Starting phenix.real_space_refine on Sun Jul 21 10:15:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtb_19485/07_2024/8rtb_19485.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtb_19485/07_2024/8rtb_19485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtb_19485/07_2024/8rtb_19485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtb_19485/07_2024/8rtb_19485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtb_19485/07_2024/8rtb_19485.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtb_19485/07_2024/8rtb_19485.cif" } resolution = 3.83 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.029 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 57 5.16 5 C 9069 2.51 5 N 2413 2.21 5 O 2593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 9": "OE1" <-> "OE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ASP 68": "OD1" <-> "OD2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A ASP 297": "OD1" <-> "OD2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A ASP 645": "OD1" <-> "OD2" Residue "A ARG 648": "NH1" <-> "NH2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 758": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ARG 101": "NH1" <-> "NH2" 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 ARG 222": "NH1" <-> "NH2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ASP 297": "OD1" <-> "OD2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 479": "OD1" <-> "OD2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B ASP 618": "OD1" <-> "OD2" Residue "B ARG 677": "NH1" <-> "NH2" Residue "B GLU 741": "OE1" <-> "OE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "G PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 25": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H ARG 38": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14132 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 835 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 94} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 5992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5992 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 36, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5284 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 630} Chain breaks: 5 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 367 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 49} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 450 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "F" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 279 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 40} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 240 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 40} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 350 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 46} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "J" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 335 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 9.52, per 1000 atoms: 0.67 Number of scatterers: 14132 At special positions: 0 Unit cell: (134.442, 89.628, 158.983, 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 57 16.00 O 2593 8.00 N 2413 7.00 C 9069 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: 5.29 Conformation dependent library (CDL) restraints added in 2.5 seconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 19 sheets defined 52.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'C' and resid 28 through 45 Processing helix chain 'C' and resid 47 through 51 removed outlier: 4.019A pdb=" N TRP C 50 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 51 " --> pdb=" O TRP C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 51' Processing helix chain 'C' and resid 52 through 67 removed outlier: 3.950A pdb=" N LEU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.788A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 4.071A pdb=" N TRP C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.791A pdb=" N SER A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 53 through 72 removed outlier: 3.576A pdb=" N PHE A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 3.982A 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 132 through 140 removed outlier: 3.822A pdb=" N PHE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 171 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.934A pdb=" N GLY A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.834A pdb=" N GLU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.946A pdb=" N TYR A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 266 removed outlier: 4.300A pdb=" N VAL A 262 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 263 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 265 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 266 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 297 Processing helix chain 'A' and resid 305 through 318 removed outlier: 4.066A pdb=" N ILE A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 354 removed outlier: 3.550A pdb=" N VAL A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 469 through 472 Processing helix chain 'A' and resid 484 through 491 Processing helix chain 'A' and resid 507 through 511 removed outlier: 4.527A pdb=" N GLN A 510 " --> pdb=" O ASN A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.534A pdb=" N LEU A 623 " --> pdb=" O THR A 620 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP A 624 " --> pdb=" O GLU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 642 removed outlier: 3.607A pdb=" N SER A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 689 through 695 removed outlier: 3.519A pdb=" N ALA A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU A 695 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 705 removed outlier: 3.832A pdb=" N LYS A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 702 " --> pdb=" O ILE A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 removed outlier: 3.635A pdb=" N TYR A 722 " --> pdb=" O ASP A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 738 Processing helix chain 'A' and resid 777 through 785 removed outlier: 4.305A pdb=" N VAL A 783 " --> pdb=" O ASP A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 801 removed outlier: 3.782A pdb=" N SER A 796 " --> pdb=" O GLU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 820 Proline residue: A 810 - end of helix Processing helix chain 'B' and resid 53 through 71 removed outlier: 3.926A pdb=" N VAL B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 71 " --> pdb=" O THR B 67 " (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: 4.061A pdb=" N PHE B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 196 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 removed outlier: 4.353A pdb=" N TYR B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 280 through 297 Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.858A pdb=" N ASN B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 353 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 469 through 472 Processing helix chain 'B' and resid 484 through 491 Processing helix chain 'B' and resid 628 through 643 removed outlier: 3.584A pdb=" N MET B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 662 through 677 removed outlier: 4.195A pdb=" N ASP B 667 " --> pdb=" O GLU B 663 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 695 removed outlier: 3.802A pdb=" N ALA B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 705 removed outlier: 3.920A pdb=" N LYS B 700 " --> pdb=" O SER B 696 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 701 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 725 removed outlier: 3.630A pdb=" N TYR B 722 " --> pdb=" O ASP B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 739 removed outlier: 3.607A pdb=" N LEU B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 785 Processing helix chain 'B' and resid 787 through 802 Processing helix chain 'B' and resid 804 through 821 removed outlier: 4.283A pdb=" N TRP B 808 " --> pdb=" O ASP B 804 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 809 " --> pdb=" O PRO B 805 " (cutoff:3.500A) Proline residue: B 810 - end of helix Processing helix chain 'E' and resid 16 through 25 Processing helix chain 'E' and resid 27 through 62 removed outlier: 4.357A pdb=" N SER E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 60 removed outlier: 3.644A pdb=" N TYR D 17 " --> pdb=" O GLN D 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 61 Processing helix chain 'G' and resid 23 through 61 Processing helix chain 'H' and resid 43 through 69 Processing helix chain 'J' and resid 31 through 49 Processing helix chain 'J' and resid 49 through 54 Processing helix chain 'J' and resid 60 through 82 removed outlier: 4.515A pdb=" N CYS J 67 " --> pdb=" O PHE J 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.587A pdb=" N ARG A 222 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.754A pdb=" N ILE A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 127 removed outlier: 3.534A pdb=" N SER A 40 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 38 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA6, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 242 through 245 Processing sheet with id=AA8, first strand: chain 'A' and resid 248 through 250 removed outlier: 3.523A pdb=" N ARG A 249 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 357 " --> pdb=" O ARG A 249 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.555A pdb=" N HIS A 326 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 415 through 417 Processing sheet with id=AB2, first strand: chain 'A' and resid 495 through 496 removed outlier: 5.897A pdb=" N ILE A 475 " --> pdb=" O TYR A 615 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE A 617 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ALA A 477 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A 474 " --> pdb=" O MET A 650 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 652 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL A 476 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL A 684 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR A 651 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A 447 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N MET A 448 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR A 709 " --> pdb=" O LYS A 749 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 767 through 768 removed outlier: 3.648A pdb=" N VAL A 768 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 22 through 27 removed outlier: 4.660A pdb=" N HIS B 24 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 177 through 178 removed outlier: 3.693A pdb=" N TYR B 38 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 121 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR B 331 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 183 through 184 Processing sheet with id=AB7, first strand: chain 'B' and resid 277 through 278 Processing sheet with id=AB8, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.878A pdb=" N THR B 415 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 684 through 687 removed outlier: 6.002A pdb=" N THR B 447 " --> pdb=" O PHE B 685 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR B 687 " --> pdb=" O THR B 447 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU B 449 " --> pdb=" O THR B 687 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N MET B 448 " --> pdb=" O ILE B 710 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 615 through 618 removed outlier: 6.269A pdb=" N ALA B 477 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL B 476 " --> pdb=" O VAL B 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 703 hydrogen bonds defined for protein. 2004 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: 5.65 Time building geometry restraints manager: 5.79 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: 4603 1.34 - 1.46: 2939 1.46 - 1.58: 6825 1.58 - 1.70: 1 1.70 - 1.81: 99 Bond restraints: 14467 Sorted by residual: bond pdb=" CB PRO A 497 " pdb=" CG PRO A 497 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.06e+01 bond pdb=" N PRO A 497 " pdb=" CA PRO A 497 " ideal model delta sigma weight residual 1.481 1.444 0.038 1.85e-02 2.92e+03 4.12e+00 bond pdb=" CD LYS H 65 " pdb=" CE LYS H 65 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CG GLU A 154 " pdb=" CD GLU A 154 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.86e+00 bond pdb=" CG1 ILE A 82 " pdb=" CD1 ILE A 82 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.81e+00 ... (remaining 14462 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.16: 233 104.16 - 111.67: 6533 111.67 - 119.18: 5064 119.18 - 126.68: 7555 126.68 - 134.19: 226 Bond angle restraints: 19611 Sorted by residual: angle pdb=" CA PRO A 497 " pdb=" N PRO A 497 " pdb=" CD PRO A 497 " ideal model delta sigma weight residual 112.00 99.05 12.95 1.40e+00 5.10e-01 8.56e+01 angle pdb=" C GLU F 31 " pdb=" N PHE F 32 " pdb=" CA PHE F 32 " ideal model delta sigma weight residual 120.68 113.22 7.46 1.70e+00 3.46e-01 1.93e+01 angle pdb=" CA TYR H 64 " pdb=" CB TYR H 64 " pdb=" CG TYR H 64 " ideal model delta sigma weight residual 113.90 121.50 -7.60 1.80e+00 3.09e-01 1.78e+01 angle pdb=" N VAL B 220 " pdb=" CA VAL B 220 " pdb=" C VAL B 220 " ideal model delta sigma weight residual 112.12 108.70 3.42 8.40e-01 1.42e+00 1.65e+01 angle pdb=" N VAL A 26 " pdb=" CA VAL A 26 " pdb=" C VAL A 26 " ideal model delta sigma weight residual 111.81 108.37 3.44 8.60e-01 1.35e+00 1.60e+01 ... (remaining 19606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7703 17.87 - 35.75: 727 35.75 - 53.62: 106 53.62 - 71.49: 18 71.49 - 89.36: 14 Dihedral angle restraints: 8568 sinusoidal: 3357 harmonic: 5211 Sorted by residual: dihedral pdb=" CA GLN A 305 " pdb=" C GLN A 305 " pdb=" N ILE A 306 " pdb=" CA ILE A 306 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA TYR A 664 " pdb=" C TYR A 664 " pdb=" N PHE A 665 " pdb=" CA PHE A 665 " ideal model delta harmonic sigma weight residual 180.00 -157.12 -22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ASN B 314 " pdb=" C ASN B 314 " pdb=" N GLN B 315 " pdb=" CA GLN B 315 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 8565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1704 0.054 - 0.108: 381 0.108 - 0.162: 56 0.162 - 0.215: 5 0.215 - 0.269: 2 Chirality restraints: 2148 Sorted by residual: chirality pdb=" CB ILE A 82 " pdb=" CA ILE A 82 " pdb=" CG1 ILE A 82 " pdb=" CG2 ILE A 82 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 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 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TYR D 18 " pdb=" N TYR D 18 " pdb=" C TYR D 18 " pdb=" CB TYR D 18 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2145 not shown) Planarity restraints: 2531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 20 " -0.073 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO B 21 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO B 21 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 21 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 496 " -0.080 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO A 497 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 497 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 497 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 33 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO J 34 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO J 34 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO J 34 " 0.061 5.00e-02 4.00e+02 ... (remaining 2528 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 249 2.68 - 3.24: 14144 3.24 - 3.79: 21172 3.79 - 4.35: 27517 4.35 - 4.90: 46506 Nonbonded interactions: 109588 Sorted by model distance: nonbonded pdb=" NH2 ARG A 211 " pdb=" OD1 ASP B 252 " model vdw 2.126 2.520 nonbonded pdb=" NH1 ARG A 222 " pdb=" OD2 ASP B 362 " model vdw 2.132 2.520 nonbonded pdb=" O LEU A 609 " pdb=" OH TYR A 615 " model vdw 2.167 2.440 nonbonded pdb=" NZ LYS A 106 " pdb=" O ASP A 776 " model vdw 2.210 2.520 nonbonded pdb=" OG1 THR A 640 " pdb=" OH TYR A 651 " model vdw 2.213 2.440 ... (remaining 109583 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 235 or resid 240 th \ rough 431 or (resid 432 through 433 and (name N or name CA or name C or name O o \ r name CB )) or resid 442 through 498 or resid 607 through 662 or (resid 663 and \ (name N or name CA or name C or name O or name CB )) or resid 664 through 688 o \ r (resid 689 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 90 through 691 or (resid 692 through 693 and (name N or name CA or name C or nam \ e O or name CB )) or resid 694 through 764 or (resid 765 and (name N or name CA \ or name C or name O or name CB )) or (resid 776 and (name N or name CA or name C \ or name O or name CB )) or resid 777 or (resid 778 and (name N or name CA or na \ me C or name O or name CB )) or resid 779 through 816 or (resid 817 through 818 \ and (name N or name CA or name C or name O or name CB )) or resid 819 or (resid \ 820 and (name N or name CA or name C or name O or name CB )) or resid 821)) selection = (chain 'B' and (resid 15 through 254 or (resid 255 and (name N or name CA or nam \ e C or name O or name CB )) or resid 256 through 607 or (resid 608 and (name N o \ r name CA or name C or name O or name CB )) or resid 609 through 720 or (resid 7 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 722 through \ 731 or (resid 732 and (name N or name CA or name C or name O or name CB )) or r \ esid 733 through 821)) } ncs_group { reference = (chain 'D' and ((resid 13 and (name N or name CA or name C or name O or name CB \ )) or resid 14 or (resid 15 and (name N or name CA or name C or name O or name C \ B )) or resid 16 through 33 or (resid 34 and (name N or name CA or name C or nam \ e O or name CB )) or resid 35 through 40 or (resid 41 and (name N or name CA or \ name C or name O or name CB )) or resid 42 through 47 or (resid 48 and (name N o \ r name CA or name C or name O or name CB )) or resid 49 through 62)) selection = chain 'E' } ncs_group { reference = (chain 'F' and ((resid 22 through 29 and (name N or name CA or name C or name O \ or name CB )) or resid 30 or (resid 31 and (name N or name CA or name C or name \ O or name CB )) or resid 32 or (resid 33 through 39 and (name N or name CA or na \ me C or name O or name CB )) or resid 40 or (resid 41 through 45 and (name N or \ name CA or name C or name O or name CB )) or resid 46 through 55 or (resid 56 an \ d (name N or name CA or name C or name O or name CB )) or resid 57 through 61 or \ (resid 62 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 22 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 57 or (resid 58 through 59 and (na \ me N or name CA or name C or name O or name CB )) or resid 60 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: 20.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 43.870 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 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 : 0.006 0.163 14467 Z= 0.373 Angle : 0.789 12.955 19611 Z= 0.455 Chirality : 0.046 0.269 2148 Planarity : 0.007 0.113 2531 Dihedral : 14.187 89.364 5208 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.38 (0.20), residues: 1774 helix: 0.50 (0.18), residues: 824 sheet: -2.74 (0.32), residues: 265 loop : -1.83 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 50 HIS 0.008 0.001 HIS A 326 PHE 0.034 0.002 PHE A 520 TYR 0.043 0.002 TYR H 64 ARG 0.010 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.6817 (tp) cc_final: 0.6581 (tp) REVERT: A 305 GLN cc_start: 0.6633 (tp40) cc_final: 0.6410 (tp-100) REVERT: A 322 VAL cc_start: 0.7554 (t) cc_final: 0.7287 (t) REVERT: B 260 LEU cc_start: 0.7453 (pt) cc_final: 0.7142 (pp) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.2725 time to fit residues: 131.6299 Evaluate side-chains 222 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.0170 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 84 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 overall best weight: 1.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14467 Z= 0.235 Angle : 0.690 11.002 19611 Z= 0.353 Chirality : 0.042 0.220 2148 Planarity : 0.006 0.108 2531 Dihedral : 5.092 25.720 1953 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.26 % Allowed : 11.04 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.84 (0.20), residues: 1774 helix: 0.92 (0.18), residues: 856 sheet: -2.32 (0.32), residues: 250 loop : -1.74 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 50 HIS 0.004 0.001 HIS B 274 PHE 0.025 0.002 PHE B 391 TYR 0.034 0.002 TYR D 18 ARG 0.011 0.001 ARG B 745 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 250 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 LEU cc_start: 0.7481 (pt) cc_final: 0.7280 (pp) REVERT: D 17 TYR cc_start: 0.6804 (t80) cc_final: 0.6450 (t80) REVERT: D 18 TYR cc_start: 0.6004 (p90) cc_final: 0.5674 (p90) REVERT: J 40 LEU cc_start: 0.7617 (tp) cc_final: 0.7154 (tp) outliers start: 33 outliers final: 16 residues processed: 268 average time/residue: 0.2519 time to fit residues: 100.0836 Evaluate side-chains 234 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 218 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain J residue 58 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN A 704 GLN B 75 ASN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 14467 Z= 0.473 Angle : 0.783 9.329 19611 Z= 0.412 Chirality : 0.044 0.230 2148 Planarity : 0.006 0.074 2531 Dihedral : 5.156 29.841 1953 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.43 % Allowed : 15.36 % 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: -0.96 (0.20), residues: 1774 helix: 0.70 (0.18), residues: 868 sheet: -2.32 (0.31), residues: 268 loop : -1.65 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 657 HIS 0.014 0.002 HIS A 320 PHE 0.029 0.002 PHE J 44 TYR 0.043 0.002 TYR H 64 ARG 0.014 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 212 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 TYR cc_start: 0.7086 (t80) cc_final: 0.6590 (t80) outliers start: 50 outliers final: 32 residues processed: 241 average time/residue: 0.2362 time to fit residues: 84.8501 Evaluate side-chains 226 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 194 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 0.9980 chunk 121 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 84 optimal weight: 0.1980 chunk 153 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14467 Z= 0.202 Angle : 0.670 10.556 19611 Z= 0.331 Chirality : 0.043 0.369 2148 Planarity : 0.004 0.049 2531 Dihedral : 4.776 26.162 1953 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.61 % Allowed : 18.04 % Favored : 79.36 % 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: -0.49 (0.20), residues: 1774 helix: 1.13 (0.18), residues: 857 sheet: -1.98 (0.32), residues: 268 loop : -1.51 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 370 HIS 0.006 0.001 HIS B 274 PHE 0.035 0.002 PHE J 44 TYR 0.049 0.002 TYR D 18 ARG 0.015 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 221 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 MET cc_start: 0.6320 (tpt) cc_final: 0.6071 (tpt) outliers start: 38 outliers final: 21 residues processed: 244 average time/residue: 0.2627 time to fit residues: 96.9408 Evaluate side-chains 226 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14467 Z= 0.246 Angle : 0.665 10.564 19611 Z= 0.334 Chirality : 0.043 0.362 2148 Planarity : 0.004 0.055 2531 Dihedral : 4.634 26.535 1953 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.02 % Allowed : 19.96 % Favored : 77.02 % 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: -0.33 (0.20), residues: 1774 helix: 1.25 (0.18), residues: 858 sheet: -1.80 (0.31), residues: 276 loop : -1.45 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 808 HIS 0.006 0.001 HIS B 274 PHE 0.036 0.001 PHE J 44 TYR 0.032 0.002 TYR D 18 ARG 0.016 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 213 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.6315 (p0) cc_final: 0.6024 (p0) REVERT: A 448 MET cc_start: 0.6469 (tpt) cc_final: 0.6185 (tpt) outliers start: 44 outliers final: 32 residues processed: 242 average time/residue: 0.2509 time to fit residues: 90.9110 Evaluate side-chains 228 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14467 Z= 0.229 Angle : 0.661 11.511 19611 Z= 0.330 Chirality : 0.043 0.368 2148 Planarity : 0.004 0.052 2531 Dihedral : 4.538 24.867 1953 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.36 % Allowed : 20.85 % Favored : 75.79 % 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 (0.20), residues: 1774 helix: 1.34 (0.18), residues: 856 sheet: -1.63 (0.31), residues: 276 loop : -1.34 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 50 HIS 0.006 0.001 HIS B 274 PHE 0.042 0.001 PHE J 44 TYR 0.027 0.001 TYR D 18 ARG 0.005 0.000 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 206 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.6310 (p0) cc_final: 0.5993 (p0) REVERT: A 268 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.6081 (p90) REVERT: E 61 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.7008 (m-80) outliers start: 49 outliers final: 35 residues processed: 241 average time/residue: 0.2328 time to fit residues: 85.5194 Evaluate side-chains 228 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 191 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** A 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14467 Z= 0.212 Angle : 0.688 15.621 19611 Z= 0.335 Chirality : 0.044 0.371 2148 Planarity : 0.004 0.048 2531 Dihedral : 4.471 24.837 1953 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.02 % Allowed : 22.02 % Favored : 74.97 % 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 (0.20), residues: 1774 helix: 1.43 (0.18), residues: 851 sheet: -1.39 (0.32), residues: 275 loop : -1.33 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 50 HIS 0.006 0.001 HIS B 274 PHE 0.046 0.001 PHE J 44 TYR 0.032 0.001 TYR D 18 ARG 0.006 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 204 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.6298 (p0) cc_final: 0.5966 (p0) REVERT: A 220 VAL cc_start: 0.8500 (m) cc_final: 0.8209 (p) REVERT: A 268 TYR cc_start: 0.6979 (OUTLIER) cc_final: 0.6051 (p90) REVERT: E 61 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6880 (m-80) outliers start: 44 outliers final: 33 residues processed: 235 average time/residue: 0.2314 time to fit residues: 82.9529 Evaluate side-chains 229 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 194 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14467 Z= 0.263 Angle : 0.707 11.503 19611 Z= 0.350 Chirality : 0.045 0.332 2148 Planarity : 0.004 0.047 2531 Dihedral : 4.493 25.213 1953 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.95 % Allowed : 22.98 % Favored : 74.07 % 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: -0.05 (0.20), residues: 1774 helix: 1.36 (0.18), residues: 855 sheet: -1.28 (0.32), residues: 276 loop : -1.33 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 50 HIS 0.006 0.001 HIS B 274 PHE 0.047 0.001 PHE J 44 TYR 0.025 0.002 TYR H 64 ARG 0.007 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 199 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.6130 (p0) cc_final: 0.5735 (p0) REVERT: A 220 VAL cc_start: 0.8490 (m) cc_final: 0.8168 (p) REVERT: A 268 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.6002 (p90) REVERT: A 448 MET cc_start: 0.6566 (tpt) cc_final: 0.6242 (tpt) REVERT: E 61 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6984 (m-80) REVERT: D 20 GLU cc_start: 0.6101 (pp20) cc_final: 0.5728 (pp20) outliers start: 43 outliers final: 38 residues processed: 228 average time/residue: 0.2307 time to fit residues: 80.4198 Evaluate side-chains 233 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 193 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 651 TYR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14467 Z= 0.298 Angle : 0.734 14.319 19611 Z= 0.365 Chirality : 0.045 0.292 2148 Planarity : 0.005 0.068 2531 Dihedral : 4.583 24.615 1953 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.95 % Allowed : 23.11 % Favored : 73.94 % 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: 1774 helix: 1.19 (0.18), residues: 866 sheet: -1.20 (0.32), residues: 276 loop : -1.42 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 50 HIS 0.007 0.001 HIS A 320 PHE 0.046 0.002 PHE J 44 TYR 0.028 0.002 TYR H 64 ARG 0.010 0.000 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.6061 (p0) cc_final: 0.5706 (p0) REVERT: A 220 VAL cc_start: 0.8561 (m) cc_final: 0.8242 (p) REVERT: A 268 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.6115 (p90) REVERT: A 448 MET cc_start: 0.6564 (tpt) cc_final: 0.6269 (tpt) REVERT: E 61 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7041 (m-80) outliers start: 43 outliers final: 37 residues processed: 225 average time/residue: 0.2313 time to fit residues: 79.3779 Evaluate side-chains 230 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 191 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 651 TYR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 176 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 108 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14467 Z= 0.223 Angle : 0.756 15.021 19611 Z= 0.368 Chirality : 0.045 0.352 2148 Planarity : 0.005 0.066 2531 Dihedral : 4.554 25.780 1953 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.67 % Allowed : 23.66 % Favored : 73.66 % 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 (0.20), residues: 1774 helix: 1.20 (0.18), residues: 870 sheet: -1.00 (0.33), residues: 271 loop : -1.44 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 50 HIS 0.005 0.001 HIS B 274 PHE 0.047 0.001 PHE J 44 TYR 0.031 0.001 TYR D 18 ARG 0.017 0.001 ARG C 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 201 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 ASP cc_start: 0.5368 (m-30) cc_final: 0.5064 (m-30) REVERT: A 216 ASP cc_start: 0.5963 (p0) cc_final: 0.5612 (p0) REVERT: A 220 VAL cc_start: 0.8564 (m) cc_final: 0.8286 (p) REVERT: A 268 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6005 (p90) REVERT: A 448 MET cc_start: 0.6480 (tpt) cc_final: 0.6201 (tpt) REVERT: E 61 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6910 (m-80) outliers start: 39 outliers final: 32 residues processed: 228 average time/residue: 0.2291 time to fit residues: 80.0434 Evaluate side-chains 228 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.057034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.045748 restraints weight = 82674.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.047183 restraints weight = 47159.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.048186 restraints weight = 32316.941| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14467 Z= 0.302 Angle : 0.773 12.530 19611 Z= 0.386 Chirality : 0.045 0.336 2148 Planarity : 0.004 0.049 2531 Dihedral : 4.634 24.738 1953 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.61 % Allowed : 24.42 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.17 (0.20), residues: 1774 helix: 1.19 (0.18), residues: 860 sheet: -1.05 (0.33), residues: 275 loop : -1.46 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 50 HIS 0.007 0.001 HIS A 320 PHE 0.049 0.002 PHE J 44 TYR 0.041 0.002 TYR E 18 ARG 0.019 0.001 ARG C 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3194.98 seconds wall clock time: 58 minutes 20.65 seconds (3500.65 seconds total)