Starting phenix.real_space_refine on Sat Feb 24 08:28:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr0_27667/02_2024/8dr0_27667_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr0_27667/02_2024/8dr0_27667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr0_27667/02_2024/8dr0_27667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr0_27667/02_2024/8dr0_27667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr0_27667/02_2024/8dr0_27667_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr0_27667/02_2024/8dr0_27667_trim.pdb" } resolution = 2.42 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= 0.000 sd= 0.046 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: 7 Type Number sf(0) Gaussians P 54 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 13461 2.51 5 N 3663 2.21 5 O 4231 1.98 5 H 21368 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 376": "OE1" <-> "OE2" Residue "A TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A ASP 697": "OD1" <-> "OD2" Residue "A ASP 733": "OD1" <-> "OD2" Residue "A ASP 741": "OD1" <-> "OD2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D ASP 178": "OD1" <-> "OD2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D ASP 266": "OD1" <-> "OD2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E ASP 309": "OD1" <-> "OD2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F GLU 8": "OE1" <-> "OE2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "G GLU 3": "OE1" <-> "OE2" Residue "G ASP 21": "OD1" <-> "OD2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G GLU 232": "OE1" <-> "OE2" Residue "G PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 3": "OE1" <-> "OE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H ASP 109": "OD1" <-> "OD2" Residue "H PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 223": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42882 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 7836 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5084 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 5254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5254 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 5464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5464 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5698 Classifications: {'peptide': 354} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 339} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4055 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4047 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "H" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4023 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "I" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 706 Classifications: {'DNA': 22} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 559 Classifications: {'DNA': 18} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.27, per 1000 atoms: 0.43 Number of scatterers: 42882 At special positions: 0 Unit cell: (124.726, 119.77, 140.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 54 15.00 Mg 4 11.99 O 4231 8.00 N 3663 7.00 C 13461 6.00 H 21368 1.00 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: 35.97 Conformation dependent library (CDL) restraints added in 4.3 seconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 15 sheets defined 54.9% alpha, 15.3% beta 13 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 18.79 Creating SS restraints... Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.559A pdb=" N LYS A 296 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.639A pdb=" N VAL A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.509A pdb=" N LEU A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 392 through 396 removed outlier: 3.705A pdb=" N LEU A 396 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 460 through 467 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 479 through 495 removed outlier: 3.551A pdb=" N ILE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.516A pdb=" N ILE A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 528 removed outlier: 4.302A pdb=" N THR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 573 through 584 removed outlier: 4.233A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 668 through 690 Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 704 through 714 removed outlier: 4.112A pdb=" N THR A 708 " --> pdb=" O ASP A 704 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 720 Processing helix chain 'A' and resid 721 through 723 No H-bonds generated for 'chain 'A' and resid 721 through 723' Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 738 through 746 Processing helix chain 'A' and resid 750 through 754 removed outlier: 3.523A pdb=" N VAL A 754 " --> pdb=" O GLY A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.546A pdb=" N ILE A 762 " --> pdb=" O ILE A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 776 removed outlier: 3.502A pdb=" N LYS A 767 " --> pdb=" O PRO A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 4.027A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.656A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.621A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.582A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.627A pdb=" N LEU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.650A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 89 through 102 removed outlier: 3.973A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.596A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.546A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.520A pdb=" N ARG C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.686A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.027A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 292 through 312 removed outlier: 4.006A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'D' and resid 17 through 24 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.719A pdb=" N VAL D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 56 removed outlier: 4.652A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.935A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 152 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.567A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 296 through 310 Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.573A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.405A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 97 through 103 removed outlier: 7.001A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 removed outlier: 3.827A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.600A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.503A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.689A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 3.805A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 20 removed outlier: 4.482A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.684A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 221 removed outlier: 4.045A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 20 removed outlier: 4.420A pdb=" N PHE G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 removed outlier: 4.214A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 217 removed outlier: 3.788A pdb=" N LYS G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 221 Processing helix chain 'H' and resid 8 through 20 removed outlier: 4.335A pdb=" N PHE H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 153 removed outlier: 3.845A pdb=" N GLN H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 217 through 221 removed outlier: 3.942A pdb=" N SER H 220 " --> pdb=" O LYS H 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 377 removed outlier: 6.403A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.917A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 601 Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.268A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.497A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.468A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 69 through 76 removed outlier: 6.664A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.547A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 59 through 62 removed outlier: 3.748A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE F 111 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.723A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY F 244 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 5.921A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE G 111 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG G 110 " --> pdb=" O ASP G 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.752A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 203 through 208 removed outlier: 4.367A pdb=" N ILE G 181 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILE H 111 " --> pdb=" O ILE G 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 25 through 30 Processing sheet with id=AB6, first strand: chain 'H' and resid 35 through 40 removed outlier: 4.885A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) 1158 hydrogen bonds defined for protein. 3252 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 17.82 Time building geometry restraints manager: 37.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 21329 1.05 - 1.27: 3605 1.27 - 1.49: 8551 1.49 - 1.70: 9666 1.70 - 1.92: 159 Bond restraints: 43310 Sorted by residual: bond pdb=" C2' AGS A 901 " pdb=" C3' AGS A 901 " ideal model delta sigma weight residual 1.530 1.239 0.291 1.30e-02 5.92e+03 5.01e+02 bond pdb=" C2' AGS C 402 " pdb=" C3' AGS C 402 " ideal model delta sigma weight residual 1.530 1.240 0.290 1.30e-02 5.92e+03 4.99e+02 bond pdb=" C2' AGS D 402 " pdb=" C3' AGS D 402 " ideal model delta sigma weight residual 1.530 1.240 0.290 1.30e-02 5.92e+03 4.96e+02 bond pdb=" C2' AGS B 402 " pdb=" C3' AGS B 402 " ideal model delta sigma weight residual 1.530 1.241 0.289 1.30e-02 5.92e+03 4.94e+02 bond pdb=" C6 AGS C 402 " pdb=" N6 AGS C 402 " ideal model delta sigma weight residual 1.335 1.468 -0.133 1.00e-02 1.00e+04 1.77e+02 ... (remaining 43305 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.03: 578 106.03 - 113.02: 52177 113.02 - 120.01: 11997 120.01 - 127.00: 13578 127.00 - 133.99: 253 Bond angle restraints: 78583 Sorted by residual: angle pdb=" N1 AGS A 901 " pdb=" C2 AGS A 901 " pdb=" N3 AGS A 901 " ideal model delta sigma weight residual 128.80 120.07 8.73 8.41e-01 1.41e+00 1.08e+02 angle pdb=" N1 AGS D 402 " pdb=" C2 AGS D 402 " pdb=" N3 AGS D 402 " ideal model delta sigma weight residual 128.80 120.07 8.73 8.41e-01 1.41e+00 1.08e+02 angle pdb=" N1 AGS C 402 " pdb=" C2 AGS C 402 " pdb=" N3 AGS C 402 " ideal model delta sigma weight residual 128.80 120.08 8.72 8.41e-01 1.41e+00 1.07e+02 angle pdb=" N1 AGS B 402 " pdb=" C2 AGS B 402 " pdb=" N3 AGS B 402 " ideal model delta sigma weight residual 128.80 120.10 8.70 8.41e-01 1.41e+00 1.07e+02 angle pdb=" C5 AGS D 402 " pdb=" N7 AGS D 402 " pdb=" C8 AGS D 402 " ideal model delta sigma weight residual 103.67 107.96 -4.29 4.26e-01 5.51e+00 1.01e+02 ... (remaining 78578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.56: 18952 30.56 - 61.11: 976 61.11 - 91.67: 57 91.67 - 122.22: 1 122.22 - 152.78: 5 Dihedral angle restraints: 19991 sinusoidal: 11356 harmonic: 8635 Sorted by residual: dihedral pdb=" O2B GDP E 401 " pdb=" O3A GDP E 401 " pdb=" PB GDP E 401 " pdb=" PA GDP E 401 " ideal model delta sinusoidal sigma weight residual -180.00 -39.31 -140.69 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" O1A AGS C 402 " pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sinusoidal sigma weight residual -67.73 75.91 -143.64 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" O1A AGS D 402 " pdb=" O3A AGS D 402 " pdb=" PA AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sinusoidal sigma weight residual -67.73 73.61 -141.34 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 19988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3068 0.060 - 0.121: 372 0.121 - 0.181: 29 0.181 - 0.241: 4 0.241 - 0.301: 4 Chirality restraints: 3477 Sorted by residual: chirality pdb=" C2' AGS C 402 " pdb=" C1' AGS C 402 " pdb=" C3' AGS C 402 " pdb=" O2' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.37 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C2' AGS B 402 " pdb=" C1' AGS B 402 " pdb=" C3' AGS B 402 " pdb=" O2' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.37 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C2' AGS D 402 " pdb=" C1' AGS D 402 " pdb=" C3' AGS D 402 " pdb=" O2' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 3474 not shown) Planarity restraints: 6191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 228 " -0.168 9.50e-02 1.11e+02 5.63e-02 3.77e+00 pdb=" NE ARG H 228 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG H 228 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG H 228 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG H 228 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG H 228 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG H 228 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG H 228 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 228 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 61 " 0.138 9.50e-02 1.11e+02 4.64e-02 2.65e+00 pdb=" NE ARG G 61 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG G 61 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG G 61 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG G 61 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG G 61 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG G 61 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG G 61 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG G 61 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 110 " 0.121 9.50e-02 1.11e+02 4.07e-02 2.33e+00 pdb=" NE ARG G 110 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG G 110 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 110 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 110 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG G 110 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG G 110 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG G 110 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG G 110 " 0.000 2.00e-02 2.50e+03 ... (remaining 6188 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 824 2.12 - 2.74: 76877 2.74 - 3.36: 124101 3.36 - 3.98: 162129 3.98 - 4.60: 251771 Nonbonded interactions: 615702 Sorted by model distance: nonbonded pdb=" OE1 GLU G 32 " pdb=" H GLU G 32 " model vdw 1.499 1.850 nonbonded pdb=" OE1 GLU G 232 " pdb=" H GLU G 232 " model vdw 1.529 1.850 nonbonded pdb=" O ASN C 12 " pdb="HH22 ARG D 165 " model vdw 1.572 1.850 nonbonded pdb=" O LYS H 31 " pdb=" HH TYR H 60 " model vdw 1.581 1.850 nonbonded pdb=" OE1 GLU F 8 " pdb=" H GLU F 8 " model vdw 1.594 1.850 ... (remaining 615697 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 'F' and resid 0 through 254) selection = (chain 'G' and ((resid 0 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 1 through 254)) selection = (chain 'H' and ((resid 0 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 1 through 254)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.590 Extract box with map and model: 14.340 Check model and map are aligned: 0.620 Set scattering table: 0.400 Process input model: 149.850 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.130 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.291 21942 Z= 0.487 Angle : 0.562 10.215 29842 Z= 0.387 Chirality : 0.040 0.301 3477 Planarity : 0.003 0.074 3648 Dihedral : 17.937 152.776 8389 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.04 % Allowed : 19.57 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.17), residues: 2590 helix: 2.22 (0.16), residues: 1211 sheet: 0.92 (0.22), residues: 526 loop : 0.60 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 298 HIS 0.005 0.001 HIS B 95 PHE 0.009 0.001 PHE G 6 TYR 0.011 0.001 TYR E 161 ARG 0.012 0.000 ARG G 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 310 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 286 time to evaluate : 3.483 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 outliers start: 24 outliers final: 10 residues processed: 308 average time/residue: 3.2894 time to fit residues: 1140.1606 Evaluate side-chains 194 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 184 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 236 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN A 562 GLN B 95 HIS B 250 GLN D 171 ASN E 80 ASN E 224 GLN G 94 ASN G 159 ASN G 190 HIS H 58 GLN H 84 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21942 Z= 0.173 Angle : 0.507 6.725 29842 Z= 0.269 Chirality : 0.039 0.163 3477 Planarity : 0.004 0.053 3648 Dihedral : 13.432 155.024 3288 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.65 % Allowed : 21.43 % Favored : 76.93 % 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: 1.95 (0.17), residues: 2590 helix: 2.04 (0.15), residues: 1246 sheet: 0.98 (0.22), residues: 522 loop : 0.46 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 4 HIS 0.004 0.001 HIS E 18 PHE 0.009 0.001 PHE E 328 TYR 0.012 0.001 TYR A 352 ARG 0.010 0.000 ARG G 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 3.608 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: A 467 ASP cc_start: 0.6976 (m-30) cc_final: 0.6694 (m-30) REVERT: E 32 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7474 (mp10) REVERT: H 2 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7745 (tt) outliers start: 38 outliers final: 16 residues processed: 223 average time/residue: 3.0904 time to fit residues: 783.0109 Evaluate side-chains 200 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 76 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 234 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN C 291 GLN E 80 ASN ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 190 HIS H 84 ASN H 153 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 21942 Z= 0.245 Angle : 0.498 6.051 29842 Z= 0.266 Chirality : 0.039 0.140 3477 Planarity : 0.003 0.049 3648 Dihedral : 13.388 160.382 3282 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.34 % Allowed : 21.21 % Favored : 77.45 % 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: 1.88 (0.17), residues: 2590 helix: 2.01 (0.15), residues: 1239 sheet: 0.99 (0.22), residues: 519 loop : 0.37 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.007 0.001 HIS E 18 PHE 0.014 0.001 PHE E 328 TYR 0.013 0.001 TYR A 352 ARG 0.009 0.000 ARG G 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 3.518 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 467 ASP cc_start: 0.7103 (m-30) cc_final: 0.6801 (m-30) REVERT: E 32 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7640 (mp10) outliers start: 31 outliers final: 21 residues processed: 203 average time/residue: 3.3026 time to fit residues: 764.1177 Evaluate side-chains 196 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 76 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 224 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 291 GLN G 94 ASN G 190 HIS H 58 GLN H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21942 Z= 0.254 Angle : 0.501 7.148 29842 Z= 0.267 Chirality : 0.040 0.136 3477 Planarity : 0.004 0.059 3648 Dihedral : 13.481 168.939 3280 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.86 % Allowed : 19.91 % Favored : 78.23 % 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: 1.81 (0.17), residues: 2590 helix: 1.95 (0.15), residues: 1234 sheet: 0.96 (0.22), residues: 519 loop : 0.34 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.007 0.001 HIS B 232 PHE 0.014 0.001 PHE E 305 TYR 0.013 0.001 TYR A 352 ARG 0.009 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 177 time to evaluate : 3.350 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 467 ASP cc_start: 0.7085 (m-30) cc_final: 0.6815 (m-30) REVERT: E 32 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7686 (mp10) outliers start: 43 outliers final: 25 residues processed: 213 average time/residue: 3.1558 time to fit residues: 762.3716 Evaluate side-chains 201 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 185 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 214 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN C 291 GLN E 121 GLN G 94 ASN G 190 HIS H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21942 Z= 0.288 Angle : 0.506 7.931 29842 Z= 0.270 Chirality : 0.040 0.142 3477 Planarity : 0.004 0.054 3648 Dihedral : 13.532 166.733 3278 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.65 % Allowed : 20.00 % Favored : 78.35 % 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: 1.73 (0.17), residues: 2590 helix: 1.87 (0.15), residues: 1239 sheet: 0.97 (0.22), residues: 520 loop : 0.28 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.007 0.001 HIS B 232 PHE 0.014 0.001 PHE E 305 TYR 0.015 0.001 TYR A 352 ARG 0.009 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 3.586 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: A 467 ASP cc_start: 0.7132 (m-30) cc_final: 0.6868 (m-30) REVERT: E 32 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7726 (mp10) outliers start: 38 outliers final: 29 residues processed: 209 average time/residue: 3.4415 time to fit residues: 810.4773 Evaluate side-chains 200 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 3.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 185 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 0.3980 chunk 226 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 291 GLN E 121 GLN G 94 ASN G 190 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21942 Z= 0.236 Angle : 0.496 8.295 29842 Z= 0.264 Chirality : 0.039 0.136 3477 Planarity : 0.004 0.062 3648 Dihedral : 13.541 167.026 3278 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.73 % Allowed : 20.00 % Favored : 78.27 % 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: 1.79 (0.17), residues: 2590 helix: 1.93 (0.15), residues: 1236 sheet: 0.99 (0.22), residues: 515 loop : 0.32 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.006 0.001 HIS E 18 PHE 0.013 0.001 PHE E 305 TYR 0.014 0.001 TYR A 352 ARG 0.009 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 3.277 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: A 467 ASP cc_start: 0.7053 (m-30) cc_final: 0.6827 (m-30) outliers start: 40 outliers final: 29 residues processed: 203 average time/residue: 3.3237 time to fit residues: 774.1977 Evaluate side-chains 196 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 185 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 250 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 291 GLN E 121 GLN G 190 HIS H 58 GLN H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 21942 Z= 0.318 Angle : 0.521 9.498 29842 Z= 0.277 Chirality : 0.040 0.138 3477 Planarity : 0.004 0.065 3648 Dihedral : 13.610 166.902 3278 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.60 % Allowed : 19.78 % Favored : 78.61 % 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: 1.65 (0.17), residues: 2590 helix: 1.80 (0.15), residues: 1247 sheet: 0.97 (0.22), residues: 515 loop : 0.22 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 669 HIS 0.008 0.001 HIS B 232 PHE 0.015 0.001 PHE E 305 TYR 0.012 0.001 TYR D 286 ARG 0.010 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 4.000 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: A 467 ASP cc_start: 0.7138 (m-30) cc_final: 0.6878 (m-30) REVERT: H 161 MET cc_start: 0.7386 (mtm) cc_final: 0.6991 (mpt) outliers start: 37 outliers final: 32 residues processed: 201 average time/residue: 3.2229 time to fit residues: 734.2392 Evaluate side-chains 201 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 185 PHE Chi-restraints excluded: chain H residue 199 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 291 GLN D 24 GLN G 190 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21942 Z= 0.257 Angle : 0.502 10.172 29842 Z= 0.267 Chirality : 0.040 0.138 3477 Planarity : 0.004 0.070 3648 Dihedral : 13.619 166.581 3278 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.43 % Allowed : 20.04 % Favored : 78.53 % 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: 1.70 (0.17), residues: 2590 helix: 1.84 (0.15), residues: 1248 sheet: 0.98 (0.22), residues: 517 loop : 0.24 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.006 0.001 HIS E 18 PHE 0.014 0.001 PHE E 305 TYR 0.011 0.001 TYR D 286 ARG 0.012 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 3.987 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 467 ASP cc_start: 0.7087 (m-30) cc_final: 0.6884 (m-30) outliers start: 33 outliers final: 30 residues processed: 197 average time/residue: 3.2443 time to fit residues: 723.9177 Evaluate side-chains 198 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 3.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 185 PHE Chi-restraints excluded: chain H residue 199 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 232 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 291 GLN D 24 GLN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21942 Z= 0.174 Angle : 0.489 10.695 29842 Z= 0.258 Chirality : 0.039 0.139 3477 Planarity : 0.004 0.083 3648 Dihedral : 13.588 167.506 3278 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.95 % Allowed : 20.39 % Favored : 78.66 % 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: 1.89 (0.17), residues: 2590 helix: 2.01 (0.15), residues: 1238 sheet: 1.06 (0.22), residues: 517 loop : 0.34 (0.23), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.005 0.001 HIS E 18 PHE 0.010 0.001 PHE E 305 TYR 0.010 0.001 TYR D 286 ARG 0.012 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 3.902 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: H 161 MET cc_start: 0.7443 (mtm) cc_final: 0.6977 (mpt) outliers start: 22 outliers final: 16 residues processed: 188 average time/residue: 3.5470 time to fit residues: 746.8364 Evaluate side-chains 184 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 185 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 259 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 291 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21942 Z= 0.343 Angle : 0.538 11.153 29842 Z= 0.284 Chirality : 0.041 0.136 3477 Planarity : 0.004 0.068 3648 Dihedral : 13.649 167.060 3277 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.95 % Allowed : 20.56 % Favored : 78.48 % 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: 1.68 (0.17), residues: 2590 helix: 1.84 (0.15), residues: 1240 sheet: 1.02 (0.22), residues: 515 loop : 0.19 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 669 HIS 0.009 0.001 HIS H 190 PHE 0.016 0.001 PHE E 305 TYR 0.013 0.001 TYR D 160 ARG 0.012 0.000 ARG E 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 169 time to evaluate : 3.746 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: D 141 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: H 161 MET cc_start: 0.7469 (mtm) cc_final: 0.6896 (mpt) outliers start: 22 outliers final: 20 residues processed: 185 average time/residue: 3.4752 time to fit residues: 723.0868 Evaluate side-chains 188 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 185 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 2.9990 chunk 219 optimal weight: 0.0370 chunk 63 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 291 GLN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.057335 restraints weight = 100305.422| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.43 r_work: 0.2604 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21942 Z= 0.190 Angle : 0.499 11.245 29842 Z= 0.264 Chirality : 0.039 0.138 3477 Planarity : 0.004 0.066 3648 Dihedral : 13.614 167.918 3277 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.91 % Allowed : 20.74 % Favored : 78.35 % 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: 1.83 (0.17), residues: 2590 helix: 1.95 (0.15), residues: 1243 sheet: 1.05 (0.22), residues: 515 loop : 0.30 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.011 0.001 HIS H 190 PHE 0.012 0.001 PHE E 305 TYR 0.009 0.001 TYR D 286 ARG 0.012 0.000 ARG E 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14581.70 seconds wall clock time: 257 minutes 1.24 seconds (15421.24 seconds total)