Starting phenix.real_space_refine on Sun Nov 19 17:45:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd6_37126/11_2023/8kd6_37126_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd6_37126/11_2023/8kd6_37126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd6_37126/11_2023/8kd6_37126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd6_37126/11_2023/8kd6_37126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd6_37126/11_2023/8kd6_37126_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd6_37126/11_2023/8kd6_37126_updated.pdb" } resolution = 3.07 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= 0.002 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 563 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 328 5.49 5 S 92 5.16 5 C 16098 2.51 5 N 4797 2.21 5 O 5666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 234": "OD1" <-> "OD2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 290": "OD1" <-> "OD2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D ASP 376": "OD1" <-> "OD2" Residue "D TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 307": "OD1" <-> "OD2" Residue "F GLU 340": "OE1" <-> "OE2" Residue "O ASP 106": "OD1" <-> "OD2" Residue "R TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 73": "OE1" <-> "OE2" Residue "R GLU 102": "OE1" <-> "OE2" Residue "S PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 105": "OE1" <-> "OE2" Residue "U GLU 41": "OE1" <-> "OE2" Residue "U TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 90": "OD1" <-> "OD2" Residue "U GLU 91": "OE1" <-> "OE2" Residue "U GLU 92": "OE1" <-> "OE2" Residue "V GLU 32": "OE1" <-> "OE2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A ASP 114": "OD1" <-> "OD2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A ASP 165": "OD1" <-> "OD2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "B PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 695": "OD1" <-> "OD2" Residue "B TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 776": "OE1" <-> "OE2" Residue "B ASP 818": "OD1" <-> "OD2" Residue "B TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 920": "OE1" <-> "OE2" Residue "B PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1160": "OE1" <-> "OE2" Residue "B ASP 1243": "OD1" <-> "OD2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 323": "OE1" <-> "OE2" Residue "G PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 550": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 26982 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1875 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Chain: "F" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1627 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain breaks: 2 Chain: "O" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "Q" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "R" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "S" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3384 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "Y" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3340 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "A" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3073 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 1 Chain: "B" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4505 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 12, 'TRANS': 524} Chain breaks: 2 Chain: "E" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2475 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 283} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 718 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.77, per 1000 atoms: 0.51 Number of scatterers: 26982 At special positions: 0 Unit cell: (138.45, 158.33, 176.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 92 16.00 P 328 15.00 O 5666 8.00 N 4797 7.00 C 16098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 303 " - pdb=" SG CYS E 306 " distance=2.03 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: 12.82 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 2 sheets defined 50.6% alpha, 1.9% beta 140 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 12.53 Creating SS restraints... Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 226 through 240 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 274 through 291 Processing helix chain 'D' and resid 300 through 314 removed outlier: 4.541A pdb=" N LEU D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 343 Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 349 through 368 Processing helix chain 'D' and resid 392 through 398 Processing helix chain 'F' and resid 99 through 111 Processing helix chain 'F' and resid 230 through 238 removed outlier: 3.606A pdb=" N GLU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 261 removed outlier: 4.114A pdb=" N TYR F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 289 removed outlier: 4.371A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 313 Processing helix chain 'F' and resid 331 through 342 Proline residue: F 339 - end of helix Processing helix chain 'F' and resid 349 through 368 removed outlier: 4.480A pdb=" N MET F 368 " --> pdb=" O VAL F 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 56 removed outlier: 3.556A pdb=" N LYS O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 77 removed outlier: 4.046A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 113 removed outlier: 3.564A pdb=" N GLU O 94 " --> pdb=" O MET O 90 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA O 95 " --> pdb=" O ALA O 91 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA O 110 " --> pdb=" O ASP O 106 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA O 111 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 131 Processing helix chain 'P' and resid 26 through 28 No H-bonds generated for 'chain 'P' and resid 26 through 28' Processing helix chain 'P' and resid 31 through 40 Processing helix chain 'P' and resid 50 through 75 removed outlier: 4.016A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 91 Processing helix chain 'Q' and resid 17 through 20 No H-bonds generated for 'chain 'Q' and resid 17 through 20' Processing helix chain 'Q' and resid 27 through 36 Processing helix chain 'Q' and resid 45 through 72 removed outlier: 4.367A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 89 Processing helix chain 'Q' and resid 91 through 96 Processing helix chain 'R' and resid 35 through 45 removed outlier: 3.554A pdb=" N TYR R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL R 45 " --> pdb=" O VAL R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 80 Processing helix chain 'R' and resid 88 through 98 removed outlier: 3.550A pdb=" N ARG R 96 " --> pdb=" O GLN R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 119 removed outlier: 3.543A pdb=" N LYS R 105 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS R 106 " --> pdb=" O LEU R 103 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL R 108 " --> pdb=" O LYS R 105 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU R 110 " --> pdb=" O ALA R 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS R 113 " --> pdb=" O GLU R 110 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR R 116 " --> pdb=" O LYS R 113 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS R 117 " --> pdb=" O ALA R 114 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR R 119 " --> pdb=" O THR R 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 55 Processing helix chain 'S' and resid 64 through 77 removed outlier: 3.776A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 86 through 113 Processing helix chain 'S' and resid 121 through 131 Processing helix chain 'T' and resid 25 through 28 Processing helix chain 'T' and resid 31 through 40 Processing helix chain 'T' and resid 50 through 75 removed outlier: 3.627A pdb=" N GLY T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 91 Processing helix chain 'U' and resid 17 through 20 No H-bonds generated for 'chain 'U' and resid 17 through 20' Processing helix chain 'U' and resid 27 through 36 Processing helix chain 'U' and resid 45 through 72 removed outlier: 4.077A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 89 Processing helix chain 'U' and resid 91 through 96 removed outlier: 3.865A pdb=" N LYS U 95 " --> pdb=" O GLU U 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 45 removed outlier: 3.520A pdb=" N VAL V 45 " --> pdb=" O VAL V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 80 Processing helix chain 'V' and resid 88 through 98 Processing helix chain 'V' and resid 101 through 118 removed outlier: 3.522A pdb=" N ALA V 104 " --> pdb=" O GLY V 101 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS V 106 " --> pdb=" O LEU V 103 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL V 108 " --> pdb=" O LYS V 105 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS V 113 " --> pdb=" O GLU V 110 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR V 116 " --> pdb=" O LYS V 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 54 removed outlier: 3.571A pdb=" N ILE A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A 53 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 54 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 116 through 136 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 244 through 261 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 288 through 299 removed outlier: 4.007A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 366 through 382 removed outlier: 4.862A pdb=" N ASN A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'B' and resid 668 through 676 Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 699 through 709 removed outlier: 3.649A pdb=" N PHE B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 724 Processing helix chain 'B' and resid 772 through 777 Processing helix chain 'B' and resid 786 through 790 Processing helix chain 'B' and resid 802 through 840 removed outlier: 4.568A pdb=" N ASN B 840 " --> pdb=" O ASN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 862 through 870 Processing helix chain 'B' and resid 873 through 885 removed outlier: 3.925A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 928 removed outlier: 4.046A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 941 removed outlier: 4.768A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 966 Processing helix chain 'B' and resid 983 through 995 Processing helix chain 'B' and resid 1004 through 1021 removed outlier: 3.701A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1163 Processing helix chain 'B' and resid 1165 through 1173 removed outlier: 4.047A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1183 Processing helix chain 'B' and resid 1203 through 1216 Processing helix chain 'B' and resid 1222 through 1231 Processing helix chain 'B' and resid 1237 through 1239 No H-bonds generated for 'chain 'B' and resid 1237 through 1239' Processing helix chain 'B' and resid 1242 through 1258 removed outlier: 3.583A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B1258 " --> pdb=" O HIS B1254 " (cutoff:3.500A) Processing helix chain 'B' and resid 1260 through 1272 Processing helix chain 'B' and resid 1283 through 1293 Processing helix chain 'B' and resid 1308 through 1310 No H-bonds generated for 'chain 'B' and resid 1308 through 1310' Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 304 through 309 Processing helix chain 'E' and resid 322 through 329 Processing helix chain 'E' and resid 334 through 344 removed outlier: 4.221A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 360 removed outlier: 3.599A pdb=" N GLU E 359 " --> pdb=" O ASN E 355 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR E 360 " --> pdb=" O TYR E 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 355 through 360' Processing helix chain 'E' and resid 431 through 433 No H-bonds generated for 'chain 'E' and resid 431 through 433' Processing helix chain 'E' and resid 544 through 557 Processing helix chain 'G' and resid 305 through 311 Processing helix chain 'G' and resid 322 through 324 No H-bonds generated for 'chain 'G' and resid 322 through 324' Processing helix chain 'G' and resid 338 through 343 removed outlier: 4.074A pdb=" N ASN G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 338 through 343' Processing helix chain 'G' and resid 542 through 568 Processing sheet with id= A, first strand: chain 'A' and resid 62 through 64 removed outlier: 3.733A pdb=" N GLU A 62 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 64 " --> pdb=" O TYR A 23 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A 141 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE A 24 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL A 143 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N MET A 305 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASN A 144 " --> pdb=" O MET A 305 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 307 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 310 " --> pdb=" O CYS A 271 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 270 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A 204 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 236 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 1136 through 1140 815 hydrogen bonds defined for protein. 2358 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 369 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 15.28 Time building geometry restraints manager: 13.48 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: 7513 1.34 - 1.46: 8211 1.46 - 1.58: 11674 1.58 - 1.71: 655 1.71 - 1.83: 144 Bond restraints: 28197 Sorted by residual: bond pdb=" CG PRO E 279 " pdb=" CD PRO E 279 " ideal model delta sigma weight residual 1.503 1.374 0.129 3.40e-02 8.65e+02 1.43e+01 bond pdb=" N PRO E 279 " pdb=" CD PRO E 279 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.08e+01 bond pdb=" CB PRO E 279 " pdb=" CG PRO E 279 " ideal model delta sigma weight residual 1.492 1.646 -0.154 5.00e-02 4.00e+02 9.45e+00 bond pdb=" CB ASP B1185 " pdb=" CG ASP B1185 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 4.06e+00 bond pdb=" N PRO E 279 " pdb=" CA PRO E 279 " ideal model delta sigma weight residual 1.469 1.444 0.025 1.28e-02 6.10e+03 3.67e+00 ... (remaining 28192 not shown) Histogram of bond angle deviations from ideal: 89.18 - 101.91: 329 101.91 - 114.64: 18473 114.64 - 127.37: 19923 127.37 - 140.10: 727 140.10 - 152.82: 1 Bond angle restraints: 39453 Sorted by residual: angle pdb=" N MET F 296 " pdb=" CA MET F 296 " pdb=" C MET F 296 " ideal model delta sigma weight residual 110.80 152.82 -42.02 2.13e+00 2.20e-01 3.89e+02 angle pdb=" N LEU F 297 " pdb=" CA LEU F 297 " pdb=" CB LEU F 297 " ideal model delta sigma weight residual 110.45 89.35 21.10 1.26e+00 6.30e-01 2.80e+02 angle pdb=" CA PRO E 279 " pdb=" N PRO E 279 " pdb=" CD PRO E 279 " ideal model delta sigma weight residual 112.00 94.72 17.28 1.40e+00 5.10e-01 1.52e+02 angle pdb=" C MET F 296 " pdb=" CA MET F 296 " pdb=" CB MET F 296 " ideal model delta sigma weight residual 110.42 89.18 21.24 1.99e+00 2.53e-01 1.14e+02 angle pdb=" N PRO E 279 " pdb=" CD PRO E 279 " pdb=" CG PRO E 279 " ideal model delta sigma weight residual 103.20 92.70 10.50 1.50e+00 4.44e-01 4.90e+01 ... (remaining 39448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 13794 35.10 - 70.20: 1987 70.20 - 105.30: 59 105.30 - 140.40: 2 140.40 - 175.50: 1 Dihedral angle restraints: 15843 sinusoidal: 8536 harmonic: 7307 Sorted by residual: dihedral pdb=" N MET F 296 " pdb=" C MET F 296 " pdb=" CA MET F 296 " pdb=" CB MET F 296 " ideal model delta harmonic sigma weight residual 122.80 147.99 -25.19 0 2.50e+00 1.60e-01 1.02e+02 dihedral pdb=" N LEU F 297 " pdb=" C LEU F 297 " pdb=" CA LEU F 297 " pdb=" CB LEU F 297 " ideal model delta harmonic sigma weight residual 122.80 97.71 25.09 0 2.50e+00 1.60e-01 1.01e+02 dihedral pdb=" C MET F 296 " pdb=" N MET F 296 " pdb=" CA MET F 296 " pdb=" CB MET F 296 " ideal model delta harmonic sigma weight residual -122.60 -144.67 22.07 0 2.50e+00 1.60e-01 7.79e+01 ... (remaining 15840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.335: 4353 0.335 - 0.671: 1 0.671 - 1.006: 0 1.006 - 1.341: 0 1.341 - 1.676: 1 Chirality restraints: 4355 Sorted by residual: chirality pdb=" CA MET F 296 " pdb=" N MET F 296 " pdb=" C MET F 296 " pdb=" CB MET F 296 " both_signs ideal model delta sigma weight residual False 2.51 0.83 1.68 2.00e-01 2.50e+01 7.02e+01 chirality pdb=" CA LEU F 297 " pdb=" N LEU F 297 " pdb=" C LEU F 297 " pdb=" CB LEU F 297 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA PRO E 279 " pdb=" N PRO E 279 " pdb=" C PRO E 279 " pdb=" CB PRO E 279 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 4352 not shown) Planarity restraints: 3868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 278 " -0.072 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO E 279 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 279 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 279 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1175 " -0.237 9.50e-02 1.11e+02 1.07e-01 8.41e+00 pdb=" NE ARG B1175 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B1175 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B1175 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B1175 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 365 " 0.019 2.00e-02 2.50e+03 1.77e-02 7.81e+00 pdb=" CG TRP D 365 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP D 365 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 365 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 365 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 365 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 365 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 365 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 365 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 365 " 0.000 2.00e-02 2.50e+03 ... (remaining 3865 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 111 2.49 - 3.09: 17339 3.09 - 3.70: 45880 3.70 - 4.30: 64407 4.30 - 4.90: 96755 Nonbonded interactions: 224492 Sorted by model distance: nonbonded pdb=" CD2 LEU Q 23 " pdb=" OE1 GLU Q 56 " model vdw 1.891 3.460 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 2.114 3.880 nonbonded pdb=" CD2 HIS A 188 " pdb="ZN ZN A 501 " model vdw 2.147 1.960 nonbonded pdb=" CB HIS A 188 " pdb="ZN ZN A 501 " model vdw 2.161 2.104 nonbonded pdb=" OG1 THR A 90 " pdb=" OD1 ASN A 93 " model vdw 2.226 2.440 ... (remaining 224487 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 'D' and (resid 11 through 24 or resid 80 through 112 or resid 222 through \ 372)) selection = chain 'F' } ncs_group { reference = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = (chain 'U' and resid 11 through 116) } ncs_group { reference = (chain 'R' and resid 29 through 119) selection = chain 'V' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 33.720 Check model and map are aligned: 0.420 Set scattering table: 0.280 Process input model: 89.290 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 28197 Z= 0.235 Angle : 0.873 42.023 39453 Z= 0.451 Chirality : 0.050 1.676 4355 Planarity : 0.006 0.107 3868 Dihedral : 24.602 175.502 11116 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 0.77 % Allowed : 34.89 % Favored : 64.34 % Cbeta Deviations : 0.08 % 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: -1.98 (0.15), residues: 2433 helix: -0.96 (0.13), residues: 1333 sheet: -0.11 (0.64), residues: 84 loop : -1.79 (0.17), residues: 1016 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 311 time to evaluate : 3.111 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 320 average time/residue: 0.3817 time to fit residues: 193.8193 Evaluate side-chains 291 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 278 time to evaluate : 2.422 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2852 time to fit residues: 9.6060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 5.9990 chunk 206 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 0.0170 chunk 213 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 247 optimal weight: 0.9990 overall best weight: 0.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 259 ASN O 68 GLN O 93 GLN S 85 GLN B1222 GLN B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 459 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 28197 Z= 0.182 Angle : 0.554 9.814 39453 Z= 0.299 Chirality : 0.036 0.204 4355 Planarity : 0.004 0.050 3868 Dihedral : 26.409 174.701 6026 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.58 % Allowed : 30.63 % Favored : 65.79 % 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: -0.90 (0.16), residues: 2433 helix: 0.17 (0.14), residues: 1336 sheet: -0.16 (0.62), residues: 88 loop : -1.64 (0.18), residues: 1009 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 321 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 35 residues processed: 370 average time/residue: 0.4048 time to fit residues: 234.8829 Evaluate side-chains 325 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 290 time to evaluate : 2.552 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2667 time to fit residues: 20.1979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 chunk 84 optimal weight: 0.0370 chunk 199 optimal weight: 0.5980 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN D 275 GLN O 68 GLN ** S 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 28197 Z= 0.252 Angle : 0.596 9.484 39453 Z= 0.321 Chirality : 0.038 0.232 4355 Planarity : 0.004 0.047 3868 Dihedral : 26.802 172.922 6026 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.17 % Allowed : 29.04 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2433 helix: 0.44 (0.14), residues: 1343 sheet: -0.48 (0.59), residues: 88 loop : -1.53 (0.18), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 333 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 30 residues processed: 379 average time/residue: 0.4161 time to fit residues: 246.4324 Evaluate side-chains 318 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 288 time to evaluate : 2.744 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2718 time to fit residues: 18.1591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 249 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 HIS D 275 GLN D 350 GLN S 85 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 28197 Z= 0.306 Angle : 0.620 10.544 39453 Z= 0.335 Chirality : 0.039 0.234 4355 Planarity : 0.005 0.090 3868 Dihedral : 27.102 176.407 6026 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.04 % Allowed : 28.73 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.63 (0.17), residues: 2433 helix: 0.47 (0.14), residues: 1333 sheet: -1.05 (0.52), residues: 104 loop : -1.54 (0.18), residues: 996 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 320 time to evaluate : 2.649 Fit side-chains revert: symmetry clash outliers start: 67 outliers final: 33 residues processed: 356 average time/residue: 0.4266 time to fit residues: 237.3956 Evaluate side-chains 312 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 279 time to evaluate : 2.882 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2455 time to fit residues: 18.7059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 108 optimal weight: 0.2980 chunk 225 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 275 GLN S 108 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28197 Z= 0.321 Angle : 0.625 11.347 39453 Z= 0.338 Chirality : 0.040 0.311 4355 Planarity : 0.004 0.086 3868 Dihedral : 27.412 175.497 6026 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.58 % Allowed : 29.04 % Favored : 68.37 % 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: -0.63 (0.17), residues: 2433 helix: 0.43 (0.14), residues: 1343 sheet: -1.30 (0.51), residues: 104 loop : -1.47 (0.19), residues: 986 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 323 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 21 residues processed: 356 average time/residue: 0.4301 time to fit residues: 237.5675 Evaluate side-chains 314 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 293 time to evaluate : 2.556 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2943 time to fit residues: 14.2007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 0.6980 chunk 237 optimal weight: 7.9990 chunk 52 optimal weight: 0.3980 chunk 154 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 264 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 GLN P 25 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1299 ASN E 314 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28197 Z= 0.194 Angle : 0.573 10.961 39453 Z= 0.310 Chirality : 0.037 0.170 4355 Planarity : 0.004 0.080 3868 Dihedral : 27.223 177.069 6026 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.77 % Allowed : 28.86 % Favored : 69.37 % 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: -0.41 (0.17), residues: 2433 helix: 0.68 (0.14), residues: 1342 sheet: -1.39 (0.50), residues: 104 loop : -1.45 (0.19), residues: 987 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 324 time to evaluate : 4.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 344 average time/residue: 0.4256 time to fit residues: 229.3159 Evaluate side-chains 315 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 295 time to evaluate : 2.956 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2646 time to fit residues: 13.5670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 3.9990 chunk 29 optimal weight: 0.0050 chunk 150 optimal weight: 3.9990 chunk 192 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 147 optimal weight: 0.7980 chunk 263 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 275 GLN D 305 GLN D 350 GLN O 108 ASN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN E 517 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28197 Z= 0.199 Angle : 0.576 10.293 39453 Z= 0.310 Chirality : 0.037 0.279 4355 Planarity : 0.004 0.074 3868 Dihedral : 27.165 177.154 6026 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.18 % Allowed : 29.45 % Favored : 69.37 % 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: -0.34 (0.17), residues: 2433 helix: 0.75 (0.14), residues: 1345 sheet: -1.30 (0.49), residues: 114 loop : -1.46 (0.19), residues: 974 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 314 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 330 average time/residue: 0.4162 time to fit residues: 215.0707 Evaluate side-chains 310 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 295 time to evaluate : 2.682 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3015 time to fit residues: 11.2382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 0.0370 chunk 50 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 206 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28197 Z= 0.189 Angle : 0.576 10.628 39453 Z= 0.309 Chirality : 0.037 0.213 4355 Planarity : 0.004 0.067 3868 Dihedral : 27.106 176.905 6026 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.63 % Allowed : 29.50 % Favored : 69.87 % 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: -0.27 (0.17), residues: 2433 helix: 0.83 (0.14), residues: 1344 sheet: -1.37 (0.50), residues: 106 loop : -1.45 (0.19), residues: 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 311 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 316 average time/residue: 0.4298 time to fit residues: 212.3648 Evaluate side-chains 301 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 294 time to evaluate : 2.693 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2667 time to fit residues: 6.8574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 9.9990 chunk 252 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 221 optimal weight: 9.9990 chunk 231 optimal weight: 0.5980 chunk 244 optimal weight: 40.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 ASN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28197 Z= 0.207 Angle : 0.595 12.214 39453 Z= 0.316 Chirality : 0.037 0.264 4355 Planarity : 0.004 0.064 3868 Dihedral : 27.117 176.551 6026 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.27 % Rotamer: Outliers : 0.54 % Allowed : 29.90 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2433 helix: 0.87 (0.14), residues: 1334 sheet: -1.28 (0.51), residues: 104 loop : -1.44 (0.19), residues: 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 302 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 311 average time/residue: 0.4303 time to fit residues: 211.0632 Evaluate side-chains 304 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 297 time to evaluate : 2.813 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3385 time to fit residues: 7.4278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 271 optimal weight: 20.0000 chunk 250 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 22 optimal weight: 0.1980 chunk 167 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 108 ASN ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 28197 Z= 0.354 Angle : 0.660 13.476 39453 Z= 0.353 Chirality : 0.042 0.415 4355 Planarity : 0.004 0.085 3868 Dihedral : 27.611 175.276 6026 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.91 % Allowed : 29.18 % Favored : 69.91 % 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: -0.45 (0.17), residues: 2433 helix: 0.62 (0.14), residues: 1330 sheet: -1.61 (0.48), residues: 104 loop : -1.38 (0.19), residues: 999 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 294 time to evaluate : 2.767 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 303 average time/residue: 0.4248 time to fit residues: 201.0370 Evaluate side-chains 292 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 281 time to evaluate : 2.768 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3164 time to fit residues: 9.6030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 0.3980 chunk 230 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 216 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN O 108 ASN R 64 ASN ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.128146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.089670 restraints weight = 67819.381| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.21 r_work: 0.3308 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28197 Z= 0.190 Angle : 0.608 12.247 39453 Z= 0.324 Chirality : 0.038 0.267 4355 Planarity : 0.004 0.068 3868 Dihedral : 27.304 176.610 6026 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.36 % Allowed : 29.77 % Favored : 69.87 % 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: -0.27 (0.17), residues: 2433 helix: 0.81 (0.14), residues: 1331 sheet: -1.27 (0.52), residues: 94 loop : -1.40 (0.19), residues: 1008 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7161.80 seconds wall clock time: 130 minutes 34.61 seconds (7834.61 seconds total)