Starting phenix.real_space_refine on Tue Dec 12 10:50:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvv_23543/12_2023/7lvv_23543_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvv_23543/12_2023/7lvv_23543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvv_23543/12_2023/7lvv_23543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvv_23543/12_2023/7lvv_23543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvv_23543/12_2023/7lvv_23543_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvv_23543/12_2023/7lvv_23543_updated.pdb" } resolution = 3.25 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= 0.050 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 110 5.49 5 S 44 5.16 5 C 12960 2.51 5 N 3709 2.21 5 O 4193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A ARG 46": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A ASP 638": "OD1" <-> "OD2" Residue "A ARG 674": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A TYR 879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 890": "NH1" <-> "NH2" Residue "A GLU 900": "OE1" <-> "OE2" Residue "A ARG 988": "NH1" <-> "NH2" Residue "A GLU 989": "OE1" <-> "OE2" Residue "A GLU 1001": "OE1" <-> "OE2" Residue "A ARG 1002": "NH1" <-> "NH2" Residue "A GLU 1023": "OE1" <-> "OE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B GLU 458": "OE1" <-> "OE2" Residue "B ASP 491": "OD1" <-> "OD2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B ARG 522": "NH1" <-> "NH2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 649": "OD1" <-> "OD2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 696": "NH1" <-> "NH2" Residue "B GLU 736": "OE1" <-> "OE2" Residue "B GLU 806": "OE1" <-> "OE2" Residue "B GLU 821": "OE1" <-> "OE2" Residue "B TYR 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 845": "NH1" <-> "NH2" Residue "B TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 870": "NH1" <-> "NH2" Residue "B ARG 890": "NH1" <-> "NH2" Residue "B GLU 912": "OE1" <-> "OE2" Residue "B ASP 935": "OD1" <-> "OD2" Residue "B GLU 971": "OE1" <-> "OE2" Residue "B GLU 975": "OE1" <-> "OE2" Residue "B ASP 984": "OD1" <-> "OD2" Residue "B ARG 988": "NH1" <-> "NH2" Residue "B GLU 989": "OE1" <-> "OE2" Residue "B ASP 1005": "OD1" <-> "OD2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D ASP 82": "OD1" <-> "OD2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D ASP 108": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 21020 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8216 Classifications: {'peptide': 1011} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 969} Chain breaks: 2 Chain: "B" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8219 Classifications: {'peptide': 1012} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 970} Chain breaks: 2 Chain: "C" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "D" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1149 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "E" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "F" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "G" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.04, per 1000 atoms: 0.53 Number of scatterers: 21020 At special positions: 0 Unit cell: (106.72, 107.88, 203, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 44 16.00 P 110 15.00 O 4193 8.00 N 3709 7.00 C 12960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.73 Conformation dependent library (CDL) restraints added in 3.5 seconds 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 14 sheets defined 41.7% alpha, 6.8% beta 48 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 10.75 Creating SS restraints... Processing helix chain 'A' and resid 3 through 19 Processing helix chain 'A' and resid 25 through 28 No H-bonds generated for 'chain 'A' and resid 25 through 28' Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.703A pdb=" N GLY A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.573A pdb=" N ALA A 96 " --> pdb=" O GLN A 92 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 161 through 174 removed outlier: 3.710A pdb=" N ILE A 167 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.876A pdb=" N ASP A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 221 removed outlier: 3.582A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 233 through 242 removed outlier: 4.226A pdb=" N LEU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 259 through 262 No H-bonds generated for 'chain 'A' and resid 259 through 262' Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 275 through 292 removed outlier: 4.177A pdb=" N ARG A 280 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.576A pdb=" N ARG A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 removed outlier: 3.606A pdb=" N THR A 318 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 354 removed outlier: 3.699A pdb=" N GLU A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 375 through 392 Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 468 through 476 removed outlier: 3.585A pdb=" N ARG A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 481 No H-bonds generated for 'chain 'A' and resid 478 through 481' Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 523 through 531 removed outlier: 4.304A pdb=" N GLY A 526 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 528 " --> pdb=" O ASP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 601 through 604 No H-bonds generated for 'chain 'A' and resid 601 through 604' Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 683 through 702 removed outlier: 3.647A pdb=" N ASN A 698 " --> pdb=" O ILE A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 709 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 766 through 769 No H-bonds generated for 'chain 'A' and resid 766 through 769' Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 845 through 857 Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 883 through 897 Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 969 through 977 Processing helix chain 'A' and resid 987 through 990 No H-bonds generated for 'chain 'A' and resid 987 through 990' Processing helix chain 'A' and resid 1001 through 1023 Processing helix chain 'B' and resid 3 through 18 removed outlier: 3.523A pdb=" N PHE B 9 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 14 " --> pdb=" O GLN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 43 removed outlier: 4.904A pdb=" N ALA B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ALA B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.880A pdb=" N GLN B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 145 through 177 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 179 through 196 Processing helix chain 'B' and resid 202 through 219 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 248 through 270 removed outlier: 4.201A pdb=" N ARG B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE B 265 " --> pdb=" O TYR B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 removed outlier: 3.504A pdb=" N ARG B 280 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 300 No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 308 through 325 removed outlier: 3.535A pdb=" N LYS B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 357 through 366 removed outlier: 4.265A pdb=" N GLN B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 386 Processing helix chain 'B' and resid 389 through 392 No H-bonds generated for 'chain 'B' and resid 389 through 392' Processing helix chain 'B' and resid 428 through 438 Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 468 through 476 removed outlier: 3.550A pdb=" N ARG B 472 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ARG B 473 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 475 " --> pdb=" O ARG B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 481 No H-bonds generated for 'chain 'B' and resid 478 through 481' Processing helix chain 'B' and resid 492 through 503 removed outlier: 3.640A pdb=" N ARG B 498 " --> pdb=" O SER B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 525 Processing helix chain 'B' and resid 527 through 533 removed outlier: 5.050A pdb=" N VAL B 532 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 removed outlier: 3.725A pdb=" N LYS B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 610 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 647 through 651 Processing helix chain 'B' and resid 675 through 677 No H-bonds generated for 'chain 'B' and resid 675 through 677' Processing helix chain 'B' and resid 685 through 701 Processing helix chain 'B' and resid 705 through 709 Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 766 through 768 No H-bonds generated for 'chain 'B' and resid 766 through 768' Processing helix chain 'B' and resid 771 through 773 No H-bonds generated for 'chain 'B' and resid 771 through 773' Processing helix chain 'B' and resid 828 through 837 Processing helix chain 'B' and resid 845 through 857 Processing helix chain 'B' and resid 861 through 864 No H-bonds generated for 'chain 'B' and resid 861 through 864' Processing helix chain 'B' and resid 866 through 869 No H-bonds generated for 'chain 'B' and resid 866 through 869' Processing helix chain 'B' and resid 882 through 897 removed outlier: 3.835A pdb=" N TRP B 888 " --> pdb=" O ARG B 884 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY B 889 " --> pdb=" O TRP B 885 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG B 890 " --> pdb=" O ALA B 886 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 923 Processing helix chain 'B' and resid 969 through 976 Processing helix chain 'B' and resid 985 through 988 No H-bonds generated for 'chain 'B' and resid 985 through 988' Processing helix chain 'B' and resid 996 through 1023 removed outlier: 6.475A pdb=" N GLU B1001 " --> pdb=" O ASP B 998 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B1008 " --> pdb=" O ASP B1005 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B1010 " --> pdb=" O LEU B1007 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B1020 " --> pdb=" O THR B1017 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B1021 " --> pdb=" O VAL B1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.510A pdb=" N ALA C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 43 removed outlier: 4.786A pdb=" N ALA C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 97 removed outlier: 4.304A pdb=" N GLN C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 141 Processing helix chain 'D' and resid 6 through 9 No H-bonds generated for 'chain 'D' and resid 6 through 9' Processing helix chain 'D' and resid 11 through 19 removed outlier: 3.724A pdb=" N ILE D 16 " --> pdb=" O ARG D 12 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 43 removed outlier: 5.034A pdb=" N ALA D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE D 32 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 43 " --> pdb=" O TRP D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 97 Processing helix chain 'D' and resid 129 through 141 Processing sheet with id= A, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.889A pdb=" N ILE A 104 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 508 through 515 removed outlier: 3.570A pdb=" N GLY A 508 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 510 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 794 through 796 removed outlier: 3.655A pdb=" N GLN A 809 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 943 through 945 Processing sheet with id= E, first strand: chain 'A' and resid 740 through 746 removed outlier: 6.863A pdb=" N ASP A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 46 through 49 removed outlier: 3.541A pdb=" N GLY B 76 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 104 " --> pdb=" O MET B 115 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 368 through 370 removed outlier: 6.434A pdb=" N ILE B 337 " --> pdb=" O HIS B 369 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU B 338 " --> pdb=" O ARG B 443 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE B 445 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 508 through 514 removed outlier: 6.287A pdb=" N LYS B 589 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE B 540 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TRP B 591 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASP B 542 " --> pdb=" O TRP B 591 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N HIS B 593 " --> pdb=" O ASP B 542 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 793 through 796 Processing sheet with id= J, first strand: chain 'B' and resid 814 through 816 Processing sheet with id= K, first strand: chain 'B' and resid 908 through 911 Processing sheet with id= L, first strand: chain 'B' and resid 740 through 746 removed outlier: 6.660A pdb=" N ASP B 749 " --> pdb=" O TYR B 745 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.761A pdb=" N GLN C 122 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN C 116 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLU C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 77 through 79 removed outlier: 3.628A pdb=" N GLU D 107 " --> pdb=" O GLU D 79 " (cutoff:3.500A) 626 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 258 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 8.95 Time building geometry restraints manager: 10.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3415 1.31 - 1.44: 6258 1.44 - 1.57: 11709 1.57 - 1.70: 213 1.70 - 1.83: 86 Bond restraints: 21681 Sorted by residual: bond pdb=" C ASN A 712 " pdb=" N TRP A 713 " ideal model delta sigma weight residual 1.332 1.247 0.085 1.40e-02 5.10e+03 3.68e+01 bond pdb=" C SER B 844 " pdb=" N ARG B 845 " ideal model delta sigma weight residual 1.335 1.263 0.072 1.25e-02 6.40e+03 3.31e+01 bond pdb=" C VAL A 741 " pdb=" N PRO A 742 " ideal model delta sigma weight residual 1.331 1.397 -0.066 1.20e-02 6.94e+03 3.02e+01 bond pdb=" C LYS A 702 " pdb=" N LEU A 703 " ideal model delta sigma weight residual 1.328 1.405 -0.077 1.44e-02 4.82e+03 2.85e+01 bond pdb=" C PRO B 144 " pdb=" O PRO B 144 " ideal model delta sigma weight residual 1.240 1.182 0.058 1.12e-02 7.97e+03 2.69e+01 ... (remaining 21676 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.24: 988 105.24 - 112.57: 10052 112.57 - 119.89: 10439 119.89 - 127.22: 7911 127.22 - 134.54: 381 Bond angle restraints: 29771 Sorted by residual: angle pdb=" N ILE A 987 " pdb=" CA ILE A 987 " pdb=" C ILE A 987 " ideal model delta sigma weight residual 113.47 104.56 8.91 1.01e+00 9.80e-01 7.79e+01 angle pdb=" N GLU B 299 " pdb=" CA GLU B 299 " pdb=" C GLU B 299 " ideal model delta sigma weight residual 114.04 103.10 10.94 1.24e+00 6.50e-01 7.78e+01 angle pdb=" N GLN B 728 " pdb=" CA GLN B 728 " pdb=" C GLN B 728 " ideal model delta sigma weight residual 112.72 102.92 9.80 1.14e+00 7.69e-01 7.40e+01 angle pdb=" N ARG A 929 " pdb=" CA ARG A 929 " pdb=" C ARG A 929 " ideal model delta sigma weight residual 112.97 104.07 8.90 1.06e+00 8.90e-01 7.04e+01 angle pdb=" C LYS A 486 " pdb=" N THR A 487 " pdb=" CA THR A 487 " ideal model delta sigma weight residual 123.07 110.94 12.13 1.46e+00 4.69e-01 6.91e+01 ... (remaining 29766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.96: 11273 32.96 - 65.91: 1469 65.91 - 98.87: 60 98.87 - 131.83: 1 131.83 - 164.78: 2 Dihedral angle restraints: 12805 sinusoidal: 6033 harmonic: 6772 Sorted by residual: dihedral pdb=" N ASP C 69 " pdb=" C ASP C 69 " pdb=" CA ASP C 69 " pdb=" CB ASP C 69 " ideal model delta harmonic sigma weight residual 122.80 140.99 -18.19 0 2.50e+00 1.60e-01 5.29e+01 dihedral pdb=" C ASP C 69 " pdb=" N ASP C 69 " pdb=" CA ASP C 69 " pdb=" CB ASP C 69 " ideal model delta harmonic sigma weight residual -122.60 -139.94 17.34 0 2.50e+00 1.60e-01 4.81e+01 dihedral pdb=" C GLN B 33 " pdb=" N GLN B 33 " pdb=" CA GLN B 33 " pdb=" CB GLN B 33 " ideal model delta harmonic sigma weight residual -122.60 -107.31 -15.29 0 2.50e+00 1.60e-01 3.74e+01 ... (remaining 12802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2554 0.149 - 0.298: 629 0.298 - 0.448: 31 0.448 - 0.597: 0 0.597 - 0.746: 1 Chirality restraints: 3215 Sorted by residual: chirality pdb=" CA ASP C 69 " pdb=" N ASP C 69 " pdb=" C ASP C 69 " pdb=" CB ASP C 69 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA ASP A 88 " pdb=" N ASP A 88 " pdb=" C ASP A 88 " pdb=" CB ASP A 88 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CA THR C 49 " pdb=" N THR C 49 " pdb=" C THR C 49 " pdb=" CB THR C 49 " both_signs ideal model delta sigma weight residual False 2.53 2.09 0.43 2.00e-01 2.50e+01 4.70e+00 ... (remaining 3212 not shown) Planarity restraints: 3504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 926 " -0.027 2.00e-02 2.50e+03 5.65e-02 3.19e+01 pdb=" C LYS B 926 " 0.098 2.00e-02 2.50e+03 pdb=" O LYS B 926 " -0.037 2.00e-02 2.50e+03 pdb=" N LYS B 927 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 646 " 0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C ALA B 646 " -0.094 2.00e-02 2.50e+03 pdb=" O ALA B 646 " 0.036 2.00e-02 2.50e+03 pdb=" N ASP B 647 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 43 " 0.026 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C SER D 43 " -0.092 2.00e-02 2.50e+03 pdb=" O SER D 43 " 0.034 2.00e-02 2.50e+03 pdb=" N GLY D 44 " 0.032 2.00e-02 2.50e+03 ... (remaining 3501 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 28 2.34 - 2.98: 10860 2.98 - 3.62: 31047 3.62 - 4.26: 55627 4.26 - 4.90: 84629 Nonbonded interactions: 182191 Sorted by model distance: nonbonded pdb=" OE2 GLU D 25 " pdb="CA CA D1101 " model vdw 1.705 2.510 nonbonded pdb=" OD1 ASP B 64 " pdb="CA CA B1102 " model vdw 1.754 2.510 nonbonded pdb=" OP1 DG F 9 " pdb="CA CA C1101 " model vdw 1.874 2.510 nonbonded pdb=" OP1 DG H 9 " pdb="CA CA D1101 " model vdw 2.036 2.510 nonbonded pdb=" OD1 ASP D 69 " pdb=" N SER D 70 " model vdw 2.074 2.520 ... (remaining 182186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 578 or resid 587 through 1029 or resid 1101 thro \ ugh 1102)) selection = (chain 'B' and (resid 2 through 411 or resid 422 through 1029 or resid 1101 thro \ ugh 1102)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 2 through 144 or resid 1101)) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.300 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 66.110 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 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 : 0.013 0.085 21681 Z= 0.806 Angle : 1.795 12.133 29771 Z= 1.309 Chirality : 0.119 0.746 3215 Planarity : 0.007 0.080 3504 Dihedral : 23.618 164.782 8433 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 1.31 % Allowed : 10.32 % Favored : 88.37 % Rotamer: Outliers : 13.97 % Allowed : 16.78 % Favored : 69.25 % Cbeta Deviations : 1.46 % Peptide Plane: Cis-proline : 2.25 % 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: -4.96 (0.13), residues: 2296 helix: -3.06 (0.12), residues: 1029 sheet: -3.38 (0.35), residues: 138 loop : -3.53 (0.14), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 39 HIS 0.012 0.002 HIS B 858 PHE 0.028 0.003 PHE A 326 TYR 0.037 0.003 TYR A 573 ARG 0.005 0.001 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 507 time to evaluate : 2.308 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: 274 outliers final: 32 residues processed: 713 average time/residue: 0.4447 time to fit residues: 443.3583 Evaluate side-chains 274 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 242 time to evaluate : 2.313 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 2 residues processed: 32 average time/residue: 0.2623 time to fit residues: 16.7112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 0.1980 chunk 186 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 216 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 212 HIS A 232 ASN A 237 GLN A 288 ASN A 325 HIS ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 464 ASN A 673 ASN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 116 GLN B 229 HIS B 232 ASN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 288 ASN B 448 ASN B 537 HIS B 563 ASN B 620 HIS B 763 GLN B 765 GLN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 857 HIS ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C 60 ASN C 72 GLN D 10 GLN D 59 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21681 Z= 0.235 Angle : 0.680 8.243 29771 Z= 0.369 Chirality : 0.042 0.173 3215 Planarity : 0.005 0.060 3504 Dihedral : 22.633 172.314 3790 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 3.11 % Allowed : 21.62 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -2.82 (0.16), residues: 2296 helix: -1.07 (0.15), residues: 1044 sheet: -2.45 (0.36), residues: 178 loop : -2.57 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 713 HIS 0.009 0.001 HIS A 325 PHE 0.022 0.002 PHE B 882 TYR 0.017 0.002 TYR A 814 ARG 0.007 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 265 time to evaluate : 2.406 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 outliers start: 61 outliers final: 22 residues processed: 311 average time/residue: 0.3938 time to fit residues: 182.1997 Evaluate side-chains 213 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 2.327 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2077 time to fit residues: 11.5281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 216 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 214 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 173 optimal weight: 0.0970 overall best weight: 2.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 HIS ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 ASN ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN C 72 GLN D 24 ASN D 34 GLN D 92 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21681 Z= 0.336 Angle : 0.672 10.299 29771 Z= 0.363 Chirality : 0.043 0.173 3215 Planarity : 0.005 0.081 3504 Dihedral : 21.877 178.691 3790 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.01 % Favored : 93.95 % Rotamer: Outliers : 3.11 % Allowed : 20.45 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.97 (0.17), residues: 2296 helix: -0.32 (0.16), residues: 1043 sheet: -1.60 (0.33), residues: 208 loop : -2.27 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 39 HIS 0.006 0.002 HIS B 275 PHE 0.033 0.002 PHE B 748 TYR 0.016 0.002 TYR B 262 ARG 0.014 0.001 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 211 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 29 residues processed: 254 average time/residue: 0.3777 time to fit residues: 145.0591 Evaluate side-chains 196 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 2.419 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2057 time to fit residues: 14.1509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 1.9990 chunk 162 optimal weight: 0.0470 chunk 112 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 217 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 205 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 271 GLN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 279 GLN B 362 GLN ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 HIS C 103 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21681 Z= 0.186 Angle : 0.564 10.062 29771 Z= 0.304 Chirality : 0.039 0.168 3215 Planarity : 0.004 0.050 3504 Dihedral : 21.546 178.018 3790 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 1.53 % Allowed : 22.08 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.44 (0.17), residues: 2296 helix: 0.14 (0.16), residues: 1049 sheet: -1.41 (0.34), residues: 203 loop : -2.02 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 888 HIS 0.005 0.001 HIS A 163 PHE 0.019 0.001 PHE D 140 TYR 0.011 0.001 TYR A 451 ARG 0.008 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 2.403 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 outliers start: 30 outliers final: 7 residues processed: 222 average time/residue: 0.3655 time to fit residues: 124.8839 Evaluate side-chains 183 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 176 time to evaluate : 2.527 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2682 time to fit residues: 6.4215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 94 optimal weight: 0.0060 chunk 196 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 206 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 362 GLN ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 ASN B 565 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 ASN B 858 HIS C 72 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21681 Z= 0.239 Angle : 0.578 9.139 29771 Z= 0.309 Chirality : 0.040 0.194 3215 Planarity : 0.004 0.043 3504 Dihedral : 21.420 178.418 3790 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 1.84 % Allowed : 21.98 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.13 (0.17), residues: 2296 helix: 0.37 (0.16), residues: 1051 sheet: -1.12 (0.34), residues: 210 loop : -1.86 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 39 HIS 0.006 0.001 HIS A 163 PHE 0.014 0.001 PHE C 139 TYR 0.011 0.001 TYR A 592 ARG 0.007 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 14 residues processed: 202 average time/residue: 0.3715 time to fit residues: 114.3955 Evaluate side-chains 178 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 2.339 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1943 time to fit residues: 8.1282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 230 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS B 362 GLN ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21681 Z= 0.244 Angle : 0.569 9.625 29771 Z= 0.303 Chirality : 0.039 0.180 3215 Planarity : 0.004 0.045 3504 Dihedral : 21.324 177.027 3790 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 1.58 % Allowed : 21.32 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.17), residues: 2296 helix: 0.50 (0.16), residues: 1053 sheet: -0.98 (0.34), residues: 216 loop : -1.74 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 888 HIS 0.007 0.001 HIS A 850 PHE 0.017 0.001 PHE B 642 TYR 0.019 0.001 TYR A 814 ARG 0.007 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 2.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 209 average time/residue: 0.3846 time to fit residues: 122.4439 Evaluate side-chains 181 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 2.376 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2036 time to fit residues: 7.7429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 131 optimal weight: 0.4980 chunk 168 optimal weight: 0.8980 chunk 130 optimal weight: 0.0000 chunk 193 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 HIS B 977 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21681 Z= 0.183 Angle : 0.560 10.807 29771 Z= 0.296 Chirality : 0.038 0.198 3215 Planarity : 0.004 0.068 3504 Dihedral : 21.187 177.635 3790 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.34 % Rotamer: Outliers : 1.12 % Allowed : 22.08 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2296 helix: 0.62 (0.16), residues: 1057 sheet: -0.79 (0.33), residues: 229 loop : -1.63 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 888 HIS 0.010 0.001 HIS A 850 PHE 0.014 0.001 PHE A 326 TYR 0.019 0.001 TYR A 305 ARG 0.015 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 198 average time/residue: 0.3745 time to fit residues: 113.7698 Evaluate side-chains 173 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 2.329 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2077 time to fit residues: 6.1244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 145 optimal weight: 0.0870 chunk 156 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 HIS A 537 HIS ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21681 Z= 0.173 Angle : 0.566 10.802 29771 Z= 0.298 Chirality : 0.038 0.197 3215 Planarity : 0.004 0.044 3504 Dihedral : 21.086 177.308 3790 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 0.61 % Allowed : 22.74 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2296 helix: 0.71 (0.17), residues: 1052 sheet: -0.70 (0.36), residues: 204 loop : -1.58 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 499 HIS 0.010 0.001 HIS A 850 PHE 0.013 0.001 PHE D 32 TYR 0.018 0.001 TYR B 305 ARG 0.011 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 184 average time/residue: 0.3733 time to fit residues: 105.2594 Evaluate side-chains 179 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 172 time to evaluate : 2.463 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1934 time to fit residues: 5.7539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 6.9990 chunk 219 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 213 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 93 optimal weight: 0.0050 chunk 167 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.6808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21681 Z= 0.206 Angle : 0.583 13.791 29771 Z= 0.303 Chirality : 0.039 0.189 3215 Planarity : 0.004 0.045 3504 Dihedral : 21.024 176.879 3790 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 0.41 % Allowed : 23.71 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.18), residues: 2296 helix: 0.72 (0.17), residues: 1052 sheet: -0.68 (0.35), residues: 214 loop : -1.55 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 888 HIS 0.009 0.001 HIS A 850 PHE 0.014 0.001 PHE D 32 TYR 0.019 0.001 TYR B 305 ARG 0.014 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 180 average time/residue: 0.3798 time to fit residues: 104.1753 Evaluate side-chains 171 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 2.557 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2422 time to fit residues: 4.0214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 145 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN C 34 GLN C 92 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.6930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21681 Z= 0.189 Angle : 0.591 13.769 29771 Z= 0.306 Chirality : 0.039 0.240 3215 Planarity : 0.004 0.045 3504 Dihedral : 20.983 176.908 3790 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 0.25 % Allowed : 24.17 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2296 helix: 0.74 (0.17), residues: 1049 sheet: -0.56 (0.33), residues: 236 loop : -1.52 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 39 HIS 0.010 0.001 HIS A 850 PHE 0.034 0.001 PHE A 326 TYR 0.019 0.001 TYR B 305 ARG 0.016 0.000 ARG C 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 180 average time/residue: 0.3932 time to fit residues: 107.9757 Evaluate side-chains 172 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 168 time to evaluate : 2.559 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2551 time to fit residues: 5.3478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 448 ASN C 92 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.088750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.070529 restraints weight = 65729.059| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.88 r_work: 0.3051 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.7040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21681 Z= 0.177 Angle : 0.577 11.365 29771 Z= 0.298 Chirality : 0.038 0.189 3215 Planarity : 0.004 0.046 3504 Dihedral : 20.949 176.776 3790 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 0.15 % Allowed : 24.12 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2296 helix: 0.79 (0.17), residues: 1052 sheet: -0.41 (0.33), residues: 236 loop : -1.48 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 888 HIS 0.010 0.001 HIS A 850 PHE 0.016 0.001 PHE D 32 TYR 0.019 0.001 TYR B 305 ARG 0.015 0.000 ARG C 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4598.01 seconds wall clock time: 84 minutes 41.77 seconds (5081.77 seconds total)