Starting phenix.real_space_refine on Thu Feb 15 16:09:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiu_12933/02_2024/7oiu_12933.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiu_12933/02_2024/7oiu_12933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiu_12933/02_2024/7oiu_12933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiu_12933/02_2024/7oiu_12933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiu_12933/02_2024/7oiu_12933.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiu_12933/02_2024/7oiu_12933.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.653 sd= 4.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 8174 2.51 5 N 2197 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 648": "NH1" <-> "NH2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ASP 104": "OD1" <-> "OD2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ASP 297": "OD1" <-> "OD2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 362": "OD1" <-> "OD2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 677": "NH1" <-> "NH2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ASP 789": "OD1" <-> "OD2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 36": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12744 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 776 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 94} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 5701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5701 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 35, 'TRANS': 716} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 14, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 5318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5318 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 31, 'TRANS': 653} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 8, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 127 Chain: "D" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 346 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 49} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 355 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 248 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 40} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 7.01, per 1000 atoms: 0.55 Number of scatterers: 12744 At special positions: 0 Unit cell: (137.643, 92.829, 161.117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 2330 8.00 N 2197 7.00 C 8174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 2.4 seconds 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 13 sheets defined 50.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'C' and resid 27 through 45 removed outlier: 3.518A pdb=" N THR C 44 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 67 removed outlier: 3.561A pdb=" N LEU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.995A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.997A pdb=" N GLN A 18 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 20 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 72 removed outlier: 3.631A pdb=" N PHE A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.550A pdb=" N PHE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 171 Processing helix chain 'A' and resid 191 through 202 removed outlier: 3.607A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 280 through 297 Processing helix chain 'A' and resid 303 through 319 removed outlier: 4.105A pdb=" N GLU A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 354 removed outlier: 3.795A pdb=" N VAL A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 484 through 491 removed outlier: 3.526A pdb=" N MET A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 528 removed outlier: 4.060A pdb=" N LYS A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.964A pdb=" N MET A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 590 removed outlier: 3.816A pdb=" N ARG A 586 " --> pdb=" O THR A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 645 Proline residue: A 631 - end of helix removed outlier: 4.181A pdb=" N SER A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 664 through 679 removed outlier: 4.617A pdb=" N ASN A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS A 674 " --> pdb=" O LYS A 670 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 694 removed outlier: 3.925A pdb=" N LEU A 694 " --> pdb=" O PRO A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.670A pdb=" N LYS A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 729 through 739 Processing helix chain 'A' and resid 777 through 785 removed outlier: 4.403A pdb=" N LEU A 782 " --> pdb=" O ASP A 778 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 785 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 802 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 808 through 820 removed outlier: 4.012A pdb=" N PHE A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 71 removed outlier: 3.843A pdb=" N VAL B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 148 through 171 Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.760A pdb=" N PHE B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 removed outlier: 4.303A pdb=" N TYR B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 removed outlier: 3.772A pdb=" N GLU B 265 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 297 Processing helix chain 'B' and resid 302 through 319 removed outlier: 4.049A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 354 removed outlier: 3.614A pdb=" N VAL B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 456 through 469 Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'B' and resid 483 through 491 removed outlier: 4.200A pdb=" N SER B 487 " --> pdb=" O GLY B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 530 Processing helix chain 'B' and resid 628 through 645 removed outlier: 4.127A pdb=" N VAL B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 638 " --> pdb=" O MET B 634 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 639 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 644 " --> pdb=" O THR B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 removed outlier: 3.652A pdb=" N GLN B 661 " --> pdb=" O TRP B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 removed outlier: 4.971A pdb=" N LYS B 674 " --> pdb=" O LYS B 670 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 694 Processing helix chain 'B' and resid 699 through 705 Processing helix chain 'B' and resid 718 through 727 removed outlier: 3.514A pdb=" N PHE B 726 " --> pdb=" O TYR B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 740 Processing helix chain 'B' and resid 776 through 785 Processing helix chain 'B' and resid 787 through 802 removed outlier: 4.020A pdb=" N GLY B 802 " --> pdb=" O ILE B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 821 removed outlier: 3.877A pdb=" N ASP B 814 " --> pdb=" O PRO B 810 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 816 " --> pdb=" O PHE B 812 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 817 " --> pdb=" O LEU B 813 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU B 819 " --> pdb=" O ARG B 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 26 Processing helix chain 'D' and resid 27 through 62 removed outlier: 3.838A pdb=" N SER D 62 " --> pdb=" O ILE D 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 61 Processing helix chain 'F' and resid 23 through 62 removed outlier: 4.178A pdb=" N ARG F 36 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER F 62 " --> pdb=" O ILE F 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.683A pdb=" N ILE A 248 " --> pdb=" O CYS A 328 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS A 328 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N GLU A 250 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N HIS A 326 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 178 removed outlier: 3.842A pdb=" N TYR A 38 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 121 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 272 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 275 " --> pdb=" O HIS A 327 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS A 327 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N HIS A 326 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N GLU A 250 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS A 328 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 248 " --> pdb=" O CYS A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 184 removed outlier: 3.656A pdb=" N HIS A 187 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 425 through 427 removed outlier: 3.511A pdb=" N THR A 415 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 494 removed outlier: 6.556A pdb=" N ILE A 475 " --> pdb=" O TYR A 615 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR A 474 " --> pdb=" O MET A 650 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A 652 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL A 476 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL A 684 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TYR A 651 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA A 686 " --> pdb=" O TYR A 651 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N THR A 447 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR A 687 " --> pdb=" O THR A 447 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 449 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N MET A 448 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU A 712 " --> pdb=" O MET A 448 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A 450 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 709 " --> pdb=" O LYS A 749 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 26 removed outlier: 3.674A pdb=" N HIS B 24 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.876A pdb=" N LEU B 121 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU B 76 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 278 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 270 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 275 " --> pdb=" O HIS B 327 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 327 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 328 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY B 244 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.694A pdb=" N GLY B 244 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 328 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 181 through 182 Processing sheet with id=AB2, first strand: chain 'B' and resid 415 through 418 removed outlier: 3.520A pdb=" N THR B 415 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 447 through 450 removed outlier: 6.098A pdb=" N MET B 448 " --> pdb=" O ILE B 710 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU B 712 " --> pdb=" O MET B 448 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 450 " --> pdb=" O LEU B 712 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 614 through 618 removed outlier: 5.799A pdb=" N ILE B 475 " --> pdb=" O TYR B 615 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N PHE B 617 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ALA B 477 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL B 476 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE B 649 " --> pdb=" O ILE B 682 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL B 684 " --> pdb=" O PHE B 649 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR B 651 " --> pdb=" O VAL B 684 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 666 hydrogen bonds defined for protein. 1932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4177 1.34 - 1.46: 2629 1.46 - 1.58: 6161 1.58 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 13042 Sorted by residual: bond pdb=" CA ILE B 20 " pdb=" CB ILE B 20 " ideal model delta sigma weight residual 1.536 1.515 0.021 1.19e-02 7.06e+03 3.18e+00 bond pdb=" CA SER A 77 " pdb=" CB SER A 77 " ideal model delta sigma weight residual 1.533 1.509 0.023 1.65e-02 3.67e+03 2.01e+00 bond pdb=" N ILE A 82 " pdb=" CA ILE A 82 " ideal model delta sigma weight residual 1.474 1.454 0.020 1.57e-02 4.06e+03 1.61e+00 bond pdb=" N VAL B 684 " pdb=" CA VAL B 684 " ideal model delta sigma weight residual 1.474 1.455 0.020 1.57e-02 4.06e+03 1.55e+00 bond pdb=" N GLU B 502 " pdb=" CA GLU B 502 " ideal model delta sigma weight residual 1.462 1.451 0.011 9.30e-03 1.16e+04 1.44e+00 ... (remaining 13037 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.95: 286 105.95 - 113.01: 6939 113.01 - 120.07: 4539 120.07 - 127.13: 5792 127.13 - 134.19: 166 Bond angle restraints: 17722 Sorted by residual: angle pdb=" CA GLU B 780 " pdb=" CB GLU B 780 " pdb=" CG GLU B 780 " ideal model delta sigma weight residual 114.10 122.02 -7.92 2.00e+00 2.50e-01 1.57e+01 angle pdb=" C LEU C 13 " pdb=" N PHE C 14 " pdb=" CA PHE C 14 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C THR B 27 " pdb=" CA THR B 27 " pdb=" CB THR B 27 " ideal model delta sigma weight residual 111.23 106.01 5.22 1.63e+00 3.76e-01 1.03e+01 angle pdb=" C LEU A 609 " pdb=" N SER A 610 " pdb=" CA SER A 610 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.33e+00 angle pdb=" C TYR B 495 " pdb=" N LEU B 496 " pdb=" CA LEU B 496 " ideal model delta sigma weight residual 123.46 119.54 3.92 1.35e+00 5.49e-01 8.41e+00 ... (remaining 17717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 6984 16.78 - 33.57: 573 33.57 - 50.35: 96 50.35 - 67.14: 12 67.14 - 83.92: 8 Dihedral angle restraints: 7673 sinusoidal: 2798 harmonic: 4875 Sorted by residual: dihedral pdb=" CA PHE B 95 " pdb=" C PHE B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta harmonic sigma weight residual -180.00 -153.05 -26.95 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLU A 627 " pdb=" C GLU A 627 " pdb=" N ALA A 628 " pdb=" CA ALA A 628 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA HIS A 24 " pdb=" C HIS A 24 " pdb=" N HIS A 25 " pdb=" CA HIS A 25 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 7670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1758 0.065 - 0.130: 202 0.130 - 0.196: 7 0.196 - 0.261: 0 0.261 - 0.326: 1 Chirality restraints: 1968 Sorted by residual: chirality pdb=" CB ILE A 416 " pdb=" CA ILE A 416 " pdb=" CG1 ILE A 416 " pdb=" CG2 ILE A 416 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA GLU B 780 " pdb=" N GLU B 780 " pdb=" C GLU B 780 " pdb=" CB GLU B 780 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA PRO B 21 " pdb=" N PRO B 21 " pdb=" C PRO B 21 " pdb=" CB PRO B 21 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 1965 not shown) Planarity restraints: 2296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 804 " -0.052 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO A 805 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 805 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 805 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 40 " -0.016 2.00e-02 2.50e+03 1.16e-02 3.37e+00 pdb=" CG TRP E 40 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP E 40 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP E 40 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 40 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 40 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 40 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 40 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 809 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A 810 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 810 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 810 " -0.025 5.00e-02 4.00e+02 ... (remaining 2293 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 114 2.63 - 3.20: 12191 3.20 - 3.76: 19376 3.76 - 4.33: 25941 4.33 - 4.90: 42709 Nonbonded interactions: 100331 Sorted by model distance: nonbonded pdb=" OH TYR A 38 " pdb=" OE1 GLN A 153 " model vdw 2.059 2.440 nonbonded pdb=" OG1 THR B 787 " pdb=" OD1 ASP B 789 " model vdw 2.179 2.440 nonbonded pdb=" OG1 THR C 80 " pdb=" OE2 GLU A 366 " model vdw 2.199 2.440 nonbonded pdb=" O ASP A 342 " pdb=" ND1 HIS A 346 " model vdw 2.212 2.520 nonbonded pdb=" OH TYR B 495 " pdb=" OD1 ASP B 618 " model vdw 2.216 2.440 ... (remaining 100326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 130 or (resid 147 through 150 and (name N or na \ me CA or name C or name O or name CB )) or resid 151 through 176 or (resid 177 a \ nd (name N or name CA or name C or name O or name CB )) or resid 178 through 237 \ or resid 241 through 431 or (resid 432 through 433 and (name N or name CA or na \ me C or name O or name CB )) or resid 441 through 498 or (resid 499 and (name N \ or name CA or name C or name O or name CB )) or resid 500 through 503 or resid 5 \ 15 through 531 or resid 607 through 622 or (resid 623 through 629 and (name N or \ name CA or name C or name O or name CB )) or resid 630 through 633 or (resid 63 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 635 through \ 638 or (resid 639 and (name N or name CA or name C or name O or name CB )) or re \ sid 640 or (resid 641 through 645 and (name N or name CA or name C or name O or \ name CB )) or (resid 646 through 648 and (name N or name CA or name C or name O \ or name CB )) or resid 649 through 662 or (resid 663 and (name N or name CA or n \ ame C or name O or name CB )) or resid 664 through 726 or (resid 727 and (name N \ or name CA or name C or name O or name CB )) or resid 728 or (resid 729 through \ 730 and (name N or name CA or name C or name O or name CB )) or resid 731 throu \ gh 740 or (resid 741 and (name N or name CA or name C or name O or name CB )) or \ resid 742 through 764 or (resid 765 through 776 and (name N or name CA or name \ C or name O or name CB )) or resid 777 through 821)) selection = (chain 'B' and (resid 15 through 53 or (resid 54 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 254 or (resid 255 throu \ gh 256 and (name N or name CA or name C or name O or name CB )) or resid 257 thr \ ough 296 or (resid 297 through 304 and (name N or name CA or name C or name O or \ name CB )) or resid 305 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 through 493 or (resid 494 and (name N o \ r name CA or name C or name O or name CB )) or resid 495 through 606 or (resid 6 \ 07 through 608 and (name N or name CA or name C or name O or name CB )) or resid \ 609 through 657 or (resid 658 and (name N or name CA or name C or name O or nam \ e CB )) or resid 659 through 660 or (resid 661 through 663 and (name N or name C \ A or name C or name O or name CB )) or resid 664 through 690 or (resid 691 throu \ gh 697 and (name N or name CA or name C or name O or name CB )) or resid 698 thr \ ough 699 or (resid 700 and (name N or name CA or name C or name O or name CB )) \ or resid 701 through 703 or (resid 704 through 705 and (name N or name CA or nam \ e C or name O or name CB )) or resid 706 through 720 or (resid 721 and (name N o \ r name CA or name C or name O or name CB )) or resid 722 through 731 or (resid 7 \ 32 and (name N or name CA or name C or name O or name CB )) or resid 733 through \ 762 or (resid 763 and (name N or name CA or name C or name O or name CB )) or r \ esid 764 through 799 or (resid 800 and (name N or name CA or name C or name O or \ name CB )) or resid 801 through 818 or (resid 819 through 821 and (name N or na \ me CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'D' and (resid 13 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 36 or (resid 37 and (name N or nam \ e CA or name C or name O or name CB )) or resid 38 through 41 or (resid 42 throu \ gh 43 and (name N or name CA or name C or name O or name CB )) or resid 44 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 62)) selection = (chain 'E' and ((resid 13 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 54 or (resid 55 through 56 and (n \ ame N or name CA or name C or name O or name CB )) or resid 57 through 62)) } 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: 0.070 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.350 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.010 Find NCS groups from input model: 0.710 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: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.004 0.040 13042 Z= 0.286 Angle : 0.680 7.924 17722 Z= 0.397 Chirality : 0.042 0.326 1968 Planarity : 0.004 0.078 2296 Dihedral : 12.595 83.919 4521 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1647 helix: 1.02 (0.19), residues: 735 sheet: -0.24 (0.33), residues: 268 loop : -1.39 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 40 HIS 0.006 0.001 HIS A 187 PHE 0.023 0.002 PHE D 61 TYR 0.018 0.002 TYR A 22 ARG 0.005 0.001 ARG F 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: D 51 LEU cc_start: 0.8660 (mt) cc_final: 0.8427 (mt) REVERT: E 26 ARG cc_start: 0.7313 (mmm160) cc_final: 0.7012 (mmm160) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2377 time to fit residues: 51.7262 Evaluate side-chains 117 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 50.0000 chunk 126 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 40.0000 chunk 50 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 151 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 97 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13042 Z= 0.244 Angle : 0.599 8.597 17722 Z= 0.319 Chirality : 0.042 0.244 1968 Planarity : 0.005 0.077 2296 Dihedral : 4.882 21.098 1806 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.23 % Allowed : 6.21 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1647 helix: 1.22 (0.19), residues: 744 sheet: -0.25 (0.33), residues: 264 loop : -1.40 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 40 HIS 0.006 0.001 HIS A 187 PHE 0.018 0.002 PHE B 478 TYR 0.017 0.002 TYR B 251 ARG 0.005 0.000 ARG F 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.551 Fit side-chains revert: symmetry clash REVERT: C 28 MET cc_start: 0.8067 (ptp) cc_final: 0.7806 (ptm) REVERT: A 311 GLU cc_start: 0.7590 (tp30) cc_final: 0.7366 (tp30) REVERT: D 51 LEU cc_start: 0.8667 (mt) cc_final: 0.8430 (mt) outliers start: 15 outliers final: 12 residues processed: 140 average time/residue: 0.2245 time to fit residues: 49.1170 Evaluate side-chains 128 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 126 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 151 optimal weight: 0.1980 chunk 164 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 51 optimal weight: 0.0170 chunk 121 optimal weight: 6.9990 overall best weight: 2.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 97 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13042 Z= 0.157 Angle : 0.541 9.355 17722 Z= 0.282 Chirality : 0.039 0.167 1968 Planarity : 0.004 0.078 2296 Dihedral : 4.536 17.842 1806 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.23 % Allowed : 9.64 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1647 helix: 1.53 (0.19), residues: 755 sheet: -0.24 (0.33), residues: 263 loop : -1.36 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 40 HIS 0.004 0.001 HIS A 187 PHE 0.017 0.001 PHE A 665 TYR 0.016 0.001 TYR B 251 ARG 0.003 0.000 ARG F 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7631 (tp30) cc_final: 0.7380 (tp30) REVERT: A 633 MET cc_start: 0.6598 (mpp) cc_final: 0.6349 (mpp) REVERT: B 218 MET cc_start: 0.8391 (ppp) cc_final: 0.8135 (ppp) REVERT: B 759 MET cc_start: 0.7676 (ptm) cc_final: 0.7218 (ppp) REVERT: D 51 LEU cc_start: 0.8708 (mt) cc_final: 0.8467 (mt) outliers start: 15 outliers final: 13 residues processed: 135 average time/residue: 0.2104 time to fit residues: 44.7794 Evaluate side-chains 133 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 144 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN B 24 HIS B 97 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13042 Z= 0.248 Angle : 0.558 8.881 17722 Z= 0.294 Chirality : 0.040 0.155 1968 Planarity : 0.005 0.075 2296 Dihedral : 4.598 18.360 1806 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.37 % Allowed : 11.85 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1647 helix: 1.50 (0.19), residues: 755 sheet: -0.38 (0.33), residues: 263 loop : -1.41 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 40 HIS 0.006 0.001 HIS A 187 PHE 0.025 0.002 PHE A 214 TYR 0.017 0.002 TYR B 251 ARG 0.003 0.000 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7732 (tp30) cc_final: 0.7466 (tp30) REVERT: B 218 MET cc_start: 0.8409 (ppp) cc_final: 0.8165 (ppp) REVERT: B 635 TYR cc_start: 0.5085 (m-80) cc_final: 0.4313 (m-10) REVERT: D 49 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.7061 (t80) REVERT: D 51 LEU cc_start: 0.8765 (mt) cc_final: 0.8559 (mt) outliers start: 29 outliers final: 23 residues processed: 138 average time/residue: 0.1950 time to fit residues: 43.2821 Evaluate side-chains 136 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 chunk 137 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 82 optimal weight: 6.9990 chunk 144 optimal weight: 30.0000 chunk 40 optimal weight: 7.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13042 Z= 0.199 Angle : 0.536 9.869 17722 Z= 0.281 Chirality : 0.039 0.157 1968 Planarity : 0.004 0.077 2296 Dihedral : 4.507 18.065 1806 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.37 % Allowed : 13.89 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1647 helix: 1.57 (0.19), residues: 756 sheet: -0.29 (0.34), residues: 253 loop : -1.42 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 40 HIS 0.005 0.001 HIS A 187 PHE 0.016 0.001 PHE A 214 TYR 0.020 0.001 TYR B 251 ARG 0.002 0.000 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.353 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.8581 (mtp) cc_final: 0.8013 (ttt) REVERT: A 311 GLU cc_start: 0.7718 (tp30) cc_final: 0.7500 (tp30) REVERT: B 218 MET cc_start: 0.8387 (ppp) cc_final: 0.8105 (ppp) REVERT: B 635 TYR cc_start: 0.5102 (m-80) cc_final: 0.4313 (m-10) REVERT: D 49 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7187 (t80) REVERT: D 51 LEU cc_start: 0.8724 (mt) cc_final: 0.8524 (mt) outliers start: 29 outliers final: 25 residues processed: 136 average time/residue: 0.2025 time to fit residues: 44.0001 Evaluate side-chains 140 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 161 optimal weight: 30.0000 chunk 134 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13042 Z= 0.234 Angle : 0.552 9.533 17722 Z= 0.290 Chirality : 0.040 0.163 1968 Planarity : 0.005 0.076 2296 Dihedral : 4.532 18.570 1806 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.94 % Allowed : 14.54 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1647 helix: 1.52 (0.19), residues: 757 sheet: -0.42 (0.33), residues: 255 loop : -1.46 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 40 HIS 0.005 0.001 HIS A 187 PHE 0.021 0.002 PHE A 665 TYR 0.020 0.002 TYR B 251 ARG 0.004 0.000 ARG F 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 118 time to evaluate : 1.628 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.8607 (mtp) cc_final: 0.8071 (ttt) REVERT: B 218 MET cc_start: 0.8400 (ppp) cc_final: 0.8119 (ppp) REVERT: B 635 TYR cc_start: 0.5177 (m-80) cc_final: 0.4446 (m-10) REVERT: D 49 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7244 (t80) REVERT: E 49 PHE cc_start: 0.7061 (OUTLIER) cc_final: 0.6532 (m-80) outliers start: 36 outliers final: 29 residues processed: 142 average time/residue: 0.2040 time to fit residues: 46.3804 Evaluate side-chains 144 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13042 Z= 0.268 Angle : 0.582 9.755 17722 Z= 0.304 Chirality : 0.041 0.176 1968 Planarity : 0.005 0.076 2296 Dihedral : 4.619 19.568 1806 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.27 % Allowed : 15.44 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1647 helix: 1.47 (0.19), residues: 757 sheet: -0.53 (0.33), residues: 255 loop : -1.52 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 40 HIS 0.006 0.001 HIS A 187 PHE 0.052 0.002 PHE A 665 TYR 0.020 0.002 TYR B 251 ARG 0.003 0.000 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 115 time to evaluate : 1.650 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.8662 (mtp) cc_final: 0.8100 (ttt) REVERT: B 218 MET cc_start: 0.8412 (ppp) cc_final: 0.8077 (ppp) REVERT: B 635 TYR cc_start: 0.5212 (m-80) cc_final: 0.4380 (m-10) REVERT: D 49 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7264 (t80) REVERT: E 49 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6573 (m-80) outliers start: 40 outliers final: 34 residues processed: 143 average time/residue: 0.2127 time to fit residues: 48.8782 Evaluate side-chains 148 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 146 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 13042 Z= 0.200 Angle : 0.548 9.869 17722 Z= 0.286 Chirality : 0.040 0.159 1968 Planarity : 0.004 0.077 2296 Dihedral : 4.484 18.810 1806 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.94 % Allowed : 15.85 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1647 helix: 1.56 (0.19), residues: 754 sheet: -0.54 (0.33), residues: 255 loop : -1.51 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 40 HIS 0.004 0.001 HIS A 187 PHE 0.026 0.001 PHE A 665 TYR 0.019 0.001 TYR B 251 ARG 0.002 0.000 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 117 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.8624 (mtp) cc_final: 0.8110 (ttt) REVERT: A 416 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8581 (tt) REVERT: B 218 MET cc_start: 0.8393 (ppp) cc_final: 0.8059 (ppp) REVERT: B 635 TYR cc_start: 0.5276 (m-80) cc_final: 0.4446 (m-10) REVERT: D 49 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7254 (t80) REVERT: E 26 ARG cc_start: 0.7283 (mmm160) cc_final: 0.6993 (mmm160) REVERT: E 49 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.6593 (m-80) outliers start: 36 outliers final: 32 residues processed: 143 average time/residue: 0.1958 time to fit residues: 45.1721 Evaluate side-chains 149 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 114 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 30.0000 chunk 140 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13042 Z= 0.217 Angle : 0.558 9.902 17722 Z= 0.291 Chirality : 0.040 0.159 1968 Planarity : 0.005 0.077 2296 Dihedral : 4.480 18.766 1806 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.43 % Allowed : 15.85 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1647 helix: 1.57 (0.19), residues: 754 sheet: -0.56 (0.34), residues: 253 loop : -1.55 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 40 HIS 0.005 0.001 HIS A 187 PHE 0.031 0.002 PHE A 665 TYR 0.019 0.001 TYR B 251 ARG 0.003 0.000 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 1.639 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.8637 (mtp) cc_final: 0.8103 (ttt) REVERT: A 377 TRP cc_start: 0.8254 (m100) cc_final: 0.7942 (m100) REVERT: A 416 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8573 (tt) REVERT: B 218 MET cc_start: 0.8375 (ppp) cc_final: 0.8067 (ppp) REVERT: B 635 TYR cc_start: 0.5291 (m-80) cc_final: 0.4451 (m-10) REVERT: D 49 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7298 (t80) REVERT: E 26 ARG cc_start: 0.7308 (mmm160) cc_final: 0.7010 (mmm160) REVERT: E 32 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7636 (t80) REVERT: E 49 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6687 (m-80) outliers start: 42 outliers final: 35 residues processed: 148 average time/residue: 0.2079 time to fit residues: 48.6314 Evaluate side-chains 153 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 114 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN A 613 GLN B 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13042 Z= 0.267 Angle : 0.588 9.757 17722 Z= 0.309 Chirality : 0.041 0.165 1968 Planarity : 0.005 0.075 2296 Dihedral : 4.612 19.853 1806 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.19 % Allowed : 15.93 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1647 helix: 1.49 (0.19), residues: 752 sheet: -0.54 (0.34), residues: 251 loop : -1.62 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 48 HIS 0.006 0.001 HIS A 187 PHE 0.027 0.002 PHE A 665 TYR 0.019 0.002 TYR B 251 ARG 0.003 0.000 ARG E 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 117 time to evaluate : 1.552 Fit side-chains REVERT: A 245 MET cc_start: 0.8677 (mtp) cc_final: 0.8113 (ttt) REVERT: A 416 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8664 (tt) REVERT: B 218 MET cc_start: 0.8372 (ppp) cc_final: 0.8057 (ppp) REVERT: B 635 TYR cc_start: 0.5380 (m-80) cc_final: 0.4502 (m-10) REVERT: D 49 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7312 (t80) REVERT: E 26 ARG cc_start: 0.7324 (mmm160) cc_final: 0.7039 (mmm160) REVERT: E 32 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7754 (t80) REVERT: E 49 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6719 (m-80) outliers start: 39 outliers final: 33 residues processed: 145 average time/residue: 0.1961 time to fit residues: 45.1940 Evaluate side-chains 154 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 117 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 49 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 132 optimal weight: 0.0470 chunk 55 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.096227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.086104 restraints weight = 42197.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.088046 restraints weight = 21157.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.089333 restraints weight = 12942.153| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13042 Z= 0.190 Angle : 0.562 10.198 17722 Z= 0.292 Chirality : 0.040 0.163 1968 Planarity : 0.004 0.077 2296 Dihedral : 4.468 18.597 1806 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.19 % Allowed : 16.42 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1647 helix: 1.62 (0.19), residues: 748 sheet: -0.51 (0.34), residues: 252 loop : -1.53 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 377 HIS 0.004 0.001 HIS A 187 PHE 0.029 0.001 PHE A 665 TYR 0.018 0.001 TYR B 251 ARG 0.011 0.000 ARG A 380 =============================================================================== Job complete usr+sys time: 2080.44 seconds wall clock time: 39 minutes 16.51 seconds (2356.51 seconds total)