Starting phenix.real_space_refine on Sat Jul 4 14:58:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ger_51305/07_2026/9ger_51305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ger_51305/07_2026/9ger_51305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ger_51305/07_2026/9ger_51305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ger_51305/07_2026/9ger_51305.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ger_51305/07_2026/9ger_51305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ger_51305/07_2026/9ger_51305.map" } resolution = 3.58 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= 0.278 sd= 1.209 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 Ca 1 9.91 5 Fe 2 7.16 5 P 290 5.49 5 S 76 5.16 5 Cl 1 4.86 5 C 12507 2.51 5 N 3918 2.21 5 O 4521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21316 Number of models: 1 Model: "" Number of chains: 20 Chain: "K" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 837 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 10, 'TRANS': 93} Chain: "L" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3732 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 429} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 837 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 10, 'TRANS': 93} Chain: "N" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3732 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 429} Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "O" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.70, per 1000 atoms: 0.22 Number of scatterers: 21316 At special positions: 0 Unit cell: (113.56, 128.52, 173.4, 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) Fe 2 26.01 Ca 1 19.99 Cl 1 17.00 S 76 16.00 P 290 15.00 O 4521 8.00 N 3918 7.00 C 12507 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS K 1 " - pdb=" SG CYS K 14 " distance=2.03 Simple disulfide: pdb=" SG CYS L 115 " - pdb=" SG CYS L 125 " distance=2.03 Simple disulfide: pdb=" SG CYS L 119 " - pdb=" SG CYS L 143 " distance=2.03 Simple disulfide: pdb=" SG CYS L 221 " - pdb=" SG CYS L 232 " distance=2.03 Simple disulfide: pdb=" SG CYS L 538 " - pdb=" SG CYS L 564 " distance=2.03 Simple disulfide: pdb=" SG CYS M 1 " - pdb=" SG CYS M 14 " distance=2.03 Simple disulfide: pdb=" SG CYS N 115 " - pdb=" SG CYS N 125 " distance=2.03 Simple disulfide: pdb=" SG CYS N 119 " - pdb=" SG CYS N 143 " distance=2.03 Simple disulfide: pdb=" SG CYS N 221 " - pdb=" SG CYS N 232 " distance=2.03 Simple disulfide: pdb=" SG CYS N 440 " - pdb=" SG CYS N 497 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " BETA1-6 " NAG O 1 " - " FUC O 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 6 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 687.5 milliseconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3550 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 10 sheets defined 53.8% alpha, 1.8% beta 139 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'K' and resid 60 through 69 Processing helix chain 'K' and resid 72 through 76 removed outlier: 3.860A pdb=" N GLN K 75 " --> pdb=" O PRO K 72 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU K 76 " --> pdb=" O THR K 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 72 through 76' Processing helix chain 'K' and resid 84 through 98 removed outlier: 4.326A pdb=" N GLN K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 178 removed outlier: 3.744A pdb=" N TYR L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 186 Processing helix chain 'L' and resid 219 through 224 removed outlier: 3.525A pdb=" N LEU L 222 " --> pdb=" O ASP L 219 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 242 removed outlier: 3.886A pdb=" N GLU L 242 " --> pdb=" O ARG L 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 239 through 242' Processing helix chain 'L' and resid 243 through 268 removed outlier: 3.545A pdb=" N THR L 247 " --> pdb=" O MET L 243 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 297 Processing helix chain 'L' and resid 298 through 300 No H-bonds generated for 'chain 'L' and resid 298 through 300' Processing helix chain 'L' and resid 302 through 310 Processing helix chain 'L' and resid 325 through 332 Processing helix chain 'L' and resid 333 through 339 removed outlier: 3.690A pdb=" N HIS L 336 " --> pdb=" O ARG L 333 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE L 339 " --> pdb=" O HIS L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 365 removed outlier: 3.811A pdb=" N PHE L 365 " --> pdb=" O SER L 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 368 through 373 removed outlier: 3.547A pdb=" N VAL L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 377 through 386 removed outlier: 3.520A pdb=" N LEU L 381 " --> pdb=" O ILE L 377 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA L 386 " --> pdb=" O ARG L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 405 Processing helix chain 'L' and resid 416 through 429 removed outlier: 3.555A pdb=" N GLY L 429 " --> pdb=" O SER L 425 " (cutoff:3.500A) Processing helix chain 'L' and resid 432 through 440 Processing helix chain 'L' and resid 447 through 456 Processing helix chain 'L' and resid 458 through 468 Processing helix chain 'L' and resid 470 through 474 Processing helix chain 'L' and resid 475 through 483 removed outlier: 3.638A pdb=" N GLU L 483 " --> pdb=" O GLY L 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 508 Processing helix chain 'L' and resid 521 through 528 Processing helix chain 'L' and resid 532 through 541 removed outlier: 3.519A pdb=" N THR L 541 " --> pdb=" O ILE L 537 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 576 Processing helix chain 'M' and resid 60 through 68 Processing helix chain 'M' and resid 72 through 76 removed outlier: 4.014A pdb=" N GLN M 75 " --> pdb=" O PRO M 72 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU M 76 " --> pdb=" O THR M 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 72 through 76' Processing helix chain 'M' and resid 84 through 98 removed outlier: 3.548A pdb=" N ASP M 98 " --> pdb=" O ASP M 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 187 Processing helix chain 'N' and resid 243 through 268 removed outlier: 3.720A pdb=" N THR N 247 " --> pdb=" O MET N 243 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN N 268 " --> pdb=" O LEU N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 272 through 297 Processing helix chain 'N' and resid 298 through 300 No H-bonds generated for 'chain 'N' and resid 298 through 300' Processing helix chain 'N' and resid 302 through 310 Processing helix chain 'N' and resid 327 through 333 removed outlier: 3.643A pdb=" N ALA N 331 " --> pdb=" O VAL N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 334 through 338 removed outlier: 3.896A pdb=" N LEU N 338 " --> pdb=" O GLY N 335 " (cutoff:3.500A) Processing helix chain 'N' and resid 368 through 374 removed outlier: 3.658A pdb=" N VAL N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 377 through 386 removed outlier: 3.727A pdb=" N ALA N 386 " --> pdb=" O ARG N 382 " (cutoff:3.500A) Processing helix chain 'N' and resid 400 through 405 removed outlier: 3.670A pdb=" N ARG N 405 " --> pdb=" O GLU N 401 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 429 Processing helix chain 'N' and resid 432 through 441 removed outlier: 3.535A pdb=" N TRP N 436 " --> pdb=" O GLY N 432 " (cutoff:3.500A) Processing helix chain 'N' and resid 447 through 456 Processing helix chain 'N' and resid 457 through 469 removed outlier: 3.861A pdb=" N GLN N 467 " --> pdb=" O LYS N 463 " (cutoff:3.500A) Processing helix chain 'N' and resid 470 through 474 Processing helix chain 'N' and resid 475 through 483 removed outlier: 3.616A pdb=" N GLU N 483 " --> pdb=" O GLY N 479 " (cutoff:3.500A) Processing helix chain 'N' and resid 492 through 508 removed outlier: 3.747A pdb=" N THR N 501 " --> pdb=" O CYS N 497 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN N 502 " --> pdb=" O ILE N 498 " (cutoff:3.500A) Processing helix chain 'N' and resid 521 through 529 Processing helix chain 'N' and resid 535 through 541 removed outlier: 3.639A pdb=" N ASP N 539 " --> pdb=" O ARG N 535 " (cutoff:3.500A) Processing helix chain 'N' and resid 572 through 576 Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.655A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 87 through 114 removed outlier: 3.574A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.811A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.824A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.819A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.939A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.559A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 71 removed outlier: 4.300A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.514A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 36 through 46 removed outlier: 3.756A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.633A pdb=" N VAL D 63 " --> pdb=" O MET D 59 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.559A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 121 removed outlier: 4.111A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 87 through 114 removed outlier: 4.041A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.597A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.719A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 4.474A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.244A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.653A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.587A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 16 through 21' Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 45 through 71 removed outlier: 4.638A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.801A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.519A pdb=" N MET H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.539A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.925A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 78 through 83 removed outlier: 6.933A pdb=" N ARG K 82 " --> pdb=" O ALA L 389 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 342 through 343 Processing sheet with id=AA3, first strand: chain 'L' and resid 545 through 546 Processing sheet with id=AA4, first strand: chain 'M' and resid 78 through 83 removed outlier: 4.110A pdb=" N ALA N 389 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 188 through 189 removed outlier: 4.457A pdb=" N LEU N 196 " --> pdb=" O ASN N 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 342 through 344 Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.564A pdb=" N THR G 101 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.210A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.345A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.558A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 619 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 355 hydrogen bonds 706 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 8597 1.39 - 1.56: 13045 1.56 - 1.74: 579 1.74 - 1.91: 122 1.91 - 2.08: 8 Bond restraints: 22351 Sorted by residual: bond pdb=" C3' DT I -67 " pdb=" C2' DT I -67 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DA J -67 " pdb=" C2' DA J -67 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DG I -19 " pdb=" C2' DG I -19 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG I 23 " pdb=" C2' DG I 23 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA I -1 " pdb=" C2' DA I -1 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.81e+00 ... (remaining 22346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 31028 2.35 - 4.70: 462 4.70 - 7.06: 37 7.06 - 9.41: 4 9.41 - 11.76: 2 Bond angle restraints: 31533 Sorted by residual: angle pdb=" N3 DT I -67 " pdb=" C4 DT I -67 " pdb=" O4 DT I -67 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 33 " pdb=" C4 DT I 33 " pdb=" O4 DT I 33 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 1 " pdb=" C4 DT J 1 " pdb=" O4 DT J 1 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT I 67 " pdb=" C4 DT I 67 " pdb=" O4 DT I 67 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 31528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.36: 10999 31.36 - 62.72: 1923 62.72 - 94.09: 53 94.09 - 125.45: 0 125.45 - 156.81: 3 Dihedral angle restraints: 12978 sinusoidal: 7491 harmonic: 5487 Sorted by residual: dihedral pdb=" CB CYS N 115 " pdb=" SG CYS N 115 " pdb=" SG CYS N 125 " pdb=" CB CYS N 125 " ideal model delta sinusoidal sigma weight residual 93.00 -179.51 -87.49 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS L 115 " pdb=" SG CYS L 115 " pdb=" SG CYS L 125 " pdb=" CB CYS L 125 " ideal model delta sinusoidal sigma weight residual -86.00 -170.85 84.85 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS M 1 " pdb=" SG CYS M 1 " pdb=" SG CYS M 14 " pdb=" CB CYS M 14 " ideal model delta sinusoidal sigma weight residual -86.00 -119.90 33.90 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 12975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2805 0.049 - 0.099: 639 0.099 - 0.148: 85 0.148 - 0.197: 5 0.197 - 0.247: 1 Chirality restraints: 3535 Sorted by residual: chirality pdb=" CA GLN N 193 " pdb=" N GLN N 193 " pdb=" C GLN N 193 " pdb=" CB GLN N 193 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE N 290 " pdb=" CA ILE N 290 " pdb=" CG1 ILE N 290 " pdb=" CG2 ILE N 290 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.09 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 3532 not shown) Planarity restraints: 3036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 77 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO K 78 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO K 78 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO K 78 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN N 193 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C GLN N 193 " -0.029 2.00e-02 2.50e+03 pdb=" O GLN N 193 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU N 194 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR N 293 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C TYR N 293 " -0.029 2.00e-02 2.50e+03 pdb=" O TYR N 293 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG N 294 " 0.010 2.00e-02 2.50e+03 ... (remaining 3033 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 281 2.65 - 3.21: 17426 3.21 - 3.77: 32707 3.77 - 4.34: 41135 4.34 - 4.90: 64201 Nonbonded interactions: 155750 Sorted by model distance: nonbonded pdb=" O2 DT I -72 " pdb=" O6 DG J 71 " model vdw 2.083 3.040 nonbonded pdb=" OD1 ASN L 549 " pdb=" N ASN L 550 " model vdw 2.171 3.120 nonbonded pdb=" NH2 ARG N 349 " pdb=" OH TYR N 557 " model vdw 2.194 3.120 nonbonded pdb=" C2 DT I -72 " pdb=" O6 DG J 71 " model vdw 2.217 3.260 nonbonded pdb=" OG SER N 521 " pdb=" OE1 GLN N 523 " model vdw 2.248 3.040 ... (remaining 155745 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = (chain 'G' and resid 13 through 117) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'K' and resid 1 through 104) selection = (chain 'M' and resid 1 through 104) } ncs_group { reference = (chain 'L' and resid 113 through 602) selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } 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 group one per residue 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: 5.760 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: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.460 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.005 0.096 22376 Z= 0.389 Angle : 0.684 11.759 31583 Z= 0.522 Chirality : 0.041 0.247 3535 Planarity : 0.004 0.052 3036 Dihedral : 24.130 156.812 9398 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 3.14 % Allowed : 29.34 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1865 helix: 2.36 (0.19), residues: 860 sheet: -2.06 (1.18), residues: 20 loop : -1.60 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 349 TYR 0.026 0.001 TYR D 80 PHE 0.019 0.001 PHE K 71 TRP 0.027 0.001 TRP N 271 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.39 (22351) covalent geometry : angle 0.68201 / 0.52 (31533) SS BOND : bond 0.00212 / 0.14 ( 10) SS BOND : angle 1.01909 / 0.49 ( 20) hydrogen bonds : bond 0.13113 / 8.45 ( 974) hydrogen bonds : angle 4.35973 / 3.10 ( 2509) Misc. bond : bond 0.04927 / 3.20 ( 5) link_ALPHA1-3 : bond 0.01009 / 0.52 ( 2) link_ALPHA1-3 : angle 1.75744 / 0.89 ( 6) link_ALPHA1-6 : bond 0.01180 / 0.62 ( 2) link_ALPHA1-6 : angle 1.42084 / 0.79 ( 6) link_BETA1-4 : bond 0.00380 / 0.19 ( 4) link_BETA1-4 : angle 1.74275 / 1.35 ( 12) link_BETA1-6 : bond 0.00342 / 0.17 ( 2) link_BETA1-6 : angle 1.27797 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7875 (pp30) cc_final: 0.7345 (pp30) REVERT: L 134 ASP cc_start: 0.7696 (t0) cc_final: 0.7285 (t70) REVERT: L 142 ASP cc_start: 0.6929 (t0) cc_final: 0.6663 (m-30) REVERT: L 293 TYR cc_start: 0.6061 (OUTLIER) cc_final: 0.4126 (t80) REVERT: L 349 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7429 (ttp80) REVERT: L 395 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.6999 (p0) REVERT: L 507 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7327 (ttm170) REVERT: L 540 ASN cc_start: 0.7305 (m110) cc_final: 0.6802 (m110) REVERT: L 561 PHE cc_start: 0.7265 (m-80) cc_final: 0.6966 (m-80) REVERT: N 175 MET cc_start: 0.7439 (pmm) cc_final: 0.6984 (pmm) REVERT: N 353 MET cc_start: 0.5447 (tpp) cc_final: 0.5118 (tpp) REVERT: B 27 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7687 (tm-30) REVERT: C 15 LYS cc_start: 0.9084 (mtpt) cc_final: 0.8624 (mtmm) REVERT: D 102 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7280 (tm-30) REVERT: G 110 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8449 (p0) outliers start: 51 outliers final: 42 residues processed: 283 average time/residue: 0.1837 time to fit residues: 76.0699 Evaluate side-chains 284 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 88 GLN Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 293 TYR Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 507 ARG Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 221 CYS Chi-restraints excluded: chain N residue 232 CYS Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 332 PHE Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 378 ASP Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.104513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.081294 restraints weight = 47982.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.083278 restraints weight = 26520.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.083875 restraints weight = 18640.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.084394 restraints weight = 15101.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084477 restraints weight = 14941.379| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 22376 Z= 0.209 Angle : 0.653 12.977 31583 Z= 0.356 Chirality : 0.043 0.219 3535 Planarity : 0.004 0.040 3036 Dihedral : 25.487 155.801 5685 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 4.92 % Allowed : 28.47 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1865 helix: 2.31 (0.18), residues: 867 sheet: -2.04 (1.17), residues: 20 loop : -1.71 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 349 TYR 0.013 0.001 TYR N 557 PHE 0.016 0.001 PHE M 71 TRP 0.013 0.001 TRP N 271 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (22351) covalent geometry : angle 0.64990 / 0.36 (31533) SS BOND : bond 0.00515 / 0.29 ( 10) SS BOND : angle 1.34671 / 0.75 ( 20) hydrogen bonds : bond 0.07377 / 4.81 ( 974) hydrogen bonds : angle 3.60308 / 2.57 ( 2509) Misc. bond : bond 0.05604 / 3.12 ( 5) link_ALPHA1-3 : bond 0.01006 / 0.52 ( 2) link_ALPHA1-3 : angle 2.12908 / 1.06 ( 6) link_ALPHA1-6 : bond 0.01179 / 0.62 ( 2) link_ALPHA1-6 : angle 1.28769 / 0.72 ( 6) link_BETA1-4 : bond 0.00510 / 0.25 ( 4) link_BETA1-4 : angle 2.03570 / 1.59 ( 12) link_BETA1-6 : bond 0.00280 / 0.14 ( 2) link_BETA1-6 : angle 1.48798 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 241 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.8022 (pp30) cc_final: 0.7486 (pp30) REVERT: L 134 ASP cc_start: 0.7574 (t0) cc_final: 0.7233 (t70) REVERT: L 293 TYR cc_start: 0.6343 (OUTLIER) cc_final: 0.4445 (t80) REVERT: L 540 ASN cc_start: 0.7504 (m110) cc_final: 0.6982 (m110) REVERT: L 561 PHE cc_start: 0.7131 (m-80) cc_final: 0.6703 (m-80) REVERT: M 85 MET cc_start: 0.7850 (tpp) cc_final: 0.7529 (tpt) REVERT: N 175 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7090 (pmm) REVERT: N 412 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6753 (ptp-170) REVERT: B 27 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7654 (tm-30) REVERT: C 15 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8553 (mtmm) REVERT: C 90 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7556 (t0) REVERT: G 33 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8609 (mp) REVERT: G 110 ASN cc_start: 0.8625 (t0) cc_final: 0.8350 (p0) outliers start: 80 outliers final: 51 residues processed: 308 average time/residue: 0.1672 time to fit residues: 76.4189 Evaluate side-chains 290 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 293 TYR Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 481 VAL Chi-restraints excluded: chain L residue 485 LEU Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 221 CYS Chi-restraints excluded: chain N residue 232 CYS Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 378 ASP Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 412 ARG Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 519 VAL Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 22 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 115 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 196 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 330 ASN N 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.109584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.085381 restraints weight = 50473.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.087755 restraints weight = 27151.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.088419 restraints weight = 16115.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088724 restraints weight = 14124.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088832 restraints weight = 13758.274| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 22376 Z= 0.133 Angle : 0.577 10.984 31583 Z= 0.321 Chirality : 0.039 0.214 3535 Planarity : 0.004 0.044 3036 Dihedral : 25.450 153.975 5646 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.30 % Rotamer: Outliers : 3.81 % Allowed : 29.70 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1865 helix: 2.39 (0.18), residues: 886 sheet: -1.89 (1.22), residues: 20 loop : -1.67 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 76 TYR 0.014 0.001 TYR F 88 PHE 0.012 0.001 PHE K 71 TRP 0.018 0.001 TRP N 271 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 (22351) covalent geometry : angle 0.57444 / 0.32 (31533) SS BOND : bond 0.00239 / 0.16 ( 10) SS BOND : angle 0.85037 / 0.50 ( 20) hydrogen bonds : bond 0.05563 / 3.61 ( 974) hydrogen bonds : angle 3.23470 / 2.33 ( 2509) Misc. bond : bond 0.06867 / 4.49 ( 5) link_ALPHA1-3 : bond 0.00939 / 0.48 ( 2) link_ALPHA1-3 : angle 2.07608 / 1.04 ( 6) link_ALPHA1-6 : bond 0.01093 / 0.57 ( 2) link_ALPHA1-6 : angle 1.37739 / 0.76 ( 6) link_BETA1-4 : bond 0.00378 / 0.18 ( 4) link_BETA1-4 : angle 1.77207 / 1.36 ( 12) link_BETA1-6 : bond 0.00371 / 0.18 ( 2) link_BETA1-6 : angle 1.26962 / 0.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 244 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7965 (pp30) cc_final: 0.7427 (pp30) REVERT: L 134 ASP cc_start: 0.7654 (t0) cc_final: 0.7322 (t70) REVERT: L 193 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7891 (tp40) REVERT: L 293 TYR cc_start: 0.6209 (OUTLIER) cc_final: 0.4210 (t80) REVERT: L 343 MET cc_start: 0.6173 (ttp) cc_final: 0.5971 (ttp) REVERT: L 540 ASN cc_start: 0.7390 (m110) cc_final: 0.6858 (m110) REVERT: M 85 MET cc_start: 0.7685 (tpp) cc_final: 0.7385 (tpt) REVERT: N 175 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6982 (pmm) REVERT: N 271 TRP cc_start: 0.8356 (m-10) cc_final: 0.7846 (m-10) REVERT: N 412 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6786 (ptp-170) REVERT: N 577 GLU cc_start: 0.7850 (tp30) cc_final: 0.7399 (tt0) REVERT: B 27 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7589 (tm-30) REVERT: B 92 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8151 (ttp80) REVERT: C 15 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8538 (mtmm) REVERT: C 90 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7510 (t0) REVERT: G 110 ASN cc_start: 0.8628 (t0) cc_final: 0.8402 (p0) outliers start: 62 outliers final: 42 residues processed: 291 average time/residue: 0.1860 time to fit residues: 78.7257 Evaluate side-chains 284 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 193 GLN Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 293 TYR Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 485 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 221 CYS Chi-restraints excluded: chain N residue 232 CYS Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 412 ARG Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 511 ARG Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 39 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 14 optimal weight: 0.1980 chunk 161 optimal weight: 0.2980 chunk 123 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 330 ASN L 450 GLN N 133 ASN N 428 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.109152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084419 restraints weight = 49995.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.086611 restraints weight = 27119.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.087278 restraints weight = 16348.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.087350 restraints weight = 14586.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.087513 restraints weight = 14600.650| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 22376 Z= 0.140 Angle : 0.583 12.264 31583 Z= 0.320 Chirality : 0.040 0.215 3535 Planarity : 0.004 0.042 3036 Dihedral : 25.492 153.994 5635 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.18 % Favored : 95.76 % Rotamer: Outliers : 4.98 % Allowed : 27.92 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1865 helix: 2.44 (0.18), residues: 888 sheet: -1.92 (1.20), residues: 20 loop : -1.65 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 349 TYR 0.014 0.001 TYR D 80 PHE 0.015 0.001 PHE K 71 TRP 0.011 0.001 TRP N 271 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (22351) covalent geometry : angle 0.58061 / 0.32 (31533) SS BOND : bond 0.00195 / 0.14 ( 10) SS BOND : angle 0.79754 / 0.49 ( 20) hydrogen bonds : bond 0.05726 / 3.72 ( 974) hydrogen bonds : angle 3.14633 / 2.27 ( 2509) Misc. bond : bond 0.05854 / 3.54 ( 5) link_ALPHA1-3 : bond 0.01042 / 0.53 ( 2) link_ALPHA1-3 : angle 2.05275 / 1.03 ( 6) link_ALPHA1-6 : bond 0.01111 / 0.58 ( 2) link_ALPHA1-6 : angle 1.35714 / 0.75 ( 6) link_BETA1-4 : bond 0.00392 / 0.19 ( 4) link_BETA1-4 : angle 1.87599 / 1.49 ( 12) link_BETA1-6 : bond 0.00271 / 0.13 ( 2) link_BETA1-6 : angle 1.35015 / 0.71 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 238 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7930 (pp30) cc_final: 0.7392 (pp30) REVERT: L 134 ASP cc_start: 0.7690 (t0) cc_final: 0.7313 (t70) REVERT: L 293 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.4290 (t80) REVERT: L 343 MET cc_start: 0.6216 (ttp) cc_final: 0.6005 (ttp) REVERT: L 540 ASN cc_start: 0.7430 (m110) cc_final: 0.6898 (m110) REVERT: N 175 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7028 (pmm) REVERT: N 271 TRP cc_start: 0.8385 (m-10) cc_final: 0.7991 (m-10) REVERT: N 412 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6767 (ptp-170) REVERT: B 27 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7531 (tm-30) REVERT: G 110 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8423 (p0) outliers start: 81 outliers final: 60 residues processed: 297 average time/residue: 0.1754 time to fit residues: 77.1375 Evaluate side-chains 298 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 234 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 293 TYR Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 319 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 485 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 221 CYS Chi-restraints excluded: chain N residue 232 CYS Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 378 ASP Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 412 ARG Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 519 VAL Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 2 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 187 optimal weight: 30.0000 chunk 192 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 99 optimal weight: 0.0370 chunk 44 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 158 optimal weight: 0.0980 chunk 103 optimal weight: 0.1980 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 193 GLN N 133 ASN N 139 ASN B 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.107984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084402 restraints weight = 47582.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.086419 restraints weight = 25729.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.087779 restraints weight = 17517.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.088605 restraints weight = 13804.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.089109 restraints weight = 12010.737| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.096 22376 Z= 0.123 Angle : 0.556 10.930 31583 Z= 0.309 Chirality : 0.039 0.216 3535 Planarity : 0.004 0.041 3036 Dihedral : 25.482 153.702 5635 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 4.06 % Allowed : 29.09 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1865 helix: 2.41 (0.18), residues: 903 sheet: -1.83 (1.23), residues: 20 loop : -1.61 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 349 TYR 0.010 0.001 TYR F 88 PHE 0.015 0.001 PHE K 71 TRP 0.016 0.001 TRP N 271 HIS 0.003 0.000 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.12 (22351) covalent geometry : angle 0.55363 / 0.31 (31533) SS BOND : bond 0.00196 / 0.14 ( 10) SS BOND : angle 0.72627 / 0.44 ( 20) hydrogen bonds : bond 0.04902 / 3.17 ( 974) hydrogen bonds : angle 3.03243 / 2.20 ( 2509) Misc. bond : bond 0.05831 / 3.76 ( 5) link_ALPHA1-3 : bond 0.01009 / 0.52 ( 2) link_ALPHA1-3 : angle 1.99210 / 1.00 ( 6) link_ALPHA1-6 : bond 0.01060 / 0.55 ( 2) link_ALPHA1-6 : angle 1.39465 / 0.77 ( 6) link_BETA1-4 : bond 0.00374 / 0.18 ( 4) link_BETA1-4 : angle 1.75539 / 1.36 ( 12) link_BETA1-6 : bond 0.00368 / 0.18 ( 2) link_BETA1-6 : angle 1.23941 / 0.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 244 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7945 (pp30) cc_final: 0.7436 (pp30) REVERT: L 134 ASP cc_start: 0.7632 (t0) cc_final: 0.7286 (t70) REVERT: L 293 TYR cc_start: 0.6088 (OUTLIER) cc_final: 0.4097 (t80) REVERT: L 540 ASN cc_start: 0.7311 (m110) cc_final: 0.6792 (m110) REVERT: N 175 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.6968 (pmm) REVERT: N 271 TRP cc_start: 0.8186 (OUTLIER) cc_final: 0.7661 (m-10) REVERT: N 412 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6718 (ptp-170) REVERT: N 488 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8252 (mtpt) REVERT: N 577 GLU cc_start: 0.7755 (tp30) cc_final: 0.7454 (tt0) REVERT: B 27 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7518 (tm-30) REVERT: B 92 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8198 (ttp80) outliers start: 66 outliers final: 45 residues processed: 288 average time/residue: 0.1830 time to fit residues: 77.5712 Evaluate side-chains 285 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 293 TYR Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 485 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 217 HIS Chi-restraints excluded: chain N residue 221 CYS Chi-restraints excluded: chain N residue 232 CYS Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 378 ASP Chi-restraints excluded: chain N residue 412 ARG Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 511 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 59 optimal weight: 0.4980 chunk 195 optimal weight: 40.0000 chunk 120 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 198 optimal weight: 30.0000 chunk 182 optimal weight: 30.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 193 GLN M 15 ASN N 133 ASN N 193 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.103674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079340 restraints weight = 47462.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.081328 restraints weight = 26186.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.082602 restraints weight = 18005.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.083396 restraints weight = 14365.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.083864 restraints weight = 12589.259| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 22376 Z= 0.197 Angle : 0.652 14.351 31583 Z= 0.350 Chirality : 0.042 0.219 3535 Planarity : 0.004 0.051 3036 Dihedral : 25.528 154.631 5627 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 5.60 % Allowed : 27.92 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1865 helix: 2.22 (0.18), residues: 897 sheet: -1.78 (1.22), residues: 20 loop : -1.68 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 349 TYR 0.024 0.002 TYR B 88 PHE 0.015 0.002 PHE K 71 TRP 0.016 0.002 TRP N 271 HIS 0.006 0.001 HIS N 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (22351) covalent geometry : angle 0.64959 / 0.35 (31533) SS BOND : bond 0.00890 / 0.32 ( 10) SS BOND : angle 0.95551 / 0.68 ( 20) hydrogen bonds : bond 0.07100 / 4.63 ( 974) hydrogen bonds : angle 3.25918 / 2.35 ( 2509) Misc. bond : bond 0.06923 / 4.23 ( 5) link_ALPHA1-3 : bond 0.01045 / 0.54 ( 2) link_ALPHA1-3 : angle 2.39607 / 1.19 ( 6) link_ALPHA1-6 : bond 0.01127 / 0.59 ( 2) link_ALPHA1-6 : angle 1.35435 / 0.75 ( 6) link_BETA1-4 : bond 0.00534 / 0.26 ( 4) link_BETA1-4 : angle 2.10502 / 1.67 ( 12) link_BETA1-6 : bond 0.00271 / 0.13 ( 2) link_BETA1-6 : angle 1.53633 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 235 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7921 (pp30) cc_final: 0.7410 (pp30) REVERT: L 134 ASP cc_start: 0.7616 (t0) cc_final: 0.7255 (t70) REVERT: L 540 ASN cc_start: 0.7549 (m110) cc_final: 0.7018 (m110) REVERT: L 561 PHE cc_start: 0.7304 (m-80) cc_final: 0.6954 (m-80) REVERT: M 85 MET cc_start: 0.7697 (tpp) cc_final: 0.7374 (mmt) REVERT: N 175 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7291 (pmm) REVERT: N 271 TRP cc_start: 0.8276 (OUTLIER) cc_final: 0.7965 (m-10) REVERT: N 353 MET cc_start: 0.5697 (OUTLIER) cc_final: 0.5449 (mmp) REVERT: N 412 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6833 (ptp-170) REVERT: B 27 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7519 (tm-30) REVERT: G 61 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7698 (tm-30) outliers start: 91 outliers final: 74 residues processed: 301 average time/residue: 0.1750 time to fit residues: 78.2088 Evaluate side-chains 312 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 234 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 319 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 373 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 485 LEU Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 221 CYS Chi-restraints excluded: chain N residue 232 CYS Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 321 ASP Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 353 MET Chi-restraints excluded: chain N residue 378 ASP Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 412 ARG Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 454 VAL Chi-restraints excluded: chain N residue 481 VAL Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 491 VAL Chi-restraints excluded: chain N residue 511 ARG Chi-restraints excluded: chain N residue 519 VAL Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 18 optimal weight: 7.9990 chunk 41 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 175 optimal weight: 0.0070 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 133 ASN B 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.110199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.085295 restraints weight = 49972.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.087385 restraints weight = 27201.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.088756 restraints weight = 18549.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.089615 restraints weight = 14629.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.090126 restraints weight = 12694.444| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.157 22376 Z= 0.128 Angle : 0.578 10.632 31583 Z= 0.320 Chirality : 0.039 0.221 3535 Planarity : 0.004 0.047 3036 Dihedral : 25.446 154.599 5625 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.54 % Favored : 96.41 % Rotamer: Outliers : 3.75 % Allowed : 30.14 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1865 helix: 2.43 (0.18), residues: 897 sheet: -1.82 (1.23), residues: 20 loop : -1.63 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 76 TYR 0.025 0.001 TYR B 88 PHE 0.014 0.001 PHE K 71 TRP 0.017 0.001 TRP N 271 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.13 (22351) covalent geometry : angle 0.57540 / 0.32 (31533) SS BOND : bond 0.00259 / 0.17 ( 10) SS BOND : angle 0.76402 / 0.52 ( 20) hydrogen bonds : bond 0.05113 / 3.29 ( 974) hydrogen bonds : angle 3.04851 / 2.21 ( 2509) Misc. bond : bond 0.08209 / 5.65 ( 5) link_ALPHA1-3 : bond 0.00980 / 0.50 ( 2) link_ALPHA1-3 : angle 2.17754 / 1.09 ( 6) link_ALPHA1-6 : bond 0.01040 / 0.54 ( 2) link_ALPHA1-6 : angle 1.40361 / 0.78 ( 6) link_BETA1-4 : bond 0.00368 / 0.18 ( 4) link_BETA1-4 : angle 1.81419 / 1.37 ( 12) link_BETA1-6 : bond 0.00418 / 0.21 ( 2) link_BETA1-6 : angle 1.23647 / 0.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 237 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7860 (pp30) cc_final: 0.7341 (pp30) REVERT: L 134 ASP cc_start: 0.7648 (t0) cc_final: 0.7271 (t70) REVERT: L 349 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7320 (ttp80) REVERT: L 540 ASN cc_start: 0.7433 (m110) cc_final: 0.6914 (m110) REVERT: L 561 PHE cc_start: 0.7219 (m-80) cc_final: 0.6869 (m-80) REVERT: N 271 TRP cc_start: 0.8269 (OUTLIER) cc_final: 0.8043 (m-10) REVERT: B 27 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7876 (tm-30) REVERT: G 61 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7668 (tm-30) outliers start: 61 outliers final: 46 residues processed: 281 average time/residue: 0.1763 time to fit residues: 72.7511 Evaluate side-chains 277 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 319 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 95 HIS Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 110 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 40.0000 chunk 50 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 71 optimal weight: 0.0980 chunk 85 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 0.4980 chunk 190 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 206 ASN M 15 ASN N 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.104796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.080716 restraints weight = 47545.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.082735 restraints weight = 26079.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.084034 restraints weight = 17844.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084840 restraints weight = 14181.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.085295 restraints weight = 12390.919| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 22376 Z= 0.163 Angle : 0.621 13.200 31583 Z= 0.335 Chirality : 0.041 0.219 3535 Planarity : 0.004 0.034 3036 Dihedral : 25.483 155.108 5623 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.17 % Rotamer: Outliers : 3.75 % Allowed : 29.70 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1865 helix: 2.32 (0.18), residues: 898 sheet: -1.69 (1.24), residues: 20 loop : -1.65 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 349 TYR 0.028 0.001 TYR D 80 PHE 0.022 0.001 PHE N 366 TRP 0.017 0.001 TRP N 271 HIS 0.003 0.001 HIS N 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (22351) covalent geometry : angle 0.61886 / 0.33 (31533) SS BOND : bond 0.00376 / 0.22 ( 10) SS BOND : angle 1.01718 / 0.74 ( 20) hydrogen bonds : bond 0.06112 / 3.97 ( 974) hydrogen bonds : angle 3.10875 / 2.26 ( 2509) Misc. bond : bond 0.06134 / 3.88 ( 5) link_ALPHA1-3 : bond 0.01049 / 0.54 ( 2) link_ALPHA1-3 : angle 2.25898 / 1.13 ( 6) link_ALPHA1-6 : bond 0.01055 / 0.55 ( 2) link_ALPHA1-6 : angle 1.37874 / 0.78 ( 6) link_BETA1-4 : bond 0.00426 / 0.21 ( 4) link_BETA1-4 : angle 1.96256 / 1.55 ( 12) link_BETA1-6 : bond 0.00216 / 0.10 ( 2) link_BETA1-6 : angle 1.44532 / 0.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 232 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7911 (pp30) cc_final: 0.7410 (pp30) REVERT: L 134 ASP cc_start: 0.7629 (t0) cc_final: 0.7280 (t70) REVERT: L 349 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7311 (ttp80) REVERT: L 540 ASN cc_start: 0.7527 (m110) cc_final: 0.7026 (m110) REVERT: L 561 PHE cc_start: 0.7273 (m-80) cc_final: 0.6896 (m-80) REVERT: M 85 MET cc_start: 0.7621 (tpt) cc_final: 0.7348 (tpt) REVERT: N 271 TRP cc_start: 0.8265 (OUTLIER) cc_final: 0.7965 (m-10) REVERT: B 27 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7495 (tm-30) REVERT: B 92 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8138 (ttp80) outliers start: 61 outliers final: 52 residues processed: 276 average time/residue: 0.1803 time to fit residues: 73.3576 Evaluate side-chains 281 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 206 ASN Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 319 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 344 PHE Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 373 LEU Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 485 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 16 optimal weight: 0.0370 chunk 203 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 185 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.104289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.080112 restraints weight = 47364.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.082139 restraints weight = 25616.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083431 restraints weight = 17429.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.084241 restraints weight = 13825.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084728 restraints weight = 12066.922| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 22376 Z= 0.181 Angle : 0.642 13.764 31583 Z= 0.345 Chirality : 0.042 0.222 3535 Planarity : 0.004 0.033 3036 Dihedral : 25.479 155.707 5623 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.85 % Rotamer: Outliers : 3.81 % Allowed : 29.70 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1865 helix: 2.25 (0.18), residues: 897 sheet: -1.65 (1.22), residues: 20 loop : -1.73 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 208 TYR 0.012 0.001 TYR F 88 PHE 0.023 0.001 PHE N 366 TRP 0.018 0.001 TRP N 271 HIS 0.003 0.001 HIS N 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (22351) covalent geometry : angle 0.63966 / 0.34 (31533) SS BOND : bond 0.00285 / 0.18 ( 10) SS BOND : angle 0.98049 / 0.68 ( 20) hydrogen bonds : bond 0.06606 / 4.29 ( 974) hydrogen bonds : angle 3.19096 / 2.31 ( 2509) Misc. bond : bond 0.07175 / 4.67 ( 5) link_ALPHA1-3 : bond 0.00985 / 0.51 ( 2) link_ALPHA1-3 : angle 2.46100 / 1.22 ( 6) link_ALPHA1-6 : bond 0.01073 / 0.56 ( 2) link_ALPHA1-6 : angle 1.38603 / 0.78 ( 6) link_BETA1-4 : bond 0.00445 / 0.22 ( 4) link_BETA1-4 : angle 1.99643 / 1.56 ( 12) link_BETA1-6 : bond 0.00240 / 0.12 ( 2) link_BETA1-6 : angle 1.49717 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7875 (pp30) cc_final: 0.7331 (pp30) REVERT: L 134 ASP cc_start: 0.7663 (t0) cc_final: 0.7301 (t70) REVERT: L 349 ARG cc_start: 0.7654 (ttp80) cc_final: 0.7319 (ttp80) REVERT: L 540 ASN cc_start: 0.7624 (m110) cc_final: 0.7138 (m110) REVERT: L 561 PHE cc_start: 0.7483 (m-80) cc_final: 0.7167 (m-80) REVERT: M 85 MET cc_start: 0.7647 (tpt) cc_final: 0.7350 (tpt) REVERT: N 175 MET cc_start: 0.7653 (pmm) cc_final: 0.7225 (pmm) REVERT: N 271 TRP cc_start: 0.8324 (OUTLIER) cc_final: 0.8122 (m-10) REVERT: N 353 MET cc_start: 0.5569 (OUTLIER) cc_final: 0.5255 (mpp) REVERT: B 27 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7510 (tm-30) REVERT: B 92 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8181 (ttp80) outliers start: 62 outliers final: 51 residues processed: 274 average time/residue: 0.1767 time to fit residues: 70.9459 Evaluate side-chains 279 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 225 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 319 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 373 LEU Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 125 CYS Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 353 MET Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 59 optimal weight: 0.0270 chunk 34 optimal weight: 7.9990 chunk 68 optimal weight: 0.0470 chunk 57 optimal weight: 0.0470 chunk 180 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 202 optimal weight: 20.0000 chunk 151 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 183 optimal weight: 50.0000 overall best weight: 0.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.110410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.085756 restraints weight = 50000.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088092 restraints weight = 26796.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.089038 restraints weight = 15788.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.088985 restraints weight = 14080.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089097 restraints weight = 13677.920| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.142 22376 Z= 0.127 Angle : 0.587 10.457 31583 Z= 0.322 Chirality : 0.039 0.226 3535 Planarity : 0.004 0.034 3036 Dihedral : 25.434 155.783 5623 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 3.01 % Allowed : 30.44 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1865 helix: 2.35 (0.18), residues: 900 sheet: -1.73 (1.23), residues: 20 loop : -1.62 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 349 TYR 0.026 0.001 TYR B 88 PHE 0.013 0.001 PHE K 71 TRP 0.017 0.001 TRP N 271 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.13 (22351) covalent geometry : angle 0.58509 / 0.32 (31533) SS BOND : bond 0.00219 / 0.15 ( 10) SS BOND : angle 0.72142 / 0.43 ( 20) hydrogen bonds : bond 0.04981 / 3.20 ( 974) hydrogen bonds : angle 3.02433 / 2.20 ( 2509) Misc. bond : bond 0.07306 / 5.08 ( 5) link_ALPHA1-3 : bond 0.00996 / 0.51 ( 2) link_ALPHA1-3 : angle 2.22535 / 1.12 ( 6) link_ALPHA1-6 : bond 0.01030 / 0.53 ( 2) link_ALPHA1-6 : angle 1.44890 / 0.80 ( 6) link_BETA1-4 : bond 0.00365 / 0.18 ( 4) link_BETA1-4 : angle 1.82997 / 1.37 ( 12) link_BETA1-6 : bond 0.00363 / 0.18 ( 2) link_BETA1-6 : angle 1.26225 / 0.67 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: L 122 GLN cc_start: 0.7854 (pp30) cc_final: 0.7346 (pp30) REVERT: L 134 ASP cc_start: 0.7682 (t0) cc_final: 0.7341 (t70) REVERT: L 349 ARG cc_start: 0.7564 (ttp80) cc_final: 0.7251 (ttp80) REVERT: L 540 ASN cc_start: 0.7457 (m110) cc_final: 0.6963 (m110) REVERT: L 561 PHE cc_start: 0.7118 (m-80) cc_final: 0.6709 (m-80) REVERT: N 175 MET cc_start: 0.7595 (pmm) cc_final: 0.7169 (pmm) REVERT: N 271 TRP cc_start: 0.8251 (OUTLIER) cc_final: 0.7957 (m-10) REVERT: N 353 MET cc_start: 0.5554 (mpp) cc_final: 0.5164 (mmp) REVERT: B 27 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7861 (tm-30) REVERT: B 92 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8157 (ttp80) outliers start: 49 outliers final: 42 residues processed: 265 average time/residue: 0.1764 time to fit residues: 68.2271 Evaluate side-chains 265 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 291 ILE Chi-restraints excluded: chain L residue 319 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 373 LEU Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 485 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 125 CYS Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 271 TRP Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 304 THR Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 488 LYS Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 9 optimal weight: 4.9990 chunk 173 optimal weight: 0.0570 chunk 114 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 151 optimal weight: 0.0000 chunk 209 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.6108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 133 ASN B 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.102821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.079148 restraints weight = 47606.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.081005 restraints weight = 26831.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082214 restraints weight = 18674.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.082974 restraints weight = 15043.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.083334 restraints weight = 13237.502| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 22376 Z= 0.194 Angle : 0.656 13.652 31583 Z= 0.351 Chirality : 0.043 0.225 3535 Planarity : 0.004 0.033 3036 Dihedral : 25.504 156.718 5623 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.90 % Favored : 94.05 % Rotamer: Outliers : 3.51 % Allowed : 29.89 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.20), residues: 1865 helix: 2.17 (0.18), residues: 895 sheet: -1.56 (1.23), residues: 20 loop : -1.71 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 76 TYR 0.021 0.002 TYR B 88 PHE 0.017 0.002 PHE K 86 TRP 0.017 0.002 TRP N 271 HIS 0.003 0.001 HIS N 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (22351) covalent geometry : angle 0.65375 / 0.35 (31533) SS BOND : bond 0.00300 / 0.19 ( 10) SS BOND : angle 0.93190 / 0.61 ( 20) hydrogen bonds : bond 0.07006 / 4.56 ( 974) hydrogen bonds : angle 3.23262 / 2.34 ( 2509) Misc. bond : bond 0.08389 / 5.44 ( 5) link_ALPHA1-3 : bond 0.01059 / 0.55 ( 2) link_ALPHA1-3 : angle 2.53713 / 1.26 ( 6) link_ALPHA1-6 : bond 0.01105 / 0.58 ( 2) link_ALPHA1-6 : angle 1.24665 / 0.70 ( 6) link_BETA1-4 : bond 0.00515 / 0.25 ( 4) link_BETA1-4 : angle 2.12513 / 1.71 ( 12) link_BETA1-6 : bond 0.00254 / 0.12 ( 2) link_BETA1-6 : angle 1.53045 / 0.79 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3503.34 seconds wall clock time: 61 minutes 1.01 seconds (3661.01 seconds total)