Starting phenix.real_space_refine on Sun Aug 24 01:10:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jyl_9718/08_2025/6jyl_9718.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jyl_9718/08_2025/6jyl_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_9718/08_2025/6jyl_9718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jyl_9718/08_2025/6jyl_9718.map" model { file = "/net/cci-nas-00/data/ceres_data/6jyl_9718/08_2025/6jyl_9718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jyl_9718/08_2025/6jyl_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-2.0-5787/lib/python3.9/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: 4.01, per 1000 atoms: 0.25 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: 1.47 Conformation dependent library (CDL) restraints added in 693.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.58 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: 4.08 Time building geometry restraints manager: 2.04 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 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.49e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.34e+00 ... (remaining 17016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 24195 4.25 - 8.50: 56 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=" 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=" N ILE K 329 " pdb=" CA ILE K 329 " pdb=" C ILE K 329 " ideal model delta sigma weight residual 111.91 108.14 3.77 8.90e-01 1.26e+00 1.79e+01 angle pdb=" C SER D 75 " pdb=" N ARG D 76 " pdb=" CA ARG D 76 " ideal model delta sigma weight residual 121.58 114.57 7.01 1.95e+00 2.63e-01 1.29e+01 angle pdb=" C SER H 75 " pdb=" N ARG H 76 " pdb=" CA ARG H 76 " ideal model delta sigma weight residual 121.58 114.72 6.86 1.95e+00 2.63e-01 1.24e+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: 2206 0.059 - 0.119: 491 0.119 - 0.178: 52 0.178 - 0.238: 5 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: 0.860 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.440 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.233 17021 Z= 0.371 Angle : 0.848 21.257 24254 Z= 0.487 Chirality : 0.048 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 aren 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 covalent geometry : bond 0.00828 (17021) covalent geometry : angle 0.84791 (24254) hydrogen bonds : bond 0.14999 ( 883) hydrogen bonds : angle 4.99289 ( 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 : 0.363 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: 0.1837 time to fit residues: 55.6871 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 : 0.488 ------------------------------------------------------------------------------- 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: 7.9990 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: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.3980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN K 205 ASN K 230 GLN ** K 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 437 GLN K 526 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.068142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.044016 restraints weight = 63726.210| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.67 r_work: 0.2585 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17021 Z= 0.210 Angle : 0.606 7.007 24254 Z= 0.350 Chirality : 0.037 0.170 2755 Planarity : 0.005 0.069 2063 Dihedral : 28.892 157.165 4604 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.39 % Allowed : 5.37 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.23), residues: 1241 helix: 0.31 (0.18), residues: 765 sheet: -2.70 (0.64), residues: 61 loop : -2.66 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 99 TYR 0.017 0.001 TYR F 51 PHE 0.015 0.002 PHE K 274 TRP 0.017 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00466 (17021) covalent geometry : angle 0.60609 (24254) hydrogen bonds : bond 0.05261 ( 883) hydrogen bonds : angle 3.17747 ( 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 178 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8759 (pm20) cc_final: 0.7982 (pm20) REVERT: A 125 GLN cc_start: 0.9454 (mt0) cc_final: 0.9221 (mt0) REVERT: B 24 ASP cc_start: 0.8796 (t0) cc_final: 0.8435 (t0) REVERT: C 90 ASP cc_start: 0.8726 (t70) cc_final: 0.8241 (t0) REVERT: C 95 LYS cc_start: 0.9520 (tppt) cc_final: 0.9243 (ttmt) REVERT: D 65 ASP cc_start: 0.9213 (t0) cc_final: 0.8949 (t0) REVERT: D 73 GLU cc_start: 0.8941 (tp30) cc_final: 0.8281 (tp30) REVERT: E 59 GLU cc_start: 0.8398 (pm20) cc_final: 0.7752 (pm20) REVERT: E 120 MET cc_start: 0.8908 (mtp) cc_final: 0.8551 (mtp) REVERT: H 39 TYR cc_start: 0.8611 (t80) cc_final: 0.8357 (t80) REVERT: H 65 ASP cc_start: 0.9284 (t0) cc_final: 0.9037 (t0) REVERT: H 102 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8371 (mm-30) REVERT: K 325 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8823 (mm-30) REVERT: K 349 LEU cc_start: 0.9095 (mt) cc_final: 0.8740 (tp) REVERT: K 470 MET cc_start: 0.9246 (tpt) cc_final: 0.9007 (mmp) REVERT: K 476 CYS cc_start: 0.9101 (m) cc_final: 0.8828 (m) outliers start: 15 outliers final: 9 residues processed: 170 average time/residue: 0.1641 time to fit residues: 39.6078 Evaluate side-chains 154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 73 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU 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: 7.9990 chunk 143 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 146 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 1 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.068871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.044724 restraints weight = 64212.095| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.67 r_work: 0.2614 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17021 Z= 0.165 Angle : 0.550 6.095 24254 Z= 0.320 Chirality : 0.035 0.160 2755 Planarity : 0.004 0.058 2063 Dihedral : 28.499 154.711 4600 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.57 % Allowed : 6.30 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.24), residues: 1241 helix: 1.30 (0.19), residues: 768 sheet: -2.35 (0.65), residues: 60 loop : -2.40 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.014 0.001 TYR F 51 PHE 0.013 0.001 PHE K 274 TRP 0.015 0.001 TRP K 364 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00363 (17021) covalent geometry : angle 0.54966 (24254) hydrogen bonds : bond 0.04520 ( 883) hydrogen bonds : angle 2.82923 ( 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 174 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9447 (mt0) cc_final: 0.9222 (mt0) REVERT: B 24 ASP cc_start: 0.8844 (t0) cc_final: 0.8574 (t0) REVERT: B 92 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8461 (ttp80) REVERT: C 90 ASP cc_start: 0.8791 (t70) cc_final: 0.8428 (t70) REVERT: C 95 LYS cc_start: 0.9460 (tppt) cc_final: 0.9222 (ttmt) REVERT: D 65 ASP cc_start: 0.9199 (t0) cc_final: 0.8945 (t0) REVERT: D 73 GLU cc_start: 0.9008 (tp30) cc_final: 0.8357 (tp30) REVERT: F 84 MET cc_start: 0.9014 (mmm) cc_final: 0.8341 (mmm) REVERT: G 72 ASP cc_start: 0.9123 (t0) cc_final: 0.8877 (t0) REVERT: G 90 ASP cc_start: 0.8912 (t70) cc_final: 0.8485 (t70) REVERT: H 39 TYR cc_start: 0.8605 (t80) cc_final: 0.8320 (t80) REVERT: H 65 ASP cc_start: 0.9280 (t0) cc_final: 0.9033 (t0) REVERT: H 73 GLU cc_start: 0.9193 (tp30) cc_final: 0.8913 (mm-30) REVERT: K 276 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8650 (tt) REVERT: K 325 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8805 (mm-30) REVERT: K 349 LEU cc_start: 0.9063 (mt) cc_final: 0.8765 (tp) REVERT: K 470 MET cc_start: 0.9240 (tpt) cc_final: 0.8975 (mmp) REVERT: K 476 CYS cc_start: 0.9200 (m) cc_final: 0.8934 (m) outliers start: 17 outliers final: 8 residues processed: 169 average time/residue: 0.1516 time to fit residues: 36.2857 Evaluate side-chains 149 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER 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 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 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: 10.0000 chunk 21 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 36 optimal weight: 0.0870 chunk 88 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 601 ASN K 620 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.067901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.043698 restraints weight = 64402.546| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.69 r_work: 0.2574 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17021 Z= 0.222 Angle : 0.573 6.014 24254 Z= 0.331 Chirality : 0.037 0.152 2755 Planarity : 0.004 0.049 2063 Dihedral : 28.387 150.397 4596 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.48 % Allowed : 7.87 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.25), residues: 1241 helix: 1.69 (0.19), residues: 770 sheet: -2.14 (0.65), residues: 60 loop : -2.27 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.014 0.001 TYR G 50 PHE 0.012 0.001 PHE G 25 TRP 0.016 0.001 TRP K 364 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00500 (17021) covalent geometry : angle 0.57300 (24254) hydrogen bonds : bond 0.05040 ( 883) hydrogen bonds : angle 2.93052 ( 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 161 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.483 Fit side-chains REVERT: A 125 GLN cc_start: 0.9472 (mt0) cc_final: 0.9246 (mt0) REVERT: B 92 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.8433 (ttp80) REVERT: C 90 ASP cc_start: 0.8818 (t70) cc_final: 0.7824 (t0) REVERT: C 91 GLU cc_start: 0.8198 (pm20) cc_final: 0.7253 (pm20) REVERT: C 95 LYS cc_start: 0.9479 (tppt) cc_final: 0.9225 (ttmt) REVERT: D 65 ASP cc_start: 0.9231 (t0) cc_final: 0.8950 (t0) REVERT: D 73 GLU cc_start: 0.9024 (tp30) cc_final: 0.8388 (tp30) REVERT: D 102 GLU cc_start: 0.8589 (tp30) cc_final: 0.8047 (tm-30) REVERT: F 84 MET cc_start: 0.9076 (mmm) cc_final: 0.8385 (mmm) REVERT: G 72 ASP cc_start: 0.9142 (t0) cc_final: 0.8906 (t0) REVERT: G 90 ASP cc_start: 0.8845 (t70) cc_final: 0.8420 (t70) REVERT: H 39 TYR cc_start: 0.8604 (t80) cc_final: 0.8369 (t80) REVERT: H 65 ASP cc_start: 0.9266 (t0) cc_final: 0.9034 (t0) REVERT: K 276 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8746 (tt) REVERT: K 325 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8820 (mm-30) REVERT: K 349 LEU cc_start: 0.9073 (mt) cc_final: 0.8792 (tp) REVERT: K 436 MET cc_start: 0.8765 (tmm) cc_final: 0.8504 (tmm) REVERT: K 470 MET cc_start: 0.9277 (tpt) cc_final: 0.9048 (mmp) REVERT: K 476 CYS cc_start: 0.9219 (m) cc_final: 0.8960 (m) outliers start: 16 outliers final: 10 residues processed: 154 average time/residue: 0.1339 time to fit residues: 29.7848 Evaluate side-chains 153 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 107 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 364 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 81 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 63 optimal weight: 0.0370 chunk 106 optimal weight: 5.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN H 106 HIS K 613 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.070153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.046243 restraints weight = 63924.892| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.70 r_work: 0.2662 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2841 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= 0.132 Angle : 0.524 6.109 24254 Z= 0.307 Chirality : 0.034 0.154 2755 Planarity : 0.004 0.049 2063 Dihedral : 27.955 149.781 4596 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.48 % Allowed : 8.33 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.25), residues: 1241 helix: 1.94 (0.19), residues: 775 sheet: -1.79 (0.60), residues: 70 loop : -2.06 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.011 0.001 TYR G 50 PHE 0.011 0.001 PHE K 274 TRP 0.013 0.001 TRP K 364 HIS 0.009 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00283 (17021) covalent geometry : angle 0.52411 (24254) hydrogen bonds : bond 0.04106 ( 883) hydrogen bonds : angle 2.58797 ( 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 179 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.505 Fit side-chains REVERT: A 125 GLN cc_start: 0.9484 (mt0) cc_final: 0.9238 (mt0) REVERT: C 90 ASP cc_start: 0.8459 (t70) cc_final: 0.8141 (t0) REVERT: C 95 LYS cc_start: 0.9400 (tppt) cc_final: 0.9182 (ttmt) REVERT: D 73 GLU cc_start: 0.8980 (tp30) cc_final: 0.8421 (tp30) REVERT: D 83 ARG cc_start: 0.9159 (mmt90) cc_final: 0.8885 (mmt-90) REVERT: F 84 MET cc_start: 0.8984 (mmm) cc_final: 0.8308 (mmm) REVERT: G 90 ASP cc_start: 0.8938 (t70) cc_final: 0.8232 (t70) REVERT: G 91 GLU cc_start: 0.8226 (pm20) cc_final: 0.7523 (pm20) REVERT: G 92 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8446 (mp0) REVERT: H 39 TYR cc_start: 0.8479 (t80) cc_final: 0.8231 (t80) REVERT: H 65 ASP cc_start: 0.9213 (t0) cc_final: 0.8997 (t0) REVERT: H 73 GLU cc_start: 0.9223 (tp30) cc_final: 0.8856 (mm-30) REVERT: K 276 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8696 (tt) REVERT: K 325 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8836 (mm-30) REVERT: K 349 LEU cc_start: 0.9090 (mt) cc_final: 0.8795 (tp) REVERT: K 436 MET cc_start: 0.8716 (tmm) cc_final: 0.8499 (tmm) REVERT: K 470 MET cc_start: 0.9290 (tpt) cc_final: 0.9060 (mmp) REVERT: K 476 CYS cc_start: 0.9135 (m) cc_final: 0.8878 (m) outliers start: 16 outliers final: 9 residues processed: 173 average time/residue: 0.1344 time to fit residues: 33.8741 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 : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 120 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 141 optimal weight: 20.0000 chunk 127 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3453 r_free = 0.3453 target = 0.066844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.042277 restraints weight = 65160.369| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.77 r_work: 0.2530 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 17021 Z= 0.340 Angle : 0.640 6.887 24254 Z= 0.363 Chirality : 0.041 0.146 2755 Planarity : 0.004 0.046 2063 Dihedral : 28.397 149.572 4596 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.94 % Allowed : 9.54 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.25), residues: 1241 helix: 1.85 (0.19), residues: 778 sheet: -1.63 (0.67), residues: 57 loop : -2.08 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 83 TYR 0.017 0.002 TYR G 50 PHE 0.017 0.002 PHE G 25 TRP 0.017 0.002 TRP K 364 HIS 0.006 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00770 (17021) covalent geometry : angle 0.64025 (24254) hydrogen bonds : bond 0.05750 ( 883) hydrogen bonds : angle 3.11667 ( 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 158 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.347 Fit side-chains REVERT: B 20 LYS cc_start: 0.8594 (ptmm) cc_final: 0.7790 (tptp) REVERT: B 53 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8452 (mm-30) REVERT: C 64 GLU cc_start: 0.9204 (tt0) cc_final: 0.8954 (tm-30) REVERT: C 90 ASP cc_start: 0.8613 (t70) cc_final: 0.8287 (t70) REVERT: C 95 LYS cc_start: 0.9477 (tppt) cc_final: 0.9274 (ttmt) REVERT: D 73 GLU cc_start: 0.9027 (tp30) cc_final: 0.8421 (tp30) REVERT: E 94 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8563 (mm-30) REVERT: G 90 ASP cc_start: 0.8844 (t70) cc_final: 0.8516 (t70) REVERT: H 39 TYR cc_start: 0.8712 (t80) cc_final: 0.8476 (t80) REVERT: H 65 ASP cc_start: 0.9304 (t0) cc_final: 0.9062 (t0) REVERT: K 325 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8910 (mm-30) REVERT: K 349 LEU cc_start: 0.9094 (mt) cc_final: 0.8834 (tp) REVERT: K 436 MET cc_start: 0.8779 (tmm) cc_final: 0.8558 (tmm) REVERT: K 476 CYS cc_start: 0.9257 (m) cc_final: 0.8992 (m) outliers start: 21 outliers final: 15 residues processed: 150 average time/residue: 0.1320 time to fit residues: 28.9132 Evaluate side-chains 151 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 92 GLU 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 G residue 62 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 568 ASP Chi-restraints excluded: chain K residue 609 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 118 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN B 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.069943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.045836 restraints weight = 63533.180| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.68 r_work: 0.2653 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17021 Z= 0.135 Angle : 0.538 7.211 24254 Z= 0.313 Chirality : 0.034 0.153 2755 Planarity : 0.004 0.046 2063 Dihedral : 27.908 149.593 4596 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.20 % Allowed : 10.37 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.25), residues: 1241 helix: 2.13 (0.19), residues: 777 sheet: -1.57 (0.61), residues: 70 loop : -1.94 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.009 0.001 TYR F 51 PHE 0.014 0.001 PHE K 574 TRP 0.014 0.001 TRP K 364 HIS 0.010 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00291 (17021) covalent geometry : angle 0.53794 (24254) hydrogen bonds : bond 0.04164 ( 883) hydrogen bonds : angle 2.58139 ( 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 163 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.369 Fit side-chains REVERT: C 90 ASP cc_start: 0.8591 (t70) cc_final: 0.8132 (t0) REVERT: D 73 GLU cc_start: 0.8924 (tp30) cc_final: 0.8323 (tp30) REVERT: D 83 ARG cc_start: 0.9169 (mmt90) cc_final: 0.8939 (mmt-90) REVERT: E 59 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: E 107 THR cc_start: 0.9582 (m) cc_final: 0.9372 (t) REVERT: G 90 ASP cc_start: 0.8906 (t70) cc_final: 0.8264 (t70) REVERT: G 91 GLU cc_start: 0.8174 (pm20) cc_final: 0.7569 (pm20) REVERT: G 92 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8534 (mp0) REVERT: H 39 TYR cc_start: 0.8459 (t80) cc_final: 0.8218 (t80) REVERT: K 276 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8900 (tt) REVERT: K 325 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8843 (mm-30) REVERT: K 349 LEU cc_start: 0.9083 (mt) cc_final: 0.8810 (tp) REVERT: K 469 MET cc_start: 0.8485 (tmm) cc_final: 0.8269 (ppp) REVERT: K 470 MET cc_start: 0.9010 (mmp) cc_final: 0.8500 (mmp) REVERT: K 476 CYS cc_start: 0.9160 (m) cc_final: 0.8909 (m) outliers start: 13 outliers final: 9 residues processed: 158 average time/residue: 0.1163 time to fit residues: 27.4267 Evaluate side-chains 152 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 276 LEU 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: 0.9990 chunk 31 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 147 optimal weight: 0.0370 chunk 128 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.069004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.044757 restraints weight = 63745.589| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.68 r_work: 0.2619 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17021 Z= 0.168 Angle : 0.553 7.585 24254 Z= 0.319 Chirality : 0.035 0.148 2755 Planarity : 0.004 0.042 2063 Dihedral : 28.013 149.081 4596 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.20 % Allowed : 11.11 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.25), residues: 1241 helix: 2.17 (0.19), residues: 782 sheet: -1.19 (0.64), residues: 67 loop : -1.83 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.010 0.001 TYR G 50 PHE 0.014 0.001 PHE K 574 TRP 0.014 0.001 TRP K 364 HIS 0.009 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00376 (17021) covalent geometry : angle 0.55331 (24254) hydrogen bonds : bond 0.04511 ( 883) hydrogen bonds : angle 2.65498 ( 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: 13 poor density : 139 time to evaluate : 0.402 Fit side-chains REVERT: A 120 MET cc_start: 0.8520 (mmm) cc_final: 0.8193 (mtt) REVERT: B 20 LYS cc_start: 0.8549 (ptmm) cc_final: 0.7798 (tptp) REVERT: C 90 ASP cc_start: 0.8612 (t70) cc_final: 0.8258 (t70) REVERT: D 73 GLU cc_start: 0.8971 (tp30) cc_final: 0.8363 (tp30) REVERT: D 83 ARG cc_start: 0.9182 (mmt90) cc_final: 0.8949 (mmt-90) REVERT: F 84 MET cc_start: 0.8969 (mmm) cc_final: 0.8433 (mmm) REVERT: G 90 ASP cc_start: 0.8822 (t70) cc_final: 0.8525 (t70) REVERT: H 39 TYR cc_start: 0.8529 (t80) cc_final: 0.8301 (t80) REVERT: K 325 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8862 (mm-30) REVERT: K 349 LEU cc_start: 0.9073 (mt) cc_final: 0.8695 (tt) REVERT: K 470 MET cc_start: 0.9006 (mmp) cc_final: 0.8803 (mmp) REVERT: K 476 CYS cc_start: 0.9168 (m) cc_final: 0.8912 (m) outliers start: 13 outliers final: 7 residues processed: 149 average time/residue: 0.1258 time to fit residues: 27.8002 Evaluate side-chains 146 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain K residue 118 LEU 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: 2.9990 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 0.0970 chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.070147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.046083 restraints weight = 63323.447| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.66 r_work: 0.2657 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17021 Z= 0.137 Angle : 0.544 8.200 24254 Z= 0.314 Chirality : 0.034 0.145 2755 Planarity : 0.003 0.042 2063 Dihedral : 27.896 148.581 4596 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.02 % Allowed : 11.48 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.25), residues: 1241 helix: 2.28 (0.19), residues: 776 sheet: -1.12 (0.64), residues: 70 loop : -1.78 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.009 0.001 TYR K 191 PHE 0.014 0.001 PHE K 574 TRP 0.013 0.001 TRP K 364 HIS 0.010 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00298 (17021) covalent geometry : angle 0.54381 (24254) hydrogen bonds : bond 0.04172 ( 883) hydrogen bonds : angle 2.55436 ( 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 156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.486 Fit side-chains REVERT: A 125 GLN cc_start: 0.9334 (mt0) cc_final: 0.9004 (mt0) REVERT: B 20 LYS cc_start: 0.8538 (ptmm) cc_final: 0.7811 (tptp) REVERT: C 90 ASP cc_start: 0.8567 (t70) cc_final: 0.8133 (t0) REVERT: D 73 GLU cc_start: 0.8932 (tp30) cc_final: 0.8346 (tp30) REVERT: D 83 ARG cc_start: 0.9115 (mmt90) cc_final: 0.8897 (mmt-90) REVERT: E 59 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: F 84 MET cc_start: 0.8925 (mmm) cc_final: 0.8371 (mmm) REVERT: G 90 ASP cc_start: 0.8865 (t70) cc_final: 0.8240 (t70) REVERT: G 91 GLU cc_start: 0.8157 (pm20) cc_final: 0.7605 (pm20) REVERT: G 92 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8530 (mp0) REVERT: H 39 TYR cc_start: 0.8465 (t80) cc_final: 0.8200 (t80) REVERT: K 325 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8841 (mm-30) REVERT: K 349 LEU cc_start: 0.9038 (mt) cc_final: 0.8700 (tt) REVERT: K 469 MET cc_start: 0.8474 (tmm) cc_final: 0.8225 (ppp) REVERT: K 470 MET cc_start: 0.8985 (mmp) cc_final: 0.8532 (mmp) REVERT: K 476 CYS cc_start: 0.9131 (m) cc_final: 0.8873 (m) outliers start: 11 outliers final: 10 residues processed: 152 average time/residue: 0.1213 time to fit residues: 27.5041 Evaluate side-chains 154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain K residue 118 LEU 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: 0.0670 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 107 optimal weight: 0.1980 chunk 9 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN K 394 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.069894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.045828 restraints weight = 63758.624| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.68 r_work: 0.2648 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17021 Z= 0.149 Angle : 0.552 7.891 24254 Z= 0.317 Chirality : 0.035 0.153 2755 Planarity : 0.004 0.042 2063 Dihedral : 27.919 148.506 4596 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.02 % Allowed : 11.67 % Favored : 87.31 % 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 aren not related in a simple way. whole: 1.38 (0.25), residues: 1241 helix: 2.35 (0.19), residues: 776 sheet: -1.03 (0.64), residues: 70 loop : -1.76 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.009 0.001 TYR K 191 PHE 0.014 0.001 PHE K 574 TRP 0.013 0.001 TRP K 364 HIS 0.009 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00329 (17021) covalent geometry : angle 0.55212 (24254) hydrogen bonds : bond 0.04302 ( 883) hydrogen bonds : angle 2.56982 ( 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 152 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.510 Fit side-chains REVERT: A 125 GLN cc_start: 0.9341 (mt0) cc_final: 0.9003 (mt0) REVERT: B 20 LYS cc_start: 0.8554 (ptmm) cc_final: 0.7839 (tptp) REVERT: C 90 ASP cc_start: 0.8565 (t70) cc_final: 0.8113 (t0) REVERT: D 73 GLU cc_start: 0.8962 (tp30) cc_final: 0.8372 (tp30) REVERT: D 83 ARG cc_start: 0.9127 (mmt90) cc_final: 0.8909 (mmt-90) REVERT: E 59 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: F 84 MET cc_start: 0.8977 (mmm) cc_final: 0.8408 (mmm) REVERT: G 90 ASP cc_start: 0.8822 (t70) cc_final: 0.8177 (t70) REVERT: G 91 GLU cc_start: 0.8149 (pm20) cc_final: 0.7534 (pm20) REVERT: G 92 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8494 (mp0) REVERT: H 39 TYR cc_start: 0.8497 (t80) cc_final: 0.8251 (t80) REVERT: K 325 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8874 (mm-30) REVERT: K 349 LEU cc_start: 0.9035 (mt) cc_final: 0.8819 (tp) REVERT: K 469 MET cc_start: 0.8478 (tmm) cc_final: 0.8248 (ppp) REVERT: K 470 MET cc_start: 0.8985 (mmp) cc_final: 0.8557 (mmp) REVERT: K 476 CYS cc_start: 0.9142 (m) cc_final: 0.8887 (m) outliers start: 11 outliers final: 10 residues processed: 147 average time/residue: 0.1229 time to fit residues: 27.1350 Evaluate side-chains 150 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 118 LEU 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.7328 > 50: distance: 27 - 68: 3.435 distance: 70 - 73: 25.913 distance: 73 - 74: 7.594 distance: 74 - 75: 42.827 distance: 74 - 77: 42.058 distance: 75 - 76: 42.480 distance: 75 - 79: 30.261 distance: 77 - 78: 48.776 distance: 79 - 80: 19.456 distance: 80 - 81: 9.845 distance: 80 - 83: 40.792 distance: 81 - 82: 23.364 distance: 81 - 91: 34.902 distance: 83 - 84: 19.181 distance: 84 - 85: 45.408 distance: 84 - 86: 24.923 distance: 85 - 87: 40.569 distance: 86 - 88: 54.450 distance: 87 - 89: 46.676 distance: 88 - 89: 55.573 distance: 89 - 90: 38.495 distance: 91 - 92: 37.758 distance: 92 - 93: 23.101 distance: 92 - 95: 33.655 distance: 93 - 94: 52.001 distance: 93 - 100: 44.890 distance: 94 - 124: 34.818 distance: 95 - 96: 38.524 distance: 96 - 97: 29.159 distance: 97 - 98: 40.421 distance: 97 - 99: 27.983 distance: 100 - 101: 29.158 distance: 101 - 102: 26.018 distance: 101 - 104: 14.301 distance: 102 - 103: 57.710 distance: 102 - 108: 22.815 distance: 103 - 135: 52.881 distance: 104 - 105: 42.009 distance: 104 - 106: 42.781 distance: 105 - 107: 43.839 distance: 108 - 109: 24.356 distance: 109 - 110: 30.624 distance: 109 - 112: 30.571 distance: 110 - 111: 42.282 distance: 110 - 116: 44.430 distance: 112 - 113: 34.531 distance: 112 - 114: 25.875 distance: 113 - 115: 12.826 distance: 116 - 117: 27.357 distance: 117 - 118: 46.030 distance: 117 - 120: 29.185 distance: 118 - 119: 37.653 distance: 118 - 124: 53.815 distance: 120 - 121: 56.686 distance: 120 - 122: 48.848 distance: 121 - 123: 34.903 distance: 124 - 125: 10.305 distance: 125 - 126: 14.796 distance: 125 - 128: 38.267 distance: 126 - 127: 17.637 distance: 126 - 135: 28.859 distance: 128 - 129: 36.170 distance: 129 - 130: 41.292 distance: 130 - 131: 43.826 distance: 131 - 132: 21.691 distance: 132 - 133: 14.342 distance: 132 - 134: 16.149 distance: 135 - 136: 28.245 distance: 136 - 137: 31.100 distance: 136 - 139: 40.880 distance: 137 - 138: 37.237 distance: 137 - 144: 50.432 distance: 139 - 140: 50.097 distance: 140 - 141: 42.830 distance: 141 - 142: 43.562 distance: 141 - 143: 36.821 distance: 144 - 145: 21.566 distance: 145 - 146: 38.683 distance: 145 - 148: 11.413 distance: 146 - 147: 28.748 distance: 146 - 153: 24.098 distance: 148 - 149: 18.831 distance: 149 - 150: 25.978 distance: 150 - 151: 14.335 distance: 151 - 152: 36.433 distance: 153 - 154: 34.496 distance: 154 - 155: 34.162 distance: 154 - 157: 28.480 distance: 155 - 156: 13.114 distance: 155 - 159: 21.877 distance: 157 - 158: 29.981