYR C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 334 through 338 removed outlier: 3.547A pdb=" N LEU C 337 " --> pdb=" O PRO C 334 " (cutoff:3.500A) removed outlier: 3.587A 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: 3.648A pdb=" N GLU C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.806A pdb=" N TRP C 366 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE C 367 " --> pdb=" O THR C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 367' Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 398 through 412 removed outlier: 3.563A pdb=" N ASN C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 498 removed outlier: 3.977A pdb=" N LEU C 473 " --> pdb=" O PHE C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 531 removed outlier: 3.668A pdb=" N ILE C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 525 " --> pdb=" O ALA C 521 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 526 " --> pdb=" O ILE C 522 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 572 removed outlier: 3.954A pdb=" N GLN C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE C 556 " --> pdb=" O ALA C 552 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN C 559 " --> pdb=" O GLN C 555 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE C 561 " --> pdb=" O GLN C 557 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL C 564 " --> pdb=" O ASN C 560 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 566 " --> pdb=" O ALA C 562 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 572 " --> pdb=" O PHE C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 576 Processing helix chain 'C' and resid 580 through 593 removed outlier: 3.634A pdb=" N CYS C 593 " --> pdb=" O THR C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 619 removed outlier: 3.602A pdb=" N ILE C 602 " --> pdb=" O PHE C 598 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 642 Processing helix chain 'C' and resid 648 through 653 removed outlier: 3.561A pdb=" N ASN C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 670 Processing helix chain 'C' and resid 673 through 698 removed outlier: 3.884A pdb=" N ALA C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 240 Processing helix chain 'D' and resid 243 through 258 removed outlier: 3.512A pdb=" N TYR D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.992A pdb=" N LEU D 273 " --> pdb=" O PHE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 284 removed outlier: 4.365A pdb=" N TRP D 280 " --> pdb=" O MET D 276 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 284 " --> pdb=" O TRP D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 291 removed outlier: 3.540A pdb=" N LEU D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 492 Processing helix chain 'D' and resid 507 through 529 removed outlier: 4.171A pdb=" N ASP D 511 " --> pdb=" O TRP D 507 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 512 " --> pdb=" O ASN D 508 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR D 529 " --> pdb=" O ASN D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 541 removed outlier: 4.002A pdb=" N LEU D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 576 Processing helix chain 'D' and resid 586 through 619 removed outlier: 3.515A pdb=" N ILE D 602 " --> pdb=" O PHE D 598 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET D 603 " --> pdb=" O GLY D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 642 removed outlier: 3.663A pdb=" N ILE D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 removed outlier: 4.062A pdb=" N GLU D 650 " --> pdb=" O PHE D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 670 Processing helix chain 'D' and resid 673 through 698 removed outlier: 3.886A pdb=" N ALA D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 680 " --> pdb=" O PHE D 676 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA D 696 " --> pdb=" O ALA D 692 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3135 through 3140 removed outlier: 4.541A pdb=" N THR A3135 " --> pdb=" O LYS A3189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3748 through 3749 removed outlier: 3.608A pdb=" N ARG A3748 " --> pdb=" O GLU A3853 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A3853 " --> pdb=" O ARG A3748 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3748 through 3749 removed outlier: 3.608A pdb=" N ARG A3748 " --> pdb=" O GLU A3853 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A3853 " --> pdb=" O ARG A3748 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.640A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.539A 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: 6.652A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 368 through 369 removed outlier: 3.596A pdb=" N GLY D 390 " --> pdb=" O THR D 369 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL D 318 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER D 427 " --> pdb=" O VAL D 318 " (cutoff:3.500A) 865 hydrogen bonds defined for protein. 2511 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.90 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: 5244 1.34 - 1.46: 4287 1.46 - 1.58: 6985 1.58 - 1.70: 0 1.70 - 1.82: 103 Bond restraints: 16619 Sorted by residual: bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CA ARG C 464 " pdb=" C ARG C 464 " ideal model delta sigma weight residual 1.517 1.526 -0.009 6.30e-03 2.52e+04 1.97e+00 bond pdb=" C1 NAG C1001 " pdb=" O5 NAG C1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" N ASP B 624 " pdb=" CA ASP B 624 " ideal model delta sigma weight residual 1.460 1.477 -0.017 1.28e-02 6.10e+03 1.86e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 ... (remaining 16614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 22417 2.53 - 5.06: 198 5.06 - 7.58: 19 7.58 - 10.11: 7 10.11 - 12.64: 2 Bond angle restraints: 22643 Sorted by residual: angle pdb=" N SER A3740 " pdb=" CA SER A3740 " pdb=" C SER A3740 " ideal model delta sigma weight residual 108.24 120.88 -12.64 1.81e+00 3.05e-01 4.87e+01 angle pdb=" CA ARG C 464 " pdb=" C ARG C 464 " pdb=" N TYR C 465 " ideal model delta sigma weight residual 119.46 116.24 3.22 6.10e-01 2.69e+00 2.78e+01 angle pdb=" C VAL B 623 " pdb=" N ASP B 624 " pdb=" CA ASP B 624 " ideal model delta sigma weight residual 126.86 134.92 -8.06 1.57e+00 4.06e-01 2.64e+01 angle pdb=" C ASP B 624 " pdb=" CA ASP B 624 " pdb=" CB ASP B 624 " ideal model delta sigma weight residual 109.83 105.34 4.49 9.90e-01 1.02e+00 2.06e+01 angle pdb=" N GLN A3739 " pdb=" CA GLN A3739 " pdb=" C GLN A3739 " ideal model delta sigma weight residual 110.80 101.88 8.92 2.13e+00 2.20e-01 1.76e+01 ... (remaining 22638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 9269 24.95 - 49.89: 405 49.89 - 74.84: 33 74.84 - 99.78: 22 99.78 - 124.73: 5 Dihedral angle restraints: 9734 sinusoidal: 3353 harmonic: 6381 Sorted by residual: dihedral pdb=" CB CYS A3770 " pdb=" SG CYS A3770 " pdb=" SG CYS A3811 " pdb=" CB CYS A3811 " ideal model delta sinusoidal sigma weight residual 93.00 -179.93 -87.07 1 1.00e+01 1.00e-02 9.11e+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 -86.00 -153.73 67.73 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CA PHE A3275 " pdb=" C PHE A3275 " pdb=" N THR A3276 " pdb=" CA THR A3276 " ideal model delta harmonic sigma weight residual 180.00 151.73 28.27 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 9731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2315 0.062 - 0.124: 313 0.124 - 0.186: 11 0.186 - 0.248: 1 0.248 - 0.310: 1 Chirality restraints: 2641 Sorted by residual: chirality pdb=" CA SER A3740 " pdb=" N SER A3740 " pdb=" C SER A3740 " pdb=" CB SER A3740 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA GLN A3739 " pdb=" N GLN A3739 " pdb=" C GLN A3739 " pdb=" CB GLN A3739 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA THR A3276 " pdb=" N THR A3276 " pdb=" C THR A3276 " pdb=" CB THR A3276 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2638 not shown) Planarity restraints: 2876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 623 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.63e+00 pdb=" C VAL B 623 " -0.051 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 " 0.035 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A3582 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A3582 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A3582 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A3741 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO A3742 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A3742 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A3742 " -0.025 5.00e-02 4.00e+02 ... (remaining 2873 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.84: 4 1.84 - 2.60: 131 2.60 - 3.37: 21154 3.37 - 4.13: 34669 4.13 - 4.90: 65503 Nonbonded interactions: 121461 Sorted by model distance: nonbonded pdb=" CH2 TRP A4096 " pdb=" CD1 PHE B 670 " model vdw 1.075 3.640 nonbonded pdb=" CH2 TRP A4096 " pdb=" CE1 PHE B 670 " model vdw 1.406 3.640 nonbonded pdb=" CZ3 TRP A4096 " pdb=" CD1 PHE B 670 " model vdw 1.502 3.640 nonbonded pdb=" CZ2 TRP A4096 " pdb=" CE1 PHE B 670 " model vdw 1.563 3.640 nonbonded pdb=" OD1 ASP C 470 " pdb=" N PHE C 471 " model vdw 1.908 3.120 ... (remaining 121456 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 215 through 239 and (name N or name CA or name C or name \ O or name CB )) or resid 240 or (resid 241 through 284 and (name N or name CA or \ name C or name O or name CB )) or resid 285 or (resid 286 through 289 and (name \ N or name CA or name C or name O or name CB )) or resid 290 or (resid 291 throu \ gh 294 and (name N or name CA or name C or name O or name CB )) or (resid 311 th \ rough 316 and (name N or name CA or name C or name O or name CB )) or resid 317 \ or (resid 318 through 328 and (name N or name CA or name C or name O or name CB \ )) or resid 329 or (resid 330 through 358 and (name N or name CA or name C or na \ me O or name CB )) or resid 359 or (resid 360 through 362 and (name N or name CA \ or name C or name O or name CB )) or resid 363 or (resid 364 through 375 and (n \ ame N or name CA or name C or name O or name CB )) or resid 376 or (resid 377 th \ rough 380 and (name N or name CA or name C or name O or name CB )) or resid 381 \ or (resid 382 through 387 and (name N or name CA or name C or name O or name CB \ )) or (resid 388 through 417 and (name N or name CA or name C or name O or name \ CB )) or resid 418 or (resid 419 through 448 and (name N or name CA or name C or \ name O or name CB )) or resid 449 through 450 or (resid 451 through 522 and (na \ me N or name CA or name C or name O or name CB )) or resid 523 or (resid 524 thr \ ough 582 and (name N or name CA or name C or name O or name CB )) or resid 583 t \ hrough 698)) selection = (chain 'C' and ((resid 215 through 239 and (name N or name CA or name C or name \ O or name CB )) or resid 240 or (resid 241 through 284 and (name N or name CA or \ name C or name O or name CB )) or resid 285 or (resid 286 through 289 and (name \ N or name CA or name C or name O or name CB )) or resid 290 or (resid 291 throu \ gh 316 and (name N or name CA or name C or name O or name CB )) or resid 317 or \ (resid 318 through 328 and (name N or name CA or name C or name O or name CB )) \ or resid 329 or (resid 330 through 358 and (name N or name CA or name C or name \ O or name CB )) or resid 359 or (resid 360 through 362 and (name N or name CA or \ name C or name O or name CB )) or resid 363 or (resid 364 through 375 and (name \ N or name CA or name C or name O or name CB )) or resid 376 or (resid 377 throu \ gh 380 and (name N or name CA or name C or name O or name CB )) or resid 381 or \ (resid 382 through 387 and (name N or name CA or name C or name O or name CB )) \ or (resid 388 through 417 and (name N or name CA or name C or name O or name CB \ )) or resid 418 or (resid 419 through 448 and (name N or name CA or name C or na \ me O or name CB )) or resid 449 through 450 or (resid 451 through 522 and (name \ N or name CA or name C or name O or name CB )) or resid 523 or (resid 524 throug \ h 582 and (name N or name CA or name C or name O or name CB )) or resid 583 thro \ ugh 698)) selection = (chain 'D' and (resid 215 through 294 or resid 311 through 698)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.120 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16628 Z= 0.155 Angle : 0.640 12.638 22667 Z= 0.370 Chirality : 0.041 0.310 2641 Planarity : 0.004 0.054 2870 Dihedral : 14.417 124.729 5587 Min Nonbonded Distance : 1.075 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.07 % Favored : 91.66 % Rotamer: Outliers : 0.34 % Allowed : 0.81 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.19), residues: 2157 helix: 0.42 (0.17), residues: 1125 sheet: -1.23 (0.39), residues: 192 loop : -3.01 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3856 TYR 0.017 0.001 TYR B 216 PHE 0.015 0.001 PHE C 669 TRP 0.020 0.001 TRP A4096 HIS 0.002 0.001 HIS A3864 Details of bonding type rmsd covalent geometry : bond 0.00291 (16619) covalent geometry : angle 0.63723 (22643) SS BOND : bond 0.00036 ( 3) SS BOND : angle 3.20076 ( 6) hydrogen bonds : bond 0.16425 ( 863) hydrogen bonds : angle 6.11502 ( 2511) link_NAG-ASN : bond 0.00219 ( 6) link_NAG-ASN : angle 0.98143 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 224 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: C 531 ASN cc_start: 0.8038 (m-40) cc_final: 0.7580 (t0) outliers start: 5 outliers final: 2 residues processed: 228 average time/residue: 0.1151 time to fit residues: 39.9831 Evaluate side-chains 173 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 466 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 chunk 200 optimal weight: 50.0000 chunk 212 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 636 GLN C 550 HIS C 694 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.124672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086447 restraints weight = 34192.739| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.33 r_work: 0.3007 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16628 Z= 0.122 Angle : 0.577 12.997 22667 Z= 0.297 Chirality : 0.041 0.258 2641 Planarity : 0.004 0.047 2870 Dihedral : 7.738 113.297 2482 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.29 % Allowed : 8.55 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.19), residues: 2157 helix: 0.74 (0.16), residues: 1155 sheet: -1.13 (0.39), residues: 189 loop : -3.02 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3856 TYR 0.009 0.001 TYR A3689 PHE 0.024 0.001 PHE B 670 TRP 0.032 0.001 TRP A4096 HIS 0.002 0.000 HIS A3864 Details of bonding type rmsd covalent geometry : bond 0.00254 (16619) covalent geometry : angle 0.57481 (22643) SS BOND : bond 0.00157 ( 3) SS BOND : angle 1.68300 ( 6) hydrogen bonds : bond 0.04174 ( 863) hydrogen bonds : angle 4.20755 ( 2511) link_NAG-ASN : bond 0.00227 ( 6) link_NAG-ASN : angle 1.46969 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.589 Fit side-chains REVERT: C 425 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8355 (m-30) REVERT: C 531 ASN cc_start: 0.8205 (m-40) cc_final: 0.7812 (t0) outliers start: 19 outliers final: 10 residues processed: 192 average time/residue: 0.1082 time to fit residues: 32.5016 Evaluate side-chains 181 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 4038 VAL Chi-restraints excluded: chain A residue 4095 LEU Chi-restraints excluded: chain A residue 4105 ILE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 672 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 3 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 191 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 181 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 190 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3623 HIS B 674 ASN C 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.120554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.082249 restraints weight = 35429.148| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.91 r_work: 0.2992 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16628 Z= 0.159 Angle : 0.564 9.518 22667 Z= 0.291 Chirality : 0.041 0.169 2641 Planarity : 0.004 0.044 2870 Dihedral : 6.604 113.027 2477 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 1.90 % Allowed : 10.79 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.19), residues: 2157 helix: 1.01 (0.16), residues: 1150 sheet: -1.20 (0.39), residues: 194 loop : -2.95 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3892 TYR 0.011 0.001 TYR B 348 PHE 0.019 0.001 PHE B 670 TRP 0.010 0.001 TRP A3298 HIS 0.003 0.001 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00366 (16619) covalent geometry : angle 0.56226 (22643) SS BOND : bond 0.00190 ( 3) SS BOND : angle 1.24094 ( 6) hydrogen bonds : bond 0.04011 ( 863) hydrogen bonds : angle 3.98086 ( 2511) link_NAG-ASN : bond 0.00143 ( 6) link_NAG-ASN : angle 1.51409 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 3268 ASP cc_start: 0.8603 (t70) cc_final: 0.8395 (t70) REVERT: C 425 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8182 (m-30) REVERT: C 531 ASN cc_start: 0.8143 (m-40) cc_final: 0.7795 (t0) REVERT: C 590 MET cc_start: 0.9236 (tpp) cc_final: 0.9006 (tpp) outliers start: 28 outliers final: 16 residues processed: 185 average time/residue: 0.1030 time to fit residues: 29.7315 Evaluate side-chains 184 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3869 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4036 LEU Chi-restraints excluded: chain A residue 4038 VAL Chi-restraints excluded: chain A residue 4095 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 672 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 141 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 7 optimal weight: 0.0060 chunk 51 optimal weight: 9.9990 chunk 83 optimal weight: 0.0000 overall best weight: 0.7004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 557 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.123369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.085415 restraints weight = 34950.092| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.87 r_work: 0.3051 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16628 Z= 0.096 Angle : 0.509 9.261 22667 Z= 0.261 Chirality : 0.039 0.250 2641 Planarity : 0.003 0.043 2870 Dihedral : 6.097 111.290 2477 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.77 % Allowed : 12.70 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.19), residues: 2157 helix: 1.31 (0.16), residues: 1143 sheet: -0.69 (0.41), residues: 170 loop : -2.86 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4100 TYR 0.007 0.001 TYR C 660 PHE 0.008 0.001 PHE C 426 TRP 0.009 0.001 TRP A3922 HIS 0.003 0.001 HIS B 501 Details of bonding type rmsd covalent geometry : bond 0.00195 (16619) covalent geometry : angle 0.50776 (22643) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.81007 ( 6) hydrogen bonds : bond 0.03165 ( 863) hydrogen bonds : angle 3.72471 ( 2511) link_NAG-ASN : bond 0.00268 ( 6) link_NAG-ASN : angle 1.42738 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.525 Fit side-chains REVERT: A 3268 ASP cc_start: 0.8553 (t70) cc_final: 0.8269 (t70) REVERT: C 425 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8065 (m-30) REVERT: C 531 ASN cc_start: 0.8136 (m-40) cc_final: 0.7841 (t0) outliers start: 26 outliers final: 8 residues processed: 207 average time/residue: 0.1101 time to fit residues: 35.0306 Evaluate side-chains 181 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3869 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain D residue 672 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 177 optimal weight: 50.0000 chunk 45 optimal weight: 0.0570 chunk 174 optimal weight: 40.0000 chunk 103 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 ASN C 323 GLN D 694 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081428 restraints weight = 35060.351| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.83 r_work: 0.2971 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16628 Z= 0.204 Angle : 0.588 13.642 22667 Z= 0.303 Chirality : 0.042 0.222 2641 Planarity : 0.004 0.044 2870 Dihedral : 6.231 111.574 2477 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.62 % Favored : 91.33 % Rotamer: Outliers : 2.10 % Allowed : 14.19 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.19), residues: 2157 helix: 1.30 (0.16), residues: 1150 sheet: -1.14 (0.39), residues: 192 loop : -2.90 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3269 TYR 0.017 0.001 TYR B 227 PHE 0.011 0.001 PHE B 538 TRP 0.010 0.001 TRP B 293 HIS 0.004 0.001 HIS A3559 Details of bonding type rmsd covalent geometry : bond 0.00477 (16619) covalent geometry : angle 0.58616 (22643) SS BOND : bond 0.00191 ( 3) SS BOND : angle 1.49108 ( 6) hydrogen bonds : bond 0.04076 ( 863) hydrogen bonds : angle 3.83601 ( 2511) link_NAG-ASN : bond 0.00151 ( 6) link_NAG-ASN : angle 1.65864 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.626 Fit side-chains REVERT: A 3258 PHE cc_start: 0.8766 (m-10) cc_final: 0.8541 (m-10) REVERT: A 3268 ASP cc_start: 0.8599 (t70) cc_final: 0.8326 (t70) REVERT: A 3563 LEU cc_start: 0.9002 (mm) cc_final: 0.8731 (mm) REVERT: C 425 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: C 531 ASN cc_start: 0.8184 (m-40) cc_final: 0.7794 (t0) REVERT: C 590 MET cc_start: 0.9297 (tpp) cc_final: 0.8989 (ttp) REVERT: D 617 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9297 (mp) outliers start: 31 outliers final: 17 residues processed: 183 average time/residue: 0.1073 time to fit residues: 30.8227 Evaluate side-chains 179 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3823 LEU Chi-restraints excluded: chain A residue 3869 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4038 VAL Chi-restraints excluded: chain A residue 4095 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 694 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 148 optimal weight: 0.9990 chunk 192 optimal weight: 50.0000 chunk 70 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 15 optimal weight: 50.0000 chunk 103 optimal weight: 0.1980 chunk 131 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 674 ASN C 323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.122438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.083205 restraints weight = 34866.008| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.93 r_work: 0.3019 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16628 Z= 0.102 Angle : 0.539 12.174 22667 Z= 0.272 Chirality : 0.040 0.211 2641 Planarity : 0.003 0.043 2870 Dihedral : 5.961 111.204 2477 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.90 % Allowed : 15.21 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.19), residues: 2157 helix: 1.52 (0.16), residues: 1151 sheet: -0.78 (0.41), residues: 175 loop : -2.82 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4114 TYR 0.014 0.001 TYR B 227 PHE 0.008 0.001 PHE C 426 TRP 0.009 0.001 TRP A3922 HIS 0.002 0.001 HIS B 501 Details of bonding type rmsd covalent geometry : bond 0.00216 (16619) covalent geometry : angle 0.53712 (22643) SS BOND : bond 0.00150 ( 3) SS BOND : angle 1.08076 ( 6) hydrogen bonds : bond 0.03292 ( 863) hydrogen bonds : angle 3.65491 ( 2511) link_NAG-ASN : bond 0.00234 ( 6) link_NAG-ASN : angle 1.44912 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.672 Fit side-chains REVERT: A 3258 PHE cc_start: 0.8732 (m-10) cc_final: 0.8480 (m-10) REVERT: A 3268 ASP cc_start: 0.8588 (t70) cc_final: 0.8330 (t70) REVERT: A 3563 LEU cc_start: 0.9014 (mm) cc_final: 0.8804 (mm) REVERT: A 4027 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8621 (tp) REVERT: C 425 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: C 531 ASN cc_start: 0.8158 (m-40) cc_final: 0.7786 (t0) REVERT: C 590 MET cc_start: 0.9306 (tpp) cc_final: 0.9033 (ttp) outliers start: 28 outliers final: 13 residues processed: 189 average time/residue: 0.1056 time to fit residues: 30.7924 Evaluate side-chains 179 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3823 LEU Chi-restraints excluded: chain A residue 3869 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 672 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 140 optimal weight: 1.9990 chunk 188 optimal weight: 50.0000 chunk 23 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 185 optimal weight: 50.0000 chunk 116 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.122406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.083051 restraints weight = 34714.162| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.91 r_work: 0.3020 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16628 Z= 0.114 Angle : 0.544 12.489 22667 Z= 0.272 Chirality : 0.040 0.295 2641 Planarity : 0.003 0.044 2870 Dihedral : 5.800 110.305 2477 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.36 % Allowed : 15.95 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.19), residues: 2157 helix: 1.64 (0.16), residues: 1147 sheet: -0.56 (0.41), residues: 170 loop : -2.83 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4114 TYR 0.014 0.001 TYR B 227 PHE 0.008 0.001 PHE B 538 TRP 0.009 0.001 TRP A3298 HIS 0.003 0.001 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00254 (16619) covalent geometry : angle 0.54202 (22643) SS BOND : bond 0.00140 ( 3) SS BOND : angle 1.00185 ( 6) hydrogen bonds : bond 0.03267 ( 863) hydrogen bonds : angle 3.59274 ( 2511) link_NAG-ASN : bond 0.00178 ( 6) link_NAG-ASN : angle 1.45057 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.423 Fit side-chains REVERT: A 3258 PHE cc_start: 0.8731 (m-10) cc_final: 0.8499 (m-10) REVERT: A 3268 ASP cc_start: 0.8606 (t70) cc_final: 0.8387 (t70) REVERT: A 3275 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8593 (t80) REVERT: A 3279 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: A 3563 LEU cc_start: 0.9010 (mm) cc_final: 0.8806 (mm) REVERT: C 425 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8029 (m-30) REVERT: C 531 ASN cc_start: 0.8150 (m-40) cc_final: 0.7800 (t0) REVERT: C 590 MET cc_start: 0.9288 (tpp) cc_final: 0.8984 (ttp) outliers start: 20 outliers final: 15 residues processed: 181 average time/residue: 0.1040 time to fit residues: 29.5115 Evaluate side-chains 186 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3279 GLN Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3823 LEU Chi-restraints excluded: chain A residue 3869 LEU Chi-restraints excluded: chain A residue 4031 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 672 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 8 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 192 optimal weight: 40.0000 chunk 160 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 179 optimal weight: 40.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 694 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.121470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083213 restraints weight = 34842.036| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.89 r_work: 0.3006 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16628 Z= 0.134 Angle : 0.553 15.917 22667 Z= 0.277 Chirality : 0.040 0.239 2641 Planarity : 0.003 0.044 2870 Dihedral : 5.788 110.260 2477 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 1.97 % Allowed : 15.34 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 2157 helix: 1.71 (0.16), residues: 1146 sheet: -0.56 (0.41), residues: 170 loop : -2.82 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4100 TYR 0.014 0.001 TYR B 227 PHE 0.009 0.001 PHE B 423 TRP 0.014 0.001 TRP A4096 HIS 0.003 0.001 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00309 (16619) covalent geometry : angle 0.55164 (22643) SS BOND : bond 0.00141 ( 3) SS BOND : angle 1.02610 ( 6) hydrogen bonds : bond 0.03390 ( 863) hydrogen bonds : angle 3.60613 ( 2511) link_NAG-ASN : bond 0.00147 ( 6) link_NAG-ASN : angle 1.45405 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.517 Fit side-chains REVERT: A 3258 PHE cc_start: 0.8756 (m-10) cc_final: 0.8528 (m-10) REVERT: A 3275 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8576 (t80) REVERT: A 3279 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: A 3563 LEU cc_start: 0.9003 (mm) cc_final: 0.8802 (mm) REVERT: A 4096 TRP cc_start: 0.7985 (t-100) cc_final: 0.7698 (t-100) REVERT: A 4101 LEU cc_start: 0.8989 (tp) cc_final: 0.8756 (tp) REVERT: C 425 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8075 (m-30) REVERT: C 531 ASN cc_start: 0.8140 (m-40) cc_final: 0.7831 (t0) REVERT: C 590 MET cc_start: 0.9267 (tpp) cc_final: 0.8872 (tpp) outliers start: 29 outliers final: 22 residues processed: 186 average time/residue: 0.1006 time to fit residues: 29.1957 Evaluate side-chains 194 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3279 GLN Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3823 LEU Chi-restraints excluded: chain A residue 3869 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4031 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain A residue 4105 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 694 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 54 optimal weight: 0.9980 chunk 186 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 175 optimal weight: 40.0000 chunk 91 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 13 optimal weight: 50.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.122481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.084186 restraints weight = 34584.699| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.93 r_work: 0.3024 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16628 Z= 0.103 Angle : 0.544 17.005 22667 Z= 0.270 Chirality : 0.040 0.236 2641 Planarity : 0.003 0.049 2870 Dihedral : 5.693 109.906 2477 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.97 % Allowed : 15.48 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.19), residues: 2157 helix: 1.81 (0.16), residues: 1146 sheet: -0.49 (0.41), residues: 170 loop : -2.80 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4114 TYR 0.027 0.001 TYR B 227 PHE 0.008 0.001 PHE C 426 TRP 0.010 0.001 TRP A3922 HIS 0.002 0.000 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00222 (16619) covalent geometry : angle 0.54271 (22643) SS BOND : bond 0.00132 ( 3) SS BOND : angle 0.85270 ( 6) hydrogen bonds : bond 0.03171 ( 863) hydrogen bonds : angle 3.54204 ( 2511) link_NAG-ASN : bond 0.00204 ( 6) link_NAG-ASN : angle 1.40713 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.402 Fit side-chains REVERT: A 3275 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8599 (t80) REVERT: A 3279 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: A 4096 TRP cc_start: 0.8006 (t-100) cc_final: 0.7667 (t-100) REVERT: A 4101 LEU cc_start: 0.8953 (tp) cc_final: 0.8733 (tp) REVERT: C 425 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: C 531 ASN cc_start: 0.8140 (m-40) cc_final: 0.7843 (t0) REVERT: C 590 MET cc_start: 0.9299 (tpp) cc_final: 0.8882 (tpp) outliers start: 29 outliers final: 21 residues processed: 189 average time/residue: 0.1052 time to fit residues: 30.9212 Evaluate side-chains 194 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3279 GLN Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3754 LEU Chi-restraints excluded: chain A residue 3823 LEU Chi-restraints excluded: chain A residue 3869 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4031 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 672 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 212 optimal weight: 0.0870 chunk 11 optimal weight: 10.0000 chunk 197 optimal weight: 50.0000 chunk 143 optimal weight: 0.7980 chunk 50 optimal weight: 0.0370 chunk 123 optimal weight: 6.9990 chunk 135 optimal weight: 0.1980 chunk 47 optimal weight: 30.0000 chunk 185 optimal weight: 50.0000 chunk 158 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 694 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.125067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.086052 restraints weight = 34737.939| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.94 r_work: 0.3061 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16628 Z= 0.093 Angle : 0.543 18.612 22667 Z= 0.267 Chirality : 0.039 0.229 2641 Planarity : 0.003 0.050 2870 Dihedral : 5.489 108.297 2477 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.77 % Allowed : 15.75 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.19), residues: 2157 helix: 1.92 (0.16), residues: 1145 sheet: -0.36 (0.42), residues: 170 loop : -2.73 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4114 TYR 0.024 0.001 TYR B 227 PHE 0.008 0.001 PHE B 670 TRP 0.012 0.001 TRP A3724 HIS 0.002 0.000 HIS A3261 Details of bonding type rmsd covalent geometry : bond 0.00190 (16619) covalent geometry : angle 0.54159 (22643) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.62642 ( 6) hydrogen bonds : bond 0.02764 ( 863) hydrogen bonds : angle 3.44609 ( 2511) link_NAG-ASN : bond 0.00258 ( 6) link_NAG-ASN : angle 1.29589 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.635 Fit side-chains REVERT: A 3279 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: A 4096 TRP cc_start: 0.7943 (t-100) cc_final: 0.7656 (t-100) REVERT: C 259 ASP cc_start: 0.8825 (m-30) cc_final: 0.8609 (m-30) REVERT: C 531 ASN cc_start: 0.8217 (m-40) cc_final: 0.7948 (t0) REVERT: C 590 MET cc_start: 0.9224 (tpp) cc_final: 0.8783 (tpp) REVERT: C 605 PHE cc_start: 0.8892 (m-80) cc_final: 0.8587 (m-10) REVERT: D 611 TYR cc_start: 0.9218 (m-80) cc_final: 0.8982 (m-80) outliers start: 26 outliers final: 19 residues processed: 201 average time/residue: 0.1117 time to fit residues: 34.9332 Evaluate side-chains 193 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3279 GLN Chi-restraints excluded: chain A residue 3315 LEU Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3754 LEU Chi-restraints excluded: chain A residue 3823 LEU Chi-restraints excluded: chain A residue 3869 LEU Chi-restraints excluded: chain A residue 4031 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 694 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 180 optimal weight: 50.0000 chunk 154 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 12 optimal weight: 40.0000 chunk 177 optimal weight: 40.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.124778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.085726 restraints weight = 34641.519| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.92 r_work: 0.3062 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 16628 Z= 0.171 Angle : 0.771 59.186 22667 Z= 0.425 Chirality : 0.041 0.224 2641 Planarity : 0.003 0.049 2870 Dihedral : 5.489 108.298 2477 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.49 % Allowed : 16.56 % Favored : 81.94 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.19), residues: 2157 helix: 1.89 (0.16), residues: 1145 sheet: -0.34 (0.42), residues: 170 loop : -2.73 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4114 TYR 0.022 0.001 TYR B 227 PHE 0.008 0.001 PHE C 426 TRP 0.010 0.001 TRP A3922 HIS 0.002 0.000 HIS A3864 Details of bonding type rmsd covalent geometry : bond 0.00347 (16619) covalent geometry : angle 0.76588 (22643) SS BOND : bond 0.05850 ( 3) SS BOND : angle 5.39716 ( 6) hydrogen bonds : bond 0.02863 ( 863) hydrogen bonds : angle 3.44203 ( 2511) link_NAG-ASN : bond 0.00269 ( 6) link_NAG-ASN : angle 1.28585 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3438.41 seconds wall clock time: 59 minutes 33.94 seconds (3573.94 seconds total)