Starting phenix.real_space_refine on Thu Feb 22 21:27:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gft_29984/02_2024/8gft_29984_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gft_29984/02_2024/8gft_29984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gft_29984/02_2024/8gft_29984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gft_29984/02_2024/8gft_29984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gft_29984/02_2024/8gft_29984_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gft_29984/02_2024/8gft_29984_trim_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 9 Type Number sf(0) Gaussians K 2 8.98 5 Mn 2 7.51 5 P 6 5.49 5 Mg 2 5.21 5 S 93 5.16 5 C 11253 2.51 5 N 3013 2.21 5 O 3426 1.98 5 H 17682 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35479 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 10411 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain breaks: 1 Chain: "B" Number of atoms: 10284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 10284 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 17, 'TRANS': 615} Chain breaks: 1 Chain: "C" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 4303 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 4, 'TRANS': 254} Chain: "D" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3101 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "E" Number of atoms: 7316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 7316 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 16, 'TRANS': 442} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.91, per 1000 atoms: 0.42 Number of scatterers: 35479 At special positions: 0 Unit cell: (149.465, 156.145, 156.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Mn 2 24.99 K 2 19.00 S 93 16.00 P 6 15.00 Mg 2 11.99 O 3426 8.00 N 3013 7.00 C 11253 6.00 H 17682 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: 29.63 Conformation dependent library (CDL) restraints added in 3.6 seconds 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 13 sheets defined 45.8% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.46 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 removed outlier: 4.064A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 58 removed outlier: 3.598A pdb=" N LEU A 43 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 44 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 58 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 132 through 139 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 398 through 421 Processing helix chain 'A' and resid 423 through 443 removed outlier: 6.031A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 454 removed outlier: 4.335A pdb=" N SER A 452 " --> pdb=" O ARG A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 498 through 505 removed outlier: 5.078A pdb=" N ARG A 502 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 504 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 522 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 561 through 570 Processing helix chain 'A' and resid 600 through 608 removed outlier: 3.605A pdb=" N ARG A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 620 removed outlier: 4.545A pdb=" N GLY A 618 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR A 619 " --> pdb=" O THR A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 644 Processing helix chain 'A' and resid 649 through 665 Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 38 through 60 removed outlier: 3.606A pdb=" N GLU B 43 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 44 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 45 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 53 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS B 54 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER B 59 " --> pdb=" O ARG B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.810A pdb=" N LEU B 66 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER B 68 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 102 Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'B' and resid 133 through 139 Processing helix chain 'B' and resid 188 through 194 removed outlier: 3.966A pdb=" N THR B 191 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU B 192 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 193 " --> pdb=" O GLN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 398 through 421 removed outlier: 3.510A pdb=" N LYS B 406 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 409 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 410 " --> pdb=" O ASN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 443 removed outlier: 6.297A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 removed outlier: 4.155A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 474 Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 498 through 505 removed outlier: 5.172A pdb=" N ARG B 502 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 504 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 3.620A pdb=" N CYS B 521 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL B 522 " --> pdb=" O GLU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 570 removed outlier: 5.341A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 574 No H-bonds generated for 'chain 'B' and resid 572 through 574' Processing helix chain 'B' and resid 600 through 608 removed outlier: 3.550A pdb=" N ARG B 604 " --> pdb=" O ALA B 600 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 620 No H-bonds generated for 'chain 'B' and resid 617 through 620' Processing helix chain 'B' and resid 633 through 644 Processing helix chain 'B' and resid 649 through 665 Processing helix chain 'B' and resid 673 through 688 Processing helix chain 'C' and resid 5 through 7 No H-bonds generated for 'chain 'C' and resid 5 through 7' Processing helix chain 'C' and resid 25 through 72 removed outlier: 3.617A pdb=" N ARG C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 111 removed outlier: 5.497A pdb=" N GLU C 82 " --> pdb=" O LYS C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 150 removed outlier: 3.550A pdb=" N GLU C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 160 removed outlier: 5.451A pdb=" N LYS C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 removed outlier: 3.825A pdb=" N LEU C 175 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 184 through 192 removed outlier: 3.592A pdb=" N VAL C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 203 through 225 removed outlier: 3.682A pdb=" N HIS C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 212 " --> pdb=" O GLN C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 235 through 242 Processing helix chain 'C' and resid 249 through 258 removed outlier: 3.879A pdb=" N ASN C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU C 256 " --> pdb=" O ASN C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 434 Processing helix chain 'D' and resid 442 through 461 Processing helix chain 'D' and resid 478 through 480 No H-bonds generated for 'chain 'D' and resid 478 through 480' Processing helix chain 'D' and resid 514 through 517 No H-bonds generated for 'chain 'D' and resid 514 through 517' Processing helix chain 'D' and resid 527 through 543 Processing helix chain 'D' and resid 554 through 562 Processing helix chain 'D' and resid 570 through 572 No H-bonds generated for 'chain 'D' and resid 570 through 572' Processing helix chain 'D' and resid 579 through 588 Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 599 through 610 Processing helix chain 'E' and resid 24 through 40 removed outlier: 4.068A pdb=" N GLU E 29 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS E 32 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 62 through 74 Processing helix chain 'E' and resid 78 through 91 Processing helix chain 'E' and resid 96 through 108 Processing helix chain 'E' and resid 112 through 125 Processing helix chain 'E' and resid 132 through 152 Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'E' and resid 206 through 220 Processing helix chain 'E' and resid 248 through 256 Processing helix chain 'E' and resid 279 through 292 removed outlier: 3.653A pdb=" N LEU E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 312 Processing helix chain 'E' and resid 315 through 322 Processing helix chain 'E' and resid 325 through 337 removed outlier: 3.511A pdb=" N VAL E 334 " --> pdb=" O PHE E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 367 Processing helix chain 'E' and resid 380 through 386 Processing helix chain 'E' and resid 408 through 418 removed outlier: 3.663A pdb=" N ALA E 413 " --> pdb=" O ASP E 409 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU E 417 " --> pdb=" O ALA E 413 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN E 418 " --> pdb=" O PHE E 414 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 277 through 279 removed outlier: 3.893A pdb=" N ILE A 277 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 215 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 73 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TYR A 216 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 75 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 220 through 222 Processing sheet with id= C, first strand: chain 'A' and resid 360 through 363 removed outlier: 7.064A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY A 379 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N TYR A 356 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 381 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 456 through 458 Processing sheet with id= E, first strand: chain 'A' and resid 532 through 535 Processing sheet with id= F, first strand: chain 'A' and resid 577 through 580 removed outlier: 4.395A pdb=" N LYS A 577 " --> pdb=" O LYS A 624 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 277 through 279 removed outlier: 6.783A pdb=" N ILE B 74 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR B 217 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE B 76 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 84 " --> pdb=" O ASN B 79 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B 143 " --> pdb=" O HIS B 185 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 360 through 363 removed outlier: 7.055A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LYS B 354 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY B 379 " --> pdb=" O LYS B 354 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N TYR B 356 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL B 381 " --> pdb=" O TYR B 356 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 532 through 535 Processing sheet with id= J, first strand: chain 'B' and resid 577 through 580 removed outlier: 4.281A pdb=" N LYS B 577 " --> pdb=" O LYS B 624 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 474 through 476 Processing sheet with id= L, first strand: chain 'E' and resid 226 through 229 removed outlier: 6.998A pdb=" N ALA E 341 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N THR E 229 " --> pdb=" O ALA E 341 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS E 343 " --> pdb=" O THR E 229 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR E 422 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 236 through 239 736 hydrogen bonds defined for protein. 1776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.27 Time building geometry restraints manager: 30.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.93: 14 0.93 - 1.16: 17639 1.16 - 1.40: 6586 1.40 - 1.63: 11404 1.63 - 1.86: 155 Bond restraints: 35798 Sorted by residual: bond pdb=" CB SER B 490 " pdb=" OG SER B 490 " ideal model delta sigma weight residual 1.417 1.099 0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" CE1 HIS E 205 " pdb=" NE2 HIS E 205 " ideal model delta sigma weight residual 1.321 1.193 0.128 1.00e-02 1.00e+04 1.65e+02 bond pdb=" CZ ARG B 612 " pdb=" NH2 ARG B 612 " ideal model delta sigma weight residual 1.330 1.177 0.153 1.30e-02 5.92e+03 1.39e+02 bond pdb=" N GLY A 127 " pdb=" CA GLY A 127 " ideal model delta sigma weight residual 1.446 1.323 0.123 1.26e-02 6.30e+03 9.51e+01 bond pdb=" N TYR C 189 " pdb=" CA TYR C 189 " ideal model delta sigma weight residual 1.457 1.357 0.100 1.17e-02 7.31e+03 7.28e+01 ... (remaining 35793 not shown) Histogram of bond angle deviations from ideal: 72.67 - 86.81: 7 86.81 - 100.96: 103 100.96 - 115.11: 43551 115.11 - 129.26: 21018 129.26 - 143.40: 100 Bond angle restraints: 64779 Sorted by residual: angle pdb=" PB ATP B 802 " pdb=" O3B ATP B 802 " pdb=" PG ATP B 802 " ideal model delta sigma weight residual 139.87 123.03 16.84 1.00e+00 1.00e+00 2.84e+02 angle pdb=" CA VAL E 402 " pdb=" CB VAL E 402 " pdb=" CG1 VAL E 402 " ideal model delta sigma weight residual 110.40 138.06 -27.66 1.70e+00 3.46e-01 2.65e+02 angle pdb=" PA ATP B 802 " pdb=" O3A ATP B 802 " pdb=" PB ATP B 802 " ideal model delta sigma weight residual 136.83 121.37 15.46 1.00e+00 1.00e+00 2.39e+02 angle pdb=" N TYR B 212 " pdb=" CA TYR B 212 " pdb=" HA TYR B 212 " ideal model delta sigma weight residual 110.00 72.67 37.33 3.00e+00 1.11e-01 1.55e+02 angle pdb=" C LYS B 435 " pdb=" N ASN B 436 " pdb=" CA ASN B 436 " ideal model delta sigma weight residual 120.65 136.98 -16.33 1.32e+00 5.74e-01 1.53e+02 ... (remaining 64774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.22: 16211 30.22 - 60.44: 428 60.44 - 90.66: 57 90.66 - 120.87: 2 120.87 - 151.09: 1 Dihedral angle restraints: 16699 sinusoidal: 9208 harmonic: 7491 Sorted by residual: dihedral pdb=" C CYS E 382 " pdb=" N CYS E 382 " pdb=" CA CYS E 382 " pdb=" CB CYS E 382 " ideal model delta harmonic sigma weight residual -122.60 -141.56 18.96 0 2.50e+00 1.60e-01 5.75e+01 dihedral pdb=" N CYS E 382 " pdb=" C CYS E 382 " pdb=" CA CYS E 382 " pdb=" CB CYS E 382 " ideal model delta harmonic sigma weight residual 122.80 140.73 -17.93 0 2.50e+00 1.60e-01 5.14e+01 dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 91.09 -151.09 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 16696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 2592 0.287 - 0.575: 53 0.575 - 0.862: 5 0.862 - 1.149: 1 1.149 - 1.437: 1 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CB VAL E 402 " pdb=" CA VAL E 402 " pdb=" CG1 VAL E 402 " pdb=" CG2 VAL E 402 " both_signs ideal model delta sigma weight residual False -2.63 -1.19 -1.44 2.00e-01 2.50e+01 5.16e+01 chirality pdb=" CA CYS E 382 " pdb=" N CYS E 382 " pdb=" C CYS E 382 " pdb=" CB CYS E 382 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA ASP E 155 " pdb=" N ASP E 155 " pdb=" C ASP E 155 " pdb=" CB ASP E 155 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 2649 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 446 " -0.359 2.00e-02 2.50e+03 1.37e-01 5.62e+02 pdb=" CG PHE E 446 " 0.120 2.00e-02 2.50e+03 pdb=" CD1 PHE E 446 " 0.119 2.00e-02 2.50e+03 pdb=" CD2 PHE E 446 " 0.133 2.00e-02 2.50e+03 pdb=" CE1 PHE E 446 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 PHE E 446 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE E 446 " -0.052 2.00e-02 2.50e+03 pdb=" HD1 PHE E 446 " 0.073 2.00e-02 2.50e+03 pdb=" HD2 PHE E 446 " 0.082 2.00e-02 2.50e+03 pdb=" HE1 PHE E 446 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE E 446 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE E 446 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 596 " 0.180 2.00e-02 2.50e+03 1.19e-01 4.27e+02 pdb=" CG TYR A 596 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR A 596 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR A 596 " -0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR A 596 " -0.142 2.00e-02 2.50e+03 pdb=" CE2 TYR A 596 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 596 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 596 " 0.160 2.00e-02 2.50e+03 pdb=" HD1 TYR A 596 " 0.150 2.00e-02 2.50e+03 pdb=" HD2 TYR A 596 " -0.155 2.00e-02 2.50e+03 pdb=" HE1 TYR A 596 " -0.127 2.00e-02 2.50e+03 pdb=" HE2 TYR A 596 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 619 " 0.241 2.00e-02 2.50e+03 9.96e-02 2.98e+02 pdb=" CG TYR A 619 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR A 619 " -0.100 2.00e-02 2.50e+03 pdb=" CD2 TYR A 619 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR A 619 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 619 " -0.044 2.00e-02 2.50e+03 pdb=" CZ TYR A 619 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 619 " 0.172 2.00e-02 2.50e+03 pdb=" HD1 TYR A 619 " -0.084 2.00e-02 2.50e+03 pdb=" HD2 TYR A 619 " -0.014 2.00e-02 2.50e+03 pdb=" HE1 TYR A 619 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR A 619 " -0.061 2.00e-02 2.50e+03 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.35: 6476 2.35 - 3.05: 102406 3.05 - 3.75: 125809 3.75 - 4.44: 191500 4.44 - 5.14: 294515 Nonbonded interactions: 720706 Sorted by model distance: nonbonded pdb=" OD1 ASP E 307 " pdb=" HH TYR E 328 " model vdw 1.655 1.850 nonbonded pdb=" HG SER B 68 " pdb=" OD1 ASN B 151 " model vdw 1.655 1.850 nonbonded pdb=" OD1 ASP B 444 " pdb=" HG1 THR B 446 " model vdw 1.660 1.850 nonbonded pdb=" HG SER A 581 " pdb=" OE1 GLU A 627 " model vdw 1.660 1.850 nonbonded pdb=" HH TYR E 422 " pdb=" O LEU E 469 " model vdw 1.660 1.850 ... (remaining 720701 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 10 through 220 or resid 273 through 691 or resid 803)) selection = (chain 'B' and (resid 11 through 691 or resid 803)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.570 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: 0.520 Extract box with map and model: 8.790 Check model and map are aligned: 0.540 Set scattering table: 0.340 Process input model: 115.490 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.017 0.318 18116 Z= 1.095 Angle : 1.959 27.660 24370 Z= 1.329 Chirality : 0.119 1.437 2652 Planarity : 0.016 0.217 3127 Dihedral : 13.211 151.092 6995 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.17), residues: 2162 helix: -0.78 (0.14), residues: 959 sheet: 0.33 (0.32), residues: 256 loop : -0.24 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.121 0.022 TRP C 114 HIS 0.012 0.003 HIS D 432 PHE 0.236 0.013 PHE E 446 TYR 0.215 0.021 TYR A 619 ARG 0.033 0.001 ARG B 449 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 602 MET cc_start: 0.9059 (ttt) cc_final: 0.8855 (tpp) REVERT: A 606 MET cc_start: 0.9570 (mmp) cc_final: 0.9327 (mmp) REVERT: C 216 MET cc_start: 0.9383 (mmm) cc_final: 0.9002 (tpp) REVERT: D 553 ASN cc_start: 0.9250 (t0) cc_final: 0.8580 (t0) REVERT: D 555 ASP cc_start: 0.8918 (m-30) cc_final: 0.8499 (p0) REVERT: E 141 LYS cc_start: 0.9209 (mtmt) cc_final: 0.8985 (tptp) REVERT: E 170 MET cc_start: 0.8427 (mmp) cc_final: 0.8124 (mpp) REVERT: E 213 LEU cc_start: 0.9126 (mt) cc_final: 0.8923 (mt) REVERT: E 327 MET cc_start: 0.9465 (tpt) cc_final: 0.8930 (mmt) REVERT: E 331 PHE cc_start: 0.9465 (m-80) cc_final: 0.9204 (t80) REVERT: E 332 SER cc_start: 0.9461 (t) cc_final: 0.9203 (p) REVERT: E 333 GLU cc_start: 0.9268 (tp30) cc_final: 0.9022 (tp30) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.8157 time to fit residues: 180.3871 Evaluate side-chains 111 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 18116 Z= 0.305 Angle : 0.684 9.849 24370 Z= 0.384 Chirality : 0.049 1.283 2652 Planarity : 0.005 0.052 3127 Dihedral : 8.406 117.750 2416 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.46 % Allowed : 3.22 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.43 (0.17), residues: 2162 helix: 0.00 (0.16), residues: 963 sheet: -0.32 (0.30), residues: 275 loop : -0.40 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 193 HIS 0.007 0.002 HIS E 296 PHE 0.036 0.002 PHE E 446 TYR 0.018 0.002 TYR E 80 ARG 0.006 0.001 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 MET cc_start: 0.9569 (mmp) cc_final: 0.9367 (mmm) REVERT: B 567 MET cc_start: 0.9083 (mtp) cc_final: 0.8870 (mtp) REVERT: C 216 MET cc_start: 0.9407 (mmm) cc_final: 0.9077 (tpp) REVERT: D 409 MET cc_start: 0.7551 (ppp) cc_final: 0.7256 (tmm) REVERT: D 456 MET cc_start: 0.9212 (mmm) cc_final: 0.8899 (mmm) REVERT: E 170 MET cc_start: 0.8550 (mmp) cc_final: 0.8317 (mpp) REVERT: E 233 GLU cc_start: 0.9637 (mp0) cc_final: 0.9412 (mm-30) REVERT: E 309 MET cc_start: 0.6004 (mmt) cc_final: 0.5398 (tmm) outliers start: 9 outliers final: 4 residues processed: 118 average time/residue: 0.7422 time to fit residues: 132.7427 Evaluate side-chains 105 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 573 LYS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 0.0870 chunk 60 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 53 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 chunk 211 optimal weight: 40.0000 chunk 174 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 156 optimal weight: 7.9990 overall best weight: 4.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 632 HIS D 422 GLN D 460 HIS E 252 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18116 Z= 0.271 Angle : 0.588 9.689 24370 Z= 0.327 Chirality : 0.047 1.317 2652 Planarity : 0.003 0.032 3127 Dihedral : 7.382 108.303 2416 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.82 % Allowed : 3.93 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2162 helix: 0.28 (0.16), residues: 968 sheet: -0.46 (0.31), residues: 279 loop : -0.48 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 158 HIS 0.007 0.001 HIS E 296 PHE 0.021 0.001 PHE E 297 TYR 0.014 0.002 TYR A 619 ARG 0.008 0.001 ARG E 395 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 MET cc_start: 0.9417 (mtm) cc_final: 0.9033 (mpp) REVERT: A 602 MET cc_start: 0.8989 (tpp) cc_final: 0.8616 (tpp) REVERT: B 567 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8866 (mtp) REVERT: C 216 MET cc_start: 0.9420 (mmm) cc_final: 0.9148 (tpp) REVERT: D 456 MET cc_start: 0.9252 (mmm) cc_final: 0.8927 (mmt) REVERT: E 170 MET cc_start: 0.8557 (mmp) cc_final: 0.8350 (mpp) REVERT: E 233 GLU cc_start: 0.9637 (mp0) cc_final: 0.9385 (mm-30) REVERT: E 309 MET cc_start: 0.6113 (mmt) cc_final: 0.5542 (tmm) outliers start: 16 outliers final: 9 residues processed: 114 average time/residue: 0.8010 time to fit residues: 137.3620 Evaluate side-chains 107 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 573 LYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 208 CYS Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 308 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 93 optimal weight: 0.3980 chunk 131 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS E 252 ASN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18116 Z= 0.311 Angle : 0.580 10.351 24370 Z= 0.319 Chirality : 0.048 1.390 2652 Planarity : 0.003 0.036 3127 Dihedral : 7.154 93.805 2416 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.82 % Allowed : 4.91 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.36 (0.17), residues: 2162 helix: 0.39 (0.17), residues: 970 sheet: -0.65 (0.31), residues: 263 loop : -0.66 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 158 HIS 0.008 0.001 HIS D 466 PHE 0.022 0.001 PHE E 335 TYR 0.015 0.001 TYR A 134 ARG 0.004 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 2.987 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: 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 394 MET cc_start: 0.8400 (ptm) cc_final: 0.8052 (ptm) REVERT: A 602 MET cc_start: 0.8997 (tpp) cc_final: 0.8582 (tpp) REVERT: A 606 MET cc_start: 0.9325 (mmm) cc_final: 0.9010 (mmt) REVERT: B 567 MET cc_start: 0.9113 (mtp) cc_final: 0.8887 (mtp) REVERT: C 249 MET cc_start: 0.7511 (tpt) cc_final: 0.7257 (tpt) REVERT: D 456 MET cc_start: 0.9300 (mmm) cc_final: 0.9000 (mmt) REVERT: E 233 GLU cc_start: 0.9667 (mp0) cc_final: 0.9417 (mm-30) REVERT: E 316 GLU cc_start: 0.8882 (tp30) cc_final: 0.8463 (tp30) outliers start: 16 outliers final: 12 residues processed: 117 average time/residue: 0.6890 time to fit residues: 123.7900 Evaluate side-chains 113 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 308 ASN Chi-restraints excluded: chain E residue 382 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 30.0000 chunk 117 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN E 196 GLN E 252 ASN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18116 Z= 0.157 Angle : 0.504 10.295 24370 Z= 0.274 Chirality : 0.047 1.392 2652 Planarity : 0.003 0.027 3127 Dihedral : 6.752 109.427 2416 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.61 % Allowed : 5.16 % Favored : 94.23 % 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: 0.04 (0.18), residues: 2162 helix: 0.80 (0.17), residues: 970 sheet: -0.57 (0.31), residues: 263 loop : -0.52 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 157 HIS 0.006 0.001 HIS E 296 PHE 0.015 0.001 PHE E 190 TYR 0.009 0.001 TYR A 457 ARG 0.003 0.000 ARG E 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8347 (ptm) cc_final: 0.7995 (ptm) REVERT: A 602 MET cc_start: 0.9014 (tpp) cc_final: 0.8736 (tpp) REVERT: A 606 MET cc_start: 0.9339 (mmm) cc_final: 0.9076 (mmt) REVERT: B 567 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8886 (mtp) REVERT: D 456 MET cc_start: 0.9313 (mmm) cc_final: 0.8997 (mmt) REVERT: E 170 MET cc_start: 0.8497 (mmp) cc_final: 0.8275 (mpp) REVERT: E 233 GLU cc_start: 0.9647 (mp0) cc_final: 0.9378 (mm-30) REVERT: E 309 MET cc_start: 0.6183 (mmt) cc_final: 0.5583 (tmm) REVERT: E 310 ASN cc_start: 0.7237 (m110) cc_final: 0.6809 (m110) REVERT: E 316 GLU cc_start: 0.8875 (tp30) cc_final: 0.8464 (tp30) REVERT: E 331 PHE cc_start: 0.9222 (t80) cc_final: 0.8989 (t80) REVERT: E 351 MET cc_start: 0.5374 (ptp) cc_final: 0.4350 (pmm) outliers start: 12 outliers final: 7 residues processed: 115 average time/residue: 0.6988 time to fit residues: 123.0442 Evaluate side-chains 111 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 382 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 HIS E 252 ASN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18116 Z= 0.265 Angle : 0.527 10.418 24370 Z= 0.289 Chirality : 0.047 1.402 2652 Planarity : 0.003 0.031 3127 Dihedral : 6.800 113.393 2416 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.72 % Allowed : 5.52 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2162 helix: 0.78 (0.17), residues: 972 sheet: -0.61 (0.32), residues: 258 loop : -0.64 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 158 HIS 0.006 0.001 HIS E 296 PHE 0.017 0.001 PHE E 190 TYR 0.013 0.001 TYR A 134 ARG 0.006 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8381 (ptm) cc_final: 0.8173 (ptm) REVERT: A 602 MET cc_start: 0.9066 (tpp) cc_final: 0.8643 (tpp) REVERT: A 606 MET cc_start: 0.9362 (mmm) cc_final: 0.9040 (mmt) REVERT: B 115 MET cc_start: 0.8681 (tmm) cc_final: 0.8471 (tmm) REVERT: B 567 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8753 (mtp) REVERT: C 216 MET cc_start: 0.9476 (mmm) cc_final: 0.9205 (tpp) REVERT: D 456 MET cc_start: 0.9333 (mmm) cc_final: 0.9017 (mmt) REVERT: E 233 GLU cc_start: 0.9655 (mp0) cc_final: 0.9380 (mm-30) REVERT: E 351 MET cc_start: 0.5934 (ptp) cc_final: 0.4723 (pmm) outliers start: 14 outliers final: 10 residues processed: 112 average time/residue: 0.6865 time to fit residues: 119.6767 Evaluate side-chains 111 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 382 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 10.0000 chunk 23 optimal weight: 0.1980 chunk 118 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 126 optimal weight: 0.0170 chunk 95 optimal weight: 4.9990 overall best weight: 3.0424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18116 Z= 0.189 Angle : 0.495 10.437 24370 Z= 0.269 Chirality : 0.047 1.407 2652 Planarity : 0.003 0.027 3127 Dihedral : 6.595 113.309 2416 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.77 % Allowed : 5.52 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 2162 helix: 0.90 (0.17), residues: 971 sheet: -0.58 (0.32), residues: 258 loop : -0.53 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 157 HIS 0.005 0.001 HIS E 296 PHE 0.017 0.001 PHE E 190 TYR 0.010 0.001 TYR A 192 ARG 0.003 0.000 ARG E 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8362 (ptm) cc_final: 0.8159 (ptm) REVERT: A 602 MET cc_start: 0.9082 (tpp) cc_final: 0.8592 (tpp) REVERT: B 115 MET cc_start: 0.8670 (tmm) cc_final: 0.8457 (tmm) REVERT: B 567 MET cc_start: 0.9120 (mtp) cc_final: 0.8756 (mtp) REVERT: C 57 CYS cc_start: 0.4198 (OUTLIER) cc_final: 0.3454 (t) REVERT: C 216 MET cc_start: 0.9461 (mmm) cc_final: 0.9187 (tpp) REVERT: D 456 MET cc_start: 0.9349 (mmm) cc_final: 0.9021 (mmt) REVERT: E 233 GLU cc_start: 0.9659 (mp0) cc_final: 0.9385 (mm-30) REVERT: E 316 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: E 351 MET cc_start: 0.5865 (ptp) cc_final: 0.4553 (pmm) outliers start: 15 outliers final: 12 residues processed: 109 average time/residue: 0.6783 time to fit residues: 115.2360 Evaluate side-chains 109 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 432 HIS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 382 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 188 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 18116 Z= 0.341 Angle : 0.558 10.458 24370 Z= 0.306 Chirality : 0.047 1.394 2652 Planarity : 0.003 0.033 3127 Dihedral : 6.771 115.517 2416 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.92 % Allowed : 5.83 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2162 helix: 0.68 (0.17), residues: 970 sheet: -0.75 (0.32), residues: 264 loop : -0.74 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 157 HIS 0.008 0.001 HIS E 296 PHE 0.017 0.001 PHE E 190 TYR 0.016 0.001 TYR A 134 ARG 0.005 0.001 ARG E 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.9074 (tpp) cc_final: 0.8702 (tpp) REVERT: B 26 MET cc_start: 0.9286 (tpp) cc_final: 0.9049 (mmm) REVERT: B 115 MET cc_start: 0.8727 (tmm) cc_final: 0.8469 (tmm) REVERT: B 567 MET cc_start: 0.9150 (mtp) cc_final: 0.8787 (mtp) REVERT: D 456 MET cc_start: 0.9358 (mmm) cc_final: 0.9039 (mmt) REVERT: E 170 MET cc_start: 0.8620 (mmp) cc_final: 0.8407 (mtm) REVERT: E 233 GLU cc_start: 0.9687 (mp0) cc_final: 0.9415 (mm-30) outliers start: 18 outliers final: 17 residues processed: 113 average time/residue: 0.6651 time to fit residues: 117.9535 Evaluate side-chains 115 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 432 HIS Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 382 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 151 optimal weight: 0.3980 chunk 59 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18116 Z= 0.177 Angle : 0.498 10.464 24370 Z= 0.269 Chirality : 0.046 1.405 2652 Planarity : 0.003 0.026 3127 Dihedral : 6.558 114.321 2416 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.77 % Allowed : 6.29 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2162 helix: 0.95 (0.17), residues: 970 sheet: -0.65 (0.32), residues: 258 loop : -0.60 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 157 HIS 0.005 0.001 HIS E 296 PHE 0.041 0.001 PHE E 335 TYR 0.014 0.001 TYR E 210 ARG 0.003 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.9075 (tpp) cc_final: 0.8630 (tpp) REVERT: A 613 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8686 (t0) REVERT: B 115 MET cc_start: 0.8703 (tmm) cc_final: 0.8495 (tmm) REVERT: B 567 MET cc_start: 0.9152 (mtp) cc_final: 0.8798 (mtp) REVERT: C 57 CYS cc_start: 0.4102 (OUTLIER) cc_final: 0.3344 (t) REVERT: C 216 MET cc_start: 0.9452 (mmm) cc_final: 0.9188 (tpp) REVERT: D 456 MET cc_start: 0.9369 (mmm) cc_final: 0.9035 (mmt) REVERT: E 170 MET cc_start: 0.8599 (mmp) cc_final: 0.8376 (mtm) REVERT: E 233 GLU cc_start: 0.9668 (mp0) cc_final: 0.9385 (mm-30) REVERT: E 351 MET cc_start: 0.6395 (ptp) cc_final: 0.5026 (pmm) outliers start: 15 outliers final: 13 residues processed: 111 average time/residue: 0.7172 time to fit residues: 123.4364 Evaluate side-chains 112 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 432 HIS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 213 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 170 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 104 optimal weight: 0.4980 chunk 135 optimal weight: 3.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18116 Z= 0.215 Angle : 0.507 10.463 24370 Z= 0.274 Chirality : 0.046 1.403 2652 Planarity : 0.003 0.026 3127 Dihedral : 6.533 117.095 2416 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.87 % Allowed : 6.08 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2162 helix: 0.97 (0.17), residues: 970 sheet: -0.71 (0.32), residues: 258 loop : -0.59 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 158 HIS 0.006 0.001 HIS E 296 PHE 0.016 0.001 PHE E 190 TYR 0.011 0.001 TYR A 134 ARG 0.003 0.000 ARG E 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 2.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.9087 (tpp) cc_final: 0.8668 (tpp) REVERT: A 613 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8706 (t0) REVERT: B 115 MET cc_start: 0.8715 (tmm) cc_final: 0.8455 (tmm) REVERT: B 567 MET cc_start: 0.9141 (mtp) cc_final: 0.8664 (mtp) REVERT: C 57 CYS cc_start: 0.4161 (OUTLIER) cc_final: 0.3463 (t) REVERT: C 216 MET cc_start: 0.9473 (mmm) cc_final: 0.9213 (tpp) REVERT: D 456 MET cc_start: 0.9374 (mmm) cc_final: 0.9045 (mmt) REVERT: E 170 MET cc_start: 0.8604 (mmp) cc_final: 0.8385 (mtm) REVERT: E 233 GLU cc_start: 0.9675 (mp0) cc_final: 0.9391 (mm-30) REVERT: E 351 MET cc_start: 0.6603 (ptp) cc_final: 0.5239 (pmm) outliers start: 17 outliers final: 15 residues processed: 111 average time/residue: 0.6736 time to fit residues: 115.3979 Evaluate side-chains 115 residues out of total 1957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 432 HIS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 382 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 149 optimal weight: 0.2980 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.059611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.043050 restraints weight = 431753.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.044323 restraints weight = 182746.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.045130 restraints weight = 111628.129| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 18116 Z= 0.302 Angle : 0.546 10.448 24370 Z= 0.297 Chirality : 0.047 1.387 2652 Planarity : 0.003 0.033 3127 Dihedral : 6.657 117.549 2416 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.02 % Allowed : 6.13 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2162 helix: 0.80 (0.17), residues: 969 sheet: -0.86 (0.32), residues: 253 loop : -0.79 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 158 HIS 0.008 0.001 HIS E 296 PHE 0.016 0.001 PHE E 190 TYR 0.015 0.001 TYR A 134 ARG 0.004 0.001 ARG E 395 =============================================================================== Job complete usr+sys time: 5636.55 seconds wall clock time: 101 minutes 46.13 seconds (6106.13 seconds total)