Starting phenix.real_space_refine on Sat Sep 12 12:46:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jyl_9718/09_2026/6jyl_9718.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jyl_9718/09_2026/6jyl_9718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jyl_9718/09_2026/6jyl_9718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jyl_9718/09_2026/6jyl_9718.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6jyl_9718/09_2026/6jyl_9718.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jyl_9718/09_2026/6jyl_9718.cif" model { file = "/net/cci-nas-00/data/ceres_data/6jyl_9718/09_2026/6jyl_9718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jyl_9718/09_2026/6jyl_9718.cif" } resolution = 3.37 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 25 5.16 5 Be 1 3.05 5 C 9259 2.51 5 N 2959 2.21 5 O 3594 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16136 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4129 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 485} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.14, per 1000 atoms: 0.19 Number of scatterers: 16136 At special positions: 0 Unit cell: (146.59, 130.54, 123.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 25 16.00 P 294 15.00 Mg 1 11.99 F 3 9.00 O 3594 8.00 N 2959 7.00 C 9259 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 506.5 milliseconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 63.8% alpha, 3.7% beta 145 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.523A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.658A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.748A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.058A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.731A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.548A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.590A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.581A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.556A pdb=" N LEU C 115 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.565A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.646A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.831A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.666A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.585A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.596A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.055A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.839A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.711A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.509A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.654A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.586A pdb=" N MET H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.739A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.880A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 113 removed outlier: 3.526A pdb=" N THR K 106 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS K 111 " --> pdb=" O LYS K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 124 removed outlier: 3.537A pdb=" N GLU K 124 " --> pdb=" O LYS K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 143 removed outlier: 3.574A pdb=" N VAL K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL K 139 " --> pdb=" O GLN K 135 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 213 removed outlier: 3.733A pdb=" N GLN K 202 " --> pdb=" O PRO K 198 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU K 207 " --> pdb=" O GLY K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 241 removed outlier: 3.826A pdb=" N GLN K 230 " --> pdb=" O GLY K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 268 removed outlier: 3.646A pdb=" N TRP K 260 " --> pdb=" O THR K 256 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU K 261 " --> pdb=" O LEU K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 289 removed outlier: 3.944A pdb=" N GLU K 285 " --> pdb=" O GLU K 281 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU K 286 " --> pdb=" O GLU K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 309 Processing helix chain 'K' and resid 327 through 331 removed outlier: 4.197A pdb=" N ASN K 331 " --> pdb=" O ARG K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 341 Processing helix chain 'K' and resid 359 through 369 removed outlier: 4.052A pdb=" N LEU K 363 " --> pdb=" O ASN K 359 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP K 364 " --> pdb=" O LEU K 360 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA K 365 " --> pdb=" O HIS K 361 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE K 369 " --> pdb=" O ALA K 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 390 removed outlier: 3.636A pdb=" N ASP K 382 " --> pdb=" O ALA K 378 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE K 385 " --> pdb=" O PHE K 381 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER K 387 " --> pdb=" O ASP K 383 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU K 388 " --> pdb=" O TRP K 384 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER K 389 " --> pdb=" O PHE K 385 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR K 390 " --> pdb=" O SER K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 406 removed outlier: 3.754A pdb=" N LEU K 401 " --> pdb=" O ILE K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 446 removed outlier: 4.126A pdb=" N LYS K 439 " --> pdb=" O SER K 435 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP K 440 " --> pdb=" O MET K 436 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE K 444 " --> pdb=" O TRP K 440 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU K 445 " --> pdb=" O TYR K 441 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU K 446 " --> pdb=" O LYS K 442 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 478 removed outlier: 3.649A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS K 475 " --> pdb=" O GLN K 471 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 482 removed outlier: 3.652A pdb=" N PHE K 482 " --> pdb=" O PRO K 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 479 through 482' Processing helix chain 'K' and resid 495 through 501 Processing helix chain 'K' and resid 502 through 518 removed outlier: 3.958A pdb=" N VAL K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU K 516 " --> pdb=" O LYS K 512 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU K 517 " --> pdb=" O LYS K 513 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 541 removed outlier: 3.889A pdb=" N LEU K 531 " --> pdb=" O MET K 527 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP K 532 " --> pdb=" O SER K 528 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 554 through 565 removed outlier: 3.560A pdb=" N ILE K 558 " --> pdb=" O HIS K 554 " (cutoff:3.500A) Processing helix chain 'K' and resid 601 through 610 removed outlier: 3.598A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP K 610 " --> pdb=" O LEU K 606 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 657 removed outlier: 3.828A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU K 646 " --> pdb=" O GLN K 642 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP K 647 " --> pdb=" O LYS K 643 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU K 649 " --> pdb=" O ARG K 645 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL K 650 " --> pdb=" O LEU K 646 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN K 653 " --> pdb=" O LEU K 649 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN K 654 " --> pdb=" O VAL K 650 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG K 655 " --> pdb=" O ILE K 651 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR K 656 " --> pdb=" O GLN K 652 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.742A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.350A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.570A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'K' and resid 217 through 219 removed outlier: 3.504A pdb=" N LEU K 350 " --> pdb=" O GLY K 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'K' and resid 425 through 431 removed outlier: 6.886A pdb=" N VAL K 593 " --> pdb=" O PHE K 624 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU K 626 " --> pdb=" O VAL K 593 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU K 595 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N THR K 628 " --> pdb=" O LEU K 595 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU K 522 " --> pdb=" O VAL K 594 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 369 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3268 1.33 - 1.45: 5062 1.45 - 1.57: 8060 1.57 - 1.69: 586 1.69 - 1.81: 45 Bond restraints: 17021 Sorted by residual: bond pdb=" F2 BEF K1202 " pdb="BE BEF K1202 " ideal model delta sigma weight residual 1.476 1.709 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" F1 BEF K1202 " pdb="BE BEF K1202 " ideal model delta sigma weight residual 1.476 1.702 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" F3 BEF K1202 " pdb="BE BEF K1202 " ideal model delta sigma weight residual 1.476 1.688 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.51e+01 bond pdb=" C1' DT I 2 " pdb=" N1 DT I 2 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.50e+01 ... (remaining 17016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 24188 4.25 - 8.50: 63 8.50 - 12.75: 1 12.75 - 17.01: 1 17.01 - 21.26: 1 Bond angle restraints: 24254 Sorted by residual: angle pdb=" F1 BEF K1202 " pdb="BE BEF K1202 " pdb=" F3 BEF K1202 " ideal model delta sigma weight residual 120.12 98.86 21.26 3.00e+00 1.11e-01 5.02e+01 angle pdb=" O5' DA I 131 " pdb=" C5' DA I 131 " pdb=" C4' DA I 131 " ideal model delta sigma weight residual 109.40 113.70 -4.30 8.00e-01 1.56e+00 2.89e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.81 -2.91 6.00e-01 2.78e+00 2.36e+01 angle pdb=" F2 BEF K1202 " pdb="BE BEF K1202 " pdb=" F3 BEF K1202 " ideal model delta sigma weight residual 119.96 105.49 14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" O5' DA J 121 " pdb=" C5' DA J 121 " pdb=" C4' DA J 121 " ideal model delta sigma weight residual 109.40 113.22 -3.82 8.00e-01 1.56e+00 2.29e+01 ... (remaining 24249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.90: 7856 30.90 - 61.80: 1612 61.80 - 92.70: 35 92.70 - 123.60: 0 123.60 - 154.50: 6 Dihedral angle restraints: 9509 sinusoidal: 5817 harmonic: 3692 Sorted by residual: dihedral pdb=" O2A ADP K1201 " pdb=" O3A ADP K1201 " pdb=" PA ADP K1201 " pdb=" PB ADP K1201 " ideal model delta sinusoidal sigma weight residual -60.00 84.35 -144.34 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O1B ADP K1201 " pdb=" O3A ADP K1201 " pdb=" PB ADP K1201 " pdb=" PA ADP K1201 " ideal model delta sinusoidal sigma weight residual -60.00 82.54 -142.54 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" C5' ADP K1201 " pdb=" O5' ADP K1201 " pdb=" PA ADP K1201 " pdb=" O2A ADP K1201 " ideal model delta sinusoidal sigma weight residual -60.00 82.45 -142.44 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 9506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2062 0.059 - 0.119: 602 0.119 - 0.178: 84 0.178 - 0.238: 6 0.238 - 0.297: 1 Chirality restraints: 2755 Sorted by residual: chirality pdb=" CA THR K 492 " pdb=" N THR K 492 " pdb=" C THR K 492 " pdb=" CB THR K 492 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE K 329 " pdb=" CA ILE K 329 " pdb=" CG1 ILE K 329 " pdb=" CG2 ILE K 329 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2752 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 488 " 0.062 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO K 489 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO K 489 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO K 489 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN K 406 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO K 407 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO K 407 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 407 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 489 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO K 490 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO K 490 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 490 " 0.036 5.00e-02 4.00e+02 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 302 2.65 - 3.21: 12770 3.21 - 3.77: 28105 3.77 - 4.34: 37153 4.34 - 4.90: 54212 Nonbonded interactions: 132542 Sorted by model distance: nonbonded pdb=" O3B ADP K1201 " pdb="MG MG K1203 " model vdw 2.086 2.170 nonbonded pdb=" N2 DG I 13 " pdb=" O2 DC J 135 " model vdw 2.254 2.496 nonbonded pdb=" N2 DG I 83 " pdb=" O2 DC J 65 " model vdw 2.310 2.496 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.334 3.040 nonbonded pdb=" O THR K 492 " pdb=" OG1 THR K 493 " model vdw 2.354 3.040 ... (remaining 132537 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 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 0.920 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: 0.050 Set scattering table: 0.040 Process input model: 15.970 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 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 : 0.009 0.233 17021 Z= 0.676 Angle : 0.959 21.257 24254 Z= 0.742 Chirality : 0.054 0.297 2755 Planarity : 0.007 0.094 2063 Dihedral : 24.561 154.504 7117 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.00 % Rotamer: Outliers : 0.28 % Allowed : 0.74 % Favored : 98.98 % 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: -3.67 (0.19), residues: 1241 helix: -1.94 (0.14), residues: 740 sheet: -3.11 (0.63), residues: 61 loop : -2.98 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 45 TYR 0.035 0.003 TYR B 51 PHE 0.029 0.003 PHE C 25 TRP 0.028 0.003 TRP K 267 HIS 0.014 0.002 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00894 / 0.68 (17021) covalent geometry : angle 0.95858 / 0.74 (24254) hydrogen bonds : bond 0.14999 / 9.79 ( 883) hydrogen bonds : angle 4.99289 / 3.48 ( 2251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 225 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 THR cc_start: 0.9247 (t) cc_final: 0.8959 (p) REVERT: A 125 GLN cc_start: 0.9102 (mt0) cc_final: 0.8842 (mt0) REVERT: C 90 ASP cc_start: 0.8648 (t70) cc_final: 0.7838 (t0) REVERT: D 65 ASP cc_start: 0.8617 (t0) cc_final: 0.8414 (t0) REVERT: D 73 GLU cc_start: 0.8266 (tp30) cc_final: 0.7550 (tp30) REVERT: G 92 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7793 (mt-10) REVERT: H 39 TYR cc_start: 0.8230 (t80) cc_final: 0.7916 (t80) REVERT: H 65 ASP cc_start: 0.8791 (t0) cc_final: 0.8529 (t0) REVERT: H 102 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7486 (mm-30) REVERT: K 325 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8265 (tm-30) REVERT: K 327 HIS cc_start: 0.7327 (m90) cc_final: 0.6792 (m-70) REVERT: K 349 LEU cc_start: 0.8971 (mt) cc_final: 0.8715 (tp) REVERT: K 470 MET cc_start: 0.9182 (tpt) cc_final: 0.8374 (tpp) REVERT: K 476 CYS cc_start: 0.9093 (m) cc_final: 0.8787 (m) outliers start: 3 outliers final: 3 residues processed: 228 average time/residue: 0.1727 time to fit residues: 52.8968 Evaluate side-chains 156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain K residue 611 ARG Chi-restraints excluded: chain K residue 614 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.3980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 46 HIS E 68 GLN E 108 ASN G 110 ASN K 205 ASN ** K 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 437 GLN ** K 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 526 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.068245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.044055 restraints weight = 63475.791| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.68 r_work: 0.2588 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17021 Z= 0.197 Angle : 0.684 7.177 24254 Z= 0.389 Chirality : 0.047 0.204 2755 Planarity : 0.005 0.067 2063 Dihedral : 29.568 158.232 4604 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.57 % Allowed : 6.02 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.40 (0.23), residues: 1241 helix: 0.18 (0.18), residues: 756 sheet: -2.74 (0.65), residues: 61 loop : -2.67 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 464 TYR 0.020 0.001 TYR F 51 PHE 0.013 0.002 PHE K 369 TRP 0.017 0.001 TRP K 364 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 (17021) covalent geometry : angle 0.68440 / 0.39 (24254) hydrogen bonds : bond 0.06223 / 3.97 ( 883) hydrogen bonds : angle 3.48096 / 2.47 ( 2251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8696 (pm20) cc_final: 0.8415 (pm20) REVERT: A 125 GLN cc_start: 0.9434 (mt0) cc_final: 0.9196 (mt0) REVERT: B 24 ASP cc_start: 0.8697 (t0) cc_final: 0.8468 (t0) REVERT: C 50 TYR cc_start: 0.9173 (t80) cc_final: 0.8958 (t80) REVERT: C 90 ASP cc_start: 0.8602 (t70) cc_final: 0.7970 (t0) REVERT: C 95 LYS cc_start: 0.9521 (tppt) cc_final: 0.9214 (ttmt) REVERT: D 65 ASP cc_start: 0.9165 (t0) cc_final: 0.8925 (t0) REVERT: D 73 GLU cc_start: 0.8906 (tp30) cc_final: 0.8178 (tp30) REVERT: E 120 MET cc_start: 0.8946 (mtp) cc_final: 0.8627 (mtp) REVERT: H 39 TYR cc_start: 0.8613 (t80) cc_final: 0.8412 (t80) REVERT: H 65 ASP cc_start: 0.9275 (t0) cc_final: 0.9051 (t0) REVERT: H 102 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8408 (mm-30) REVERT: K 325 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8884 (mm-30) REVERT: K 349 LEU cc_start: 0.9078 (mt) cc_final: 0.8691 (tp) REVERT: K 470 MET cc_start: 0.9238 (tpt) cc_final: 0.9022 (tpp) REVERT: K 476 CYS cc_start: 0.9121 (m) cc_final: 0.8808 (m) outliers start: 17 outliers final: 9 residues processed: 169 average time/residue: 0.1391 time to fit residues: 33.7823 Evaluate side-chains 159 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 611 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 26 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS K 213 ASN K 230 GLN K 500 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.068334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.044257 restraints weight = 64144.981| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.70 r_work: 0.2594 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17021 Z= 0.166 Angle : 0.616 7.101 24254 Z= 0.355 Chirality : 0.043 0.218 2755 Planarity : 0.004 0.050 2063 Dihedral : 29.281 156.571 4600 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.39 % Allowed : 6.30 % Favored : 92.31 % 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: -0.34 (0.24), residues: 1241 helix: 1.11 (0.19), residues: 762 sheet: -2.43 (0.66), residues: 60 loop : -2.45 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 29 TYR 0.016 0.001 TYR F 51 PHE 0.022 0.002 PHE K 574 TRP 0.016 0.001 TRP K 364 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (17021) covalent geometry : angle 0.61558 / 0.35 (24254) hydrogen bonds : bond 0.05452 / 3.46 ( 883) hydrogen bonds : angle 3.13787 / 2.22 ( 2251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8683 (pm20) cc_final: 0.8123 (pm20) REVERT: A 125 GLN cc_start: 0.9447 (mt0) cc_final: 0.9202 (mt0) REVERT: B 24 ASP cc_start: 0.8823 (t0) cc_final: 0.8502 (t0) REVERT: C 90 ASP cc_start: 0.8700 (t70) cc_final: 0.8078 (t0) REVERT: C 95 LYS cc_start: 0.9515 (tppt) cc_final: 0.9250 (ttmt) REVERT: D 65 ASP cc_start: 0.9180 (t0) cc_final: 0.8952 (t0) REVERT: D 73 GLU cc_start: 0.8902 (tp30) cc_final: 0.8213 (tp30) REVERT: E 59 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: E 120 MET cc_start: 0.8936 (mtp) cc_final: 0.8610 (mtp) REVERT: H 39 TYR cc_start: 0.8609 (t80) cc_final: 0.8332 (t80) REVERT: H 65 ASP cc_start: 0.9286 (t0) cc_final: 0.9050 (t0) REVERT: H 102 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8403 (mm-30) REVERT: K 325 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8879 (mm-30) REVERT: K 349 LEU cc_start: 0.9081 (mt) cc_final: 0.8705 (tp) REVERT: K 470 MET cc_start: 0.9285 (tpt) cc_final: 0.9013 (mmp) REVERT: K 476 CYS cc_start: 0.9129 (m) cc_final: 0.8866 (m) REVERT: K 609 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.9066 (mmm) outliers start: 15 outliers final: 8 residues processed: 161 average time/residue: 0.1395 time to fit residues: 32.3930 Evaluate side-chains 153 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain K residue 611 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 104 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 113 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.068487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.044344 restraints weight = 64150.157| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.69 r_work: 0.2594 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17021 Z= 0.153 Angle : 0.591 8.208 24254 Z= 0.340 Chirality : 0.042 0.207 2755 Planarity : 0.004 0.041 2063 Dihedral : 29.074 159.007 4600 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.76 % Allowed : 6.48 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.25), residues: 1241 helix: 1.57 (0.19), residues: 765 sheet: -2.12 (0.67), residues: 60 loop : -2.36 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 412 TYR 0.012 0.001 TYR F 51 PHE 0.013 0.001 PHE K 274 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (17021) covalent geometry : angle 0.59057 / 0.34 (24254) hydrogen bonds : bond 0.05062 / 3.18 ( 883) hydrogen bonds : angle 2.95498 / 2.08 ( 2251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8833 (pm20) cc_final: 0.8555 (pm20) REVERT: A 125 GLN cc_start: 0.9462 (mt0) cc_final: 0.9221 (mt0) REVERT: B 24 ASP cc_start: 0.8801 (t0) cc_final: 0.8463 (t0) REVERT: B 92 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.9031 (ttp80) REVERT: C 90 ASP cc_start: 0.8765 (t70) cc_final: 0.8159 (t0) REVERT: C 95 LYS cc_start: 0.9484 (tppt) cc_final: 0.9241 (ttmt) REVERT: D 65 ASP cc_start: 0.9178 (t0) cc_final: 0.8942 (t0) REVERT: D 73 GLU cc_start: 0.8950 (tp30) cc_final: 0.8222 (tp30) REVERT: G 72 ASP cc_start: 0.9155 (t0) cc_final: 0.8912 (t0) REVERT: G 91 GLU cc_start: 0.8066 (pm20) cc_final: 0.6877 (pm20) REVERT: G 92 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8535 (mp0) REVERT: H 39 TYR cc_start: 0.8564 (t80) cc_final: 0.8289 (t80) REVERT: H 65 ASP cc_start: 0.9287 (t0) cc_final: 0.9049 (t0) REVERT: H 102 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8365 (mm-30) REVERT: K 276 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8859 (tt) REVERT: K 325 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8893 (mm-30) REVERT: K 349 LEU cc_start: 0.9106 (mt) cc_final: 0.8737 (tp) REVERT: K 470 MET cc_start: 0.9291 (tpt) cc_final: 0.8959 (mmp) REVERT: K 476 CYS cc_start: 0.9156 (m) cc_final: 0.8890 (m) REVERT: K 609 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.9016 (mmm) outliers start: 19 outliers final: 12 residues processed: 159 average time/residue: 0.1427 time to fit residues: 32.4424 Evaluate side-chains 156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 609 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 81 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 130 optimal weight: 0.0770 chunk 46 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 0.0970 chunk 106 optimal weight: 5.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.069122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.045138 restraints weight = 64195.235| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.70 r_work: 0.2626 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17021 Z= 0.127 Angle : 0.557 8.771 24254 Z= 0.326 Chirality : 0.041 0.213 2755 Planarity : 0.004 0.042 2063 Dihedral : 28.854 155.135 4596 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.76 % Allowed : 7.41 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.61 (0.25), residues: 1241 helix: 1.84 (0.19), residues: 767 sheet: -1.82 (0.67), residues: 60 loop : -2.12 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.016 0.001 TYR G 50 PHE 0.012 0.001 PHE K 274 TRP 0.015 0.001 TRP K 364 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (17021) covalent geometry : angle 0.55707 / 0.33 (24254) hydrogen bonds : bond 0.04715 / 2.92 ( 883) hydrogen bonds : angle 2.79427 / 1.96 ( 2251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8735 (pm20) cc_final: 0.8372 (pm20) REVERT: A 125 GLN cc_start: 0.9459 (mt0) cc_final: 0.9214 (mt0) REVERT: B 24 ASP cc_start: 0.8781 (t0) cc_final: 0.8530 (t0) REVERT: B 92 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8515 (ttp80) REVERT: C 90 ASP cc_start: 0.8783 (t70) cc_final: 0.8232 (t0) REVERT: C 95 LYS cc_start: 0.9419 (tppt) cc_final: 0.9195 (ttmt) REVERT: D 65 ASP cc_start: 0.9178 (t0) cc_final: 0.8944 (t0) REVERT: D 73 GLU cc_start: 0.8955 (tp30) cc_final: 0.8283 (tp30) REVERT: E 59 GLU cc_start: 0.8690 (pm20) cc_final: 0.8474 (pm20) REVERT: F 84 MET cc_start: 0.8972 (mmm) cc_final: 0.8364 (mmm) REVERT: G 72 ASP cc_start: 0.9143 (t0) cc_final: 0.8907 (t0) REVERT: G 90 ASP cc_start: 0.8843 (t70) cc_final: 0.8082 (t70) REVERT: G 91 GLU cc_start: 0.8192 (pm20) cc_final: 0.7471 (pm20) REVERT: G 92 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8515 (mp0) REVERT: H 39 TYR cc_start: 0.8544 (t80) cc_final: 0.8284 (t80) REVERT: H 65 ASP cc_start: 0.9256 (t0) cc_final: 0.9035 (t0) REVERT: H 73 GLU cc_start: 0.9202 (tp30) cc_final: 0.8913 (mm-30) REVERT: H 102 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8340 (mm-30) REVERT: K 276 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8621 (tt) REVERT: K 325 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8885 (mm-30) REVERT: K 349 LEU cc_start: 0.9098 (mt) cc_final: 0.8762 (tp) REVERT: K 470 MET cc_start: 0.9294 (tpt) cc_final: 0.8979 (mmp) REVERT: K 476 CYS cc_start: 0.9175 (m) cc_final: 0.8912 (m) outliers start: 19 outliers final: 8 residues processed: 162 average time/residue: 0.1334 time to fit residues: 31.3284 Evaluate side-chains 151 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 364 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 141 optimal weight: 0.1980 chunk 127 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 91 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 46 HIS D 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.066694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.042432 restraints weight = 64723.148| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.65 r_work: 0.2537 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 17021 Z= 0.343 Angle : 0.737 7.315 24254 Z= 0.397 Chirality : 0.047 0.206 2755 Planarity : 0.005 0.041 2063 Dihedral : 29.127 155.612 4596 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.94 % Allowed : 8.06 % Favored : 90.00 % 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: 0.55 (0.25), residues: 1241 helix: 1.80 (0.19), residues: 768 sheet: -1.97 (0.67), residues: 60 loop : -2.13 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 76 TYR 0.020 0.002 TYR G 50 PHE 0.025 0.002 PHE G 25 TRP 0.017 0.002 TRP K 364 HIS 0.009 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.34 (17021) covalent geometry : angle 0.73723 / 0.40 (24254) hydrogen bonds : bond 0.06543 / 4.27 ( 883) hydrogen bonds : angle 3.30397 / 2.32 ( 2251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.497 Fit side-chains REVERT: A 59 GLU cc_start: 0.8899 (pm20) cc_final: 0.8575 (pm20) REVERT: A 125 GLN cc_start: 0.9451 (mt0) cc_final: 0.9243 (mt0) REVERT: C 64 GLU cc_start: 0.9199 (tt0) cc_final: 0.8908 (tm-30) REVERT: C 90 ASP cc_start: 0.8844 (t70) cc_final: 0.7361 (t70) REVERT: C 95 LYS cc_start: 0.9471 (tppt) cc_final: 0.9231 (ttmt) REVERT: D 65 ASP cc_start: 0.9230 (t0) cc_final: 0.8972 (t0) REVERT: D 73 GLU cc_start: 0.9066 (tp30) cc_final: 0.8453 (tp30) REVERT: E 59 GLU cc_start: 0.8725 (pm20) cc_final: 0.8387 (pm20) REVERT: E 76 GLN cc_start: 0.9162 (tt0) cc_final: 0.8922 (tm-30) REVERT: F 84 MET cc_start: 0.9137 (mmm) cc_final: 0.8370 (mmm) REVERT: G 72 ASP cc_start: 0.9158 (t0) cc_final: 0.8941 (t0) REVERT: G 91 GLU cc_start: 0.8280 (pm20) cc_final: 0.7711 (pm20) REVERT: G 92 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8349 (mp0) REVERT: H 39 TYR cc_start: 0.8811 (t80) cc_final: 0.8543 (t80) REVERT: H 65 ASP cc_start: 0.9321 (t0) cc_final: 0.9066 (t0) REVERT: H 73 GLU cc_start: 0.9316 (tp30) cc_final: 0.9102 (mm-30) REVERT: H 102 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8439 (mm-30) REVERT: K 276 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8767 (tt) REVERT: K 325 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8867 (mm-30) REVERT: K 349 LEU cc_start: 0.9118 (mt) cc_final: 0.8739 (tp) REVERT: K 470 MET cc_start: 0.9283 (tpt) cc_final: 0.9050 (mmp) REVERT: K 476 CYS cc_start: 0.9240 (m) cc_final: 0.8962 (m) REVERT: K 609 MET cc_start: 0.9352 (tpp) cc_final: 0.9065 (mmm) outliers start: 21 outliers final: 16 residues processed: 149 average time/residue: 0.1320 time to fit residues: 28.7754 Evaluate side-chains 148 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 92 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 23 optimal weight: 0.0970 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.068250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.044127 restraints weight = 63802.954| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.69 r_work: 0.2591 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17021 Z= 0.136 Angle : 0.576 7.459 24254 Z= 0.334 Chirality : 0.041 0.213 2755 Planarity : 0.004 0.041 2063 Dihedral : 28.886 154.947 4596 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.30 % Allowed : 8.98 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.87 (0.25), residues: 1241 helix: 2.07 (0.19), residues: 767 sheet: -1.69 (0.68), residues: 60 loop : -2.07 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.012 0.001 TYR F 51 PHE 0.011 0.001 PHE K 274 TRP 0.016 0.001 TRP K 364 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (17021) covalent geometry : angle 0.57579 / 0.33 (24254) hydrogen bonds : bond 0.05062 / 3.17 ( 883) hydrogen bonds : angle 2.85935 / 2.00 ( 2251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.469 Fit side-chains REVERT: A 59 GLU cc_start: 0.8816 (pm20) cc_final: 0.8498 (pm20) REVERT: B 92 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8464 (ttp80) REVERT: C 90 ASP cc_start: 0.8438 (t70) cc_final: 0.8186 (t70) REVERT: C 95 LYS cc_start: 0.9440 (tppt) cc_final: 0.9207 (ttmt) REVERT: D 65 ASP cc_start: 0.9196 (t0) cc_final: 0.8937 (t0) REVERT: D 73 GLU cc_start: 0.8945 (tp30) cc_final: 0.8292 (tp30) REVERT: E 59 GLU cc_start: 0.8707 (pm20) cc_final: 0.8481 (pm20) REVERT: E 76 GLN cc_start: 0.9127 (tt0) cc_final: 0.8926 (tm-30) REVERT: E 94 GLU cc_start: 0.9108 (tp30) cc_final: 0.8894 (mm-30) REVERT: F 84 MET cc_start: 0.8999 (mmm) cc_final: 0.8328 (mmm) REVERT: G 72 ASP cc_start: 0.9169 (t0) cc_final: 0.8945 (t0) REVERT: G 90 ASP cc_start: 0.8898 (t70) cc_final: 0.8177 (t70) REVERT: G 91 GLU cc_start: 0.8314 (pm20) cc_final: 0.7752 (pm20) REVERT: G 92 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8362 (mp0) REVERT: H 39 TYR cc_start: 0.8580 (t80) cc_final: 0.8321 (t80) REVERT: H 65 ASP cc_start: 0.9268 (t0) cc_final: 0.9043 (t0) REVERT: H 73 GLU cc_start: 0.9246 (tp30) cc_final: 0.9030 (mm-30) REVERT: H 102 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8412 (mm-30) REVERT: K 276 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8804 (tt) REVERT: K 325 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8891 (mm-30) REVERT: K 349 LEU cc_start: 0.9100 (mt) cc_final: 0.8763 (tp) REVERT: K 476 CYS cc_start: 0.9220 (m) cc_final: 0.8950 (m) REVERT: K 609 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9072 (mmm) outliers start: 14 outliers final: 10 residues processed: 154 average time/residue: 0.1291 time to fit residues: 29.2888 Evaluate side-chains 150 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 609 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 140 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.067615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.043497 restraints weight = 64057.693| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.66 r_work: 0.2570 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17021 Z= 0.208 Angle : 0.620 8.080 24254 Z= 0.349 Chirality : 0.043 0.208 2755 Planarity : 0.004 0.040 2063 Dihedral : 28.888 155.200 4596 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.57 % Allowed : 9.17 % Favored : 89.26 % 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: 0.90 (0.25), residues: 1241 helix: 2.08 (0.19), residues: 769 sheet: -1.70 (0.67), residues: 60 loop : -2.04 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 76 TYR 0.014 0.001 TYR G 50 PHE 0.013 0.001 PHE G 25 TRP 0.016 0.001 TRP K 364 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (17021) covalent geometry : angle 0.61982 / 0.35 (24254) hydrogen bonds : bond 0.05449 / 3.47 ( 883) hydrogen bonds : angle 2.97863 / 2.08 ( 2251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.510 Fit side-chains REVERT: A 59 GLU cc_start: 0.8840 (pm20) cc_final: 0.8523 (pm20) REVERT: B 92 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.8458 (ttp80) REVERT: C 64 GLU cc_start: 0.9209 (tt0) cc_final: 0.8953 (tm-30) REVERT: C 90 ASP cc_start: 0.8449 (t70) cc_final: 0.8117 (t0) REVERT: C 95 LYS cc_start: 0.9445 (tppt) cc_final: 0.9212 (ttmt) REVERT: D 65 ASP cc_start: 0.9213 (t0) cc_final: 0.8950 (t0) REVERT: D 73 GLU cc_start: 0.9016 (tp30) cc_final: 0.8400 (tp30) REVERT: E 59 GLU cc_start: 0.8679 (pm20) cc_final: 0.8444 (pm20) REVERT: E 76 GLN cc_start: 0.9154 (tt0) cc_final: 0.8927 (tm-30) REVERT: G 72 ASP cc_start: 0.9166 (t0) cc_final: 0.8951 (t0) REVERT: G 90 ASP cc_start: 0.8882 (t70) cc_final: 0.8091 (t70) REVERT: G 91 GLU cc_start: 0.8348 (pm20) cc_final: 0.7828 (pm20) REVERT: G 92 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8404 (mp0) REVERT: H 32 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7329 (tm-30) REVERT: H 39 TYR cc_start: 0.8654 (t80) cc_final: 0.8397 (t80) REVERT: H 65 ASP cc_start: 0.9252 (t0) cc_final: 0.9009 (t0) REVERT: H 102 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8427 (mm-30) REVERT: K 276 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8743 (tt) REVERT: K 325 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8904 (mm-30) REVERT: K 349 LEU cc_start: 0.9091 (mt) cc_final: 0.8745 (tp) REVERT: K 476 CYS cc_start: 0.9224 (m) cc_final: 0.8933 (m) REVERT: K 609 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.9067 (mmm) outliers start: 17 outliers final: 12 residues processed: 146 average time/residue: 0.1421 time to fit residues: 30.4579 Evaluate side-chains 149 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 609 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 108 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.069077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.045055 restraints weight = 63746.939| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.69 r_work: 0.2616 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17021 Z= 0.123 Angle : 0.562 8.773 24254 Z= 0.328 Chirality : 0.040 0.213 2755 Planarity : 0.004 0.040 2063 Dihedral : 28.689 154.026 4596 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.48 % Allowed : 9.54 % Favored : 88.98 % 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: 1.08 (0.25), residues: 1241 helix: 2.22 (0.19), residues: 766 sheet: -1.39 (0.70), residues: 60 loop : -1.97 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 76 TYR 0.009 0.001 TYR F 51 PHE 0.012 0.001 PHE K 274 TRP 0.014 0.001 TRP K 364 HIS 0.009 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.12 (17021) covalent geometry : angle 0.56158 / 0.33 (24254) hydrogen bonds : bond 0.04722 / 2.91 ( 883) hydrogen bonds : angle 2.72697 / 1.90 ( 2251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8766 (pm20) cc_final: 0.8466 (pm20) REVERT: B 92 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8485 (ttp80) REVERT: C 90 ASP cc_start: 0.8571 (t70) cc_final: 0.8054 (t0) REVERT: C 95 LYS cc_start: 0.9421 (tppt) cc_final: 0.9219 (ttmt) REVERT: D 65 ASP cc_start: 0.9182 (t0) cc_final: 0.8931 (t0) REVERT: D 73 GLU cc_start: 0.8917 (tp30) cc_final: 0.8261 (tp30) REVERT: E 59 GLU cc_start: 0.8602 (pm20) cc_final: 0.8382 (pm20) REVERT: F 84 MET cc_start: 0.8859 (mmm) cc_final: 0.8324 (mmm) REVERT: G 72 ASP cc_start: 0.9166 (t0) cc_final: 0.8947 (t0) REVERT: G 90 ASP cc_start: 0.8895 (t70) cc_final: 0.8111 (t70) REVERT: G 91 GLU cc_start: 0.8391 (pm20) cc_final: 0.7850 (pm20) REVERT: G 92 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8385 (mp0) REVERT: H 39 TYR cc_start: 0.8528 (t80) cc_final: 0.8285 (t80) REVERT: H 65 ASP cc_start: 0.9265 (t0) cc_final: 0.9045 (t0) REVERT: H 102 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8336 (mm-30) REVERT: K 276 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8604 (tt) REVERT: K 325 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8914 (mm-30) REVERT: K 349 LEU cc_start: 0.9109 (mt) cc_final: 0.8766 (tp) REVERT: K 436 MET cc_start: 0.8746 (tmm) cc_final: 0.8472 (tmm) REVERT: K 470 MET cc_start: 0.9004 (mmp) cc_final: 0.8729 (mmm) REVERT: K 476 CYS cc_start: 0.9216 (m) cc_final: 0.8942 (m) REVERT: K 609 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9093 (mmm) outliers start: 16 outliers final: 10 residues processed: 161 average time/residue: 0.1399 time to fit residues: 33.4031 Evaluate side-chains 156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 609 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 81 ASN ** K 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.069050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.044977 restraints weight = 63755.200| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.67 r_work: 0.2619 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 17021 Z= 0.132 Angle : 0.575 7.990 24254 Z= 0.332 Chirality : 0.040 0.258 2755 Planarity : 0.004 0.040 2063 Dihedral : 28.676 154.194 4596 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.02 % Allowed : 10.65 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.15 (0.25), residues: 1241 helix: 2.23 (0.19), residues: 771 sheet: -1.26 (0.70), residues: 60 loop : -1.93 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 76 TYR 0.009 0.001 TYR G 50 PHE 0.011 0.001 PHE K 274 TRP 0.015 0.001 TRP K 364 HIS 0.013 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (17021) covalent geometry : angle 0.57499 / 0.33 (24254) hydrogen bonds : bond 0.04752 / 2.94 ( 883) hydrogen bonds : angle 2.75160 / 1.93 ( 2251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.517 Fit side-chains REVERT: A 59 GLU cc_start: 0.8749 (pm20) cc_final: 0.8470 (pm20) REVERT: B 92 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8481 (ttp80) REVERT: C 90 ASP cc_start: 0.8589 (t70) cc_final: 0.8083 (t0) REVERT: C 95 LYS cc_start: 0.9412 (tppt) cc_final: 0.9209 (ttmt) REVERT: D 65 ASP cc_start: 0.9193 (t0) cc_final: 0.8917 (t0) REVERT: D 73 GLU cc_start: 0.8978 (tp30) cc_final: 0.8375 (tp30) REVERT: E 59 GLU cc_start: 0.8611 (pm20) cc_final: 0.8406 (pm20) REVERT: F 84 MET cc_start: 0.8915 (mmm) cc_final: 0.8296 (mmm) REVERT: G 72 ASP cc_start: 0.9149 (t0) cc_final: 0.8917 (t0) REVERT: G 90 ASP cc_start: 0.8853 (t70) cc_final: 0.8131 (t70) REVERT: G 91 GLU cc_start: 0.8407 (pm20) cc_final: 0.7846 (pm20) REVERT: G 92 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8349 (mp0) REVERT: H 39 TYR cc_start: 0.8539 (t80) cc_final: 0.8289 (t80) REVERT: H 65 ASP cc_start: 0.9253 (t0) cc_final: 0.9051 (t0) REVERT: H 102 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8355 (mm-30) REVERT: K 325 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8920 (mm-30) REVERT: K 349 LEU cc_start: 0.9097 (mt) cc_final: 0.8774 (tp) REVERT: K 436 MET cc_start: 0.8683 (tmm) cc_final: 0.8407 (tmm) REVERT: K 470 MET cc_start: 0.8978 (mmp) cc_final: 0.8716 (mmm) REVERT: K 476 CYS cc_start: 0.9221 (m) cc_final: 0.8951 (m) REVERT: K 609 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.9095 (mmm) outliers start: 11 outliers final: 8 residues processed: 148 average time/residue: 0.1407 time to fit residues: 30.7811 Evaluate side-chains 148 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 609 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 132 optimal weight: 0.4980 chunk 137 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 113 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** K 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 613 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.069316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.045142 restraints weight = 63469.005| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.69 r_work: 0.2629 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17021 Z= 0.127 Angle : 0.567 7.945 24254 Z= 0.328 Chirality : 0.040 0.201 2755 Planarity : 0.004 0.039 2063 Dihedral : 28.641 153.834 4596 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.20 % Allowed : 10.74 % Favored : 88.06 % 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: 1.23 (0.25), residues: 1241 helix: 2.24 (0.19), residues: 776 sheet: -1.08 (0.71), residues: 60 loop : -1.83 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 76 TYR 0.009 0.001 TYR G 50 PHE 0.012 0.001 PHE K 274 TRP 0.014 0.001 TRP K 364 HIS 0.012 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (17021) covalent geometry : angle 0.56667 / 0.33 (24254) hydrogen bonds : bond 0.04674 / 2.88 ( 883) hydrogen bonds : angle 2.70243 / 1.89 ( 2251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3745.67 seconds wall clock time: 65 minutes 1.88 seconds (3901.88 seconds total)