Starting phenix.real_space_refine on Mon Mar 25 18:13:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzw_27808/03_2024/8dzw_27808.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzw_27808/03_2024/8dzw_27808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzw_27808/03_2024/8dzw_27808.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzw_27808/03_2024/8dzw_27808.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzw_27808/03_2024/8dzw_27808.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzw_27808/03_2024/8dzw_27808.pdb" } resolution = 2.46 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= 0.003 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10291 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 105 5.16 5 C 12723 2.51 5 N 3378 2.21 5 O 3996 1.98 5 H 20048 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 295": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "N GLU 125": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 85": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40250 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 6917 Classifications: {'peptide': 444} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 431} Chain breaks: 2 Chain: "B" Number of atoms: 6916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 6916 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 12, 'TRANS': 431} Chain breaks: 2 Chain: "C" Number of atoms: 6917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 6917 Classifications: {'peptide': 444} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 431} Chain breaks: 2 Chain: "L" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3159 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 199} Chain: "H" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3341 Classifications: {'peptide': 225} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "M" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3159 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 199} Chain: "I" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3341 Classifications: {'peptide': 225} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "N" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3159 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 199} Chain: "J" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3341 Classifications: {'peptide': 225} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Time building chain proxies: 17.49, per 1000 atoms: 0.43 Number of scatterers: 40250 At special positions: 0 Unit cell: (189.81, 208.68, 126.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 O 3996 8.00 N 3378 7.00 C 12723 6.00 H 20048 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.00 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 290 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.04 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.04 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.04 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=1.97 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.04 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS L 212 " - pdb=" SG CYS H 216 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=1.99 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 135 " - pdb=" SG CYS M 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 212 " - pdb=" SG CYS I 216 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 196 " distance=2.01 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 135 " - pdb=" SG CYS N 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 212 " - pdb=" SG CYS J 216 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 140 " - pdb=" SG CYS J 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.07 Conformation dependent library (CDL) restraints added in 4.6 seconds 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 37 sheets defined 21.0% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 73 through 97 removed outlier: 3.759A pdb=" N MET A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.687A pdb=" N LEU A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 142' Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 195 through 201 Processing helix chain 'A' and resid 217 through 239 removed outlier: 3.533A pdb=" N ASN A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.506A pdb=" N ASP A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.546A pdb=" N CYS A 358 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 376 through 379 Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.059A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.744A pdb=" N TYR A 478 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.595A pdb=" N PHE A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 506 removed outlier: 3.600A pdb=" N ILE A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 97 removed outlier: 3.824A pdb=" N LEU B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.520A pdb=" N LEU B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 142 " --> pdb=" O GLY B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 142' Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.502A pdb=" N LEU B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 removed outlier: 3.569A pdb=" N ILE B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 227 Processing helix chain 'B' and resid 227 through 239 removed outlier: 3.665A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.140A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.527A pdb=" N ASN B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR B 478 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.609A pdb=" N PHE B 483 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 505 Processing helix chain 'C' and resid 74 through 97 removed outlier: 3.623A pdb=" N LEU C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 79 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.516A pdb=" N LEU C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU C 142 " --> pdb=" O GLY C 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 138 through 142' Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 172 removed outlier: 3.555A pdb=" N LEU C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 203 Processing helix chain 'C' and resid 217 through 239 removed outlier: 3.788A pdb=" N ASN C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 264 Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 4.122A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.716A pdb=" N TYR C 478 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 483 Processing helix chain 'C' and resid 492 through 505 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.684A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 182 through 189 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.509A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.597A pdb=" N ASP M 82 " --> pdb=" O GLN M 79 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 79 through 83' Processing helix chain 'M' and resid 122 through 128 removed outlier: 3.717A pdb=" N ALA M 128 " --> pdb=" O GLU M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 189 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.828A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.533A pdb=" N ASP N 82 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing helix chain 'N' and resid 122 through 127 Processing helix chain 'N' and resid 182 through 189 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 187 through 189 No H-bonds generated for 'chain 'J' and resid 187 through 189' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.833A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 340 " --> pdb=" O LEU A 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 349 through 352 current: chain 'A' and resid 364 through 368 Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 180 removed outlier: 11.571A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL A 300 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N MET A 289 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLN A 302 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER A 287 " --> pdb=" O GLN A 302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 322 removed outlier: 3.546A pdb=" N SER A 398 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 395 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASP A 489 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 487 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 404 through 407 Processing sheet with id=AA5, first strand: chain 'A' and resid 430 through 434 removed outlier: 6.705A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR A 434 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N CYS A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 33 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 186 through 194 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 186 through 194 current: chain 'B' and resid 286 through 293 removed outlier: 6.972A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE B 292 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP B 344 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 340 " --> pdb=" O LEU B 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 349 through 352 current: chain 'B' and resid 364 through 368 Processing sheet with id=AA7, first strand: chain 'B' and resid 321 through 322 removed outlier: 3.525A pdb=" N SER B 398 " --> pdb=" O CYS B 333 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE B 395 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP B 489 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AA9, first strand: chain 'B' and resid 430 through 434 removed outlier: 6.758A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 449 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 33 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 60 current: chain 'C' and resid 186 through 194 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 186 through 194 current: chain 'C' and resid 286 through 293 removed outlier: 5.742A pdb=" N SER C 287 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLN C 302 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N MET C 289 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL C 300 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 340 " --> pdb=" O LEU C 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 348 through 352 current: chain 'C' and resid 364 through 368 Processing sheet with id=AB2, first strand: chain 'C' and resid 321 through 322 removed outlier: 3.536A pdb=" N SER C 398 " --> pdb=" O CYS C 333 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C 395 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASP C 489 " --> pdb=" O ILE C 395 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 487 " --> pdb=" O THR C 397 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AB4, first strand: chain 'C' and resid 430 through 434 removed outlier: 6.681A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 95A through 97 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AB7, first strand: chain 'L' and resid 115 through 119 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 131 through 140 current: chain 'L' and resid 173 through 181 Processing sheet with id=AB8, first strand: chain 'L' and resid 145 through 151 removed outlier: 4.234A pdb=" N TRP L 149 " --> pdb=" O VAL L 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 154 through 156 current: chain 'L' and resid 201 through 203 Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.678A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100C through 103 Processing sheet with id=AC2, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.918A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 151 through 153 removed outlier: 3.590A pdb=" N THR H 151 " --> pdb=" O ASN H 199 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 9 through 13 current: chain 'M' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 95A through 98 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'M' and resid 18 through 24 Processing sheet with id=AC6, first strand: chain 'M' and resid 115 through 119 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 131 through 140 current: chain 'M' and resid 173 through 181 Processing sheet with id=AC7, first strand: chain 'M' and resid 146 through 151 removed outlier: 4.216A pdb=" N TRP M 149 " --> pdb=" O VAL M 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 154 through 156 current: chain 'M' and resid 201 through 203 Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'I' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 11 through 12 current: chain 'I' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 100C through 103 Processing sheet with id=AD1, first strand: chain 'I' and resid 120 through 124 removed outlier: 6.021A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 150 through 153 removed outlier: 3.545A pdb=" N THR I 151 " --> pdb=" O ASN I 199 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 9 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 95A through 98 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AD5, first strand: chain 'N' and resid 115 through 119 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 131 through 140 current: chain 'N' and resid 173 through 181 Processing sheet with id=AD6, first strand: chain 'N' and resid 146 through 151 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 154 through 155 current: chain 'N' and resid 201 through 203 Processing sheet with id=AD7, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'J' and resid 34 through 39 removed outlier: 6.597A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100C through 103 Processing sheet with id=AD9, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.007A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 150 through 152 removed outlier: 3.557A pdb=" N THR J 151 " --> pdb=" O ASN J 199 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN J 199 " --> pdb=" O THR J 151 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1674 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: 16.09 Time building geometry restraints manager: 31.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 20048 1.04 - 1.23: 1451 1.23 - 1.43: 7099 1.43 - 1.63: 11913 1.63 - 1.83: 132 Bond restraints: 40643 Sorted by residual: bond pdb=" C TYR L 49 " pdb=" O TYR L 49 " ideal model delta sigma weight residual 1.234 1.077 0.156 1.26e-02 6.30e+03 1.54e+02 bond pdb=" C VAL I 184 " pdb=" O VAL I 184 " ideal model delta sigma weight residual 1.238 1.160 0.078 7.90e-03 1.60e+04 9.83e+01 bond pdb=" C GLY C 242 " pdb=" N VAL C 243 " ideal model delta sigma weight residual 1.332 1.447 -0.116 1.36e-02 5.41e+03 7.21e+01 bond pdb=" C TRP L 35 " pdb=" O TRP L 35 " ideal model delta sigma weight residual 1.234 1.140 0.093 1.17e-02 7.31e+03 6.36e+01 bond pdb=" C ILE I 100 " pdb=" O ILE I 100 " ideal model delta sigma weight residual 1.236 1.153 0.083 1.19e-02 7.06e+03 4.86e+01 ... (remaining 40638 not shown) Histogram of bond angle deviations from ideal: 97.60 - 105.01: 442 105.01 - 112.42: 47342 112.42 - 119.83: 11062 119.83 - 127.25: 14430 127.25 - 134.66: 229 Bond angle restraints: 73505 Sorted by residual: angle pdb=" C PRO L 120 " pdb=" CA PRO L 120 " pdb=" CB PRO L 120 " ideal model delta sigma weight residual 110.92 100.42 10.50 1.22e+00 6.72e-01 7.41e+01 angle pdb=" O GLN C 501 " pdb=" C GLN C 501 " pdb=" N SER C 502 " ideal model delta sigma weight residual 122.03 130.61 -8.58 1.04e+00 9.25e-01 6.81e+01 angle pdb=" CA PRO M 142 " pdb=" C PRO M 142 " pdb=" O PRO M 142 " ideal model delta sigma weight residual 121.27 112.99 8.28 1.05e+00 9.07e-01 6.21e+01 angle pdb=" N ARG N 61 " pdb=" CA ARG N 61 " pdb=" C ARG N 61 " ideal model delta sigma weight residual 113.23 103.49 9.74 1.24e+00 6.50e-01 6.17e+01 angle pdb=" CA PRO L 142 " pdb=" C PRO L 142 " pdb=" O PRO L 142 " ideal model delta sigma weight residual 121.27 113.23 8.04 1.05e+00 9.07e-01 5.86e+01 ... (remaining 73500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17420 17.95 - 35.90: 1316 35.90 - 53.85: 484 53.85 - 71.80: 149 71.80 - 89.75: 53 Dihedral angle restraints: 19422 sinusoidal: 10596 harmonic: 8826 Sorted by residual: dihedral pdb=" CB CYS C 69 " pdb=" SG CYS C 69 " pdb=" SG CYS C 212 " pdb=" CB CYS C 212 " ideal model delta sinusoidal sigma weight residual -86.00 -141.26 55.26 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS B 155 " pdb=" SG CYS B 155 " pdb=" SG CYS B 290 " pdb=" CB CYS B 290 " ideal model delta sinusoidal sigma weight residual -86.00 -133.95 47.95 1 1.00e+01 1.00e-02 3.17e+01 dihedral pdb=" CB CYS A 155 " pdb=" SG CYS A 155 " pdb=" SG CYS A 290 " pdb=" CB CYS A 290 " ideal model delta sinusoidal sigma weight residual -86.00 -131.42 45.42 1 1.00e+01 1.00e-02 2.86e+01 ... (remaining 19419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2777 0.086 - 0.172: 407 0.172 - 0.257: 66 0.257 - 0.343: 7 0.343 - 0.429: 4 Chirality restraints: 3261 Sorted by residual: chirality pdb=" CB THR H 98 " pdb=" CA THR H 98 " pdb=" OG1 THR H 98 " pdb=" CG2 THR H 98 " both_signs ideal model delta sigma weight residual False 2.55 2.12 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CB THR J 98 " pdb=" CA THR J 98 " pdb=" OG1 THR J 98 " pdb=" CG2 THR J 98 " both_signs ideal model delta sigma weight residual False 2.55 2.12 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CB THR I 98 " pdb=" CA THR I 98 " pdb=" OG1 THR I 98 " pdb=" CG2 THR I 98 " both_signs ideal model delta sigma weight residual False 2.55 2.12 0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 3258 not shown) Planarity restraints: 6075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN I 1 " -0.063 2.00e-02 2.50e+03 4.27e-01 2.74e+03 pdb=" CD GLN I 1 " 0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN I 1 " 0.059 2.00e-02 2.50e+03 pdb=" NE2 GLN I 1 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN I 1 " 0.734 2.00e-02 2.50e+03 pdb="HE22 GLN I 1 " -0.741 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN N 37 " -0.074 2.00e-02 2.50e+03 4.26e-01 2.73e+03 pdb=" CD GLN N 37 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN N 37 " 0.071 2.00e-02 2.50e+03 pdb=" NE2 GLN N 37 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN N 37 " 0.733 2.00e-02 2.50e+03 pdb="HE22 GLN N 37 " -0.737 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN L 29 " -0.077 2.00e-02 2.50e+03 4.26e-01 2.73e+03 pdb=" CG ASN L 29 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN L 29 " 0.067 2.00e-02 2.50e+03 pdb=" ND2 ASN L 29 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN L 29 " -0.744 2.00e-02 2.50e+03 pdb="HD22 ASN L 29 " 0.726 2.00e-02 2.50e+03 ... (remaining 6072 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.93: 146 1.93 - 2.60: 43346 2.60 - 3.26: 115548 3.26 - 3.93: 150714 3.93 - 4.60: 235185 Nonbonded interactions: 544939 Sorted by model distance: nonbonded pdb=" HG1 THR M 146 " pdb=" HG1 THR M 197 " model vdw 1.259 2.100 nonbonded pdb=" HG1 THR M 146 " pdb=" OG1 THR M 197 " model vdw 1.372 1.850 nonbonded pdb=" O PRO N 7 " pdb=" HG1 THR N 102 " model vdw 1.421 1.850 nonbonded pdb=" O GLY C 329 " pdb=" HG SER C 330 " model vdw 1.452 1.850 nonbonded pdb="HD22 ASN B 426 " pdb=" O GLY B 446 " model vdw 1.482 1.850 ... (remaining 544934 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 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 27 through 509)) selection = chain 'B' selection = (chain 'C' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 27 through 509)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 0.010 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.590 Extract box with map and model: 9.290 Check model and map are aligned: 0.600 Set scattering table: 0.390 Process input model: 122.310 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.170 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.007 0.156 20595 Z= 0.447 Angle : 1.159 11.425 27987 Z= 0.781 Chirality : 0.062 0.429 3261 Planarity : 0.007 0.045 3555 Dihedral : 14.155 89.751 7452 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 1.29 % Allowed : 3.14 % Favored : 95.56 % Cbeta Deviations : 0.36 % 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: -0.58 (0.16), residues: 2625 helix: 0.78 (0.26), residues: 447 sheet: 0.51 (0.17), residues: 834 loop : -1.42 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP I 154 HIS 0.021 0.002 HIS N 198 PHE 0.022 0.001 PHE A 190 TYR 0.040 0.002 TYR N 36 ARG 0.006 0.000 ARG N 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 241 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 171 GLN cc_start: 0.7068 (mt0) cc_final: 0.6805 (mt0) REVERT: N 51 ASP cc_start: 0.7412 (m-30) cc_final: 0.7116 (m-30) REVERT: J 98 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8619 (m) outliers start: 30 outliers final: 6 residues processed: 266 average time/residue: 2.5858 time to fit residues: 787.4093 Evaluate side-chains 177 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 207 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 98 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 GLN J 155 ASN J 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20595 Z= 0.207 Angle : 0.589 7.524 27987 Z= 0.309 Chirality : 0.045 0.164 3261 Planarity : 0.004 0.039 3555 Dihedral : 5.049 57.675 2825 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.08 % Allowed : 8.18 % Favored : 90.74 % 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: -0.35 (0.16), residues: 2625 helix: 0.87 (0.26), residues: 459 sheet: 0.73 (0.18), residues: 819 loop : -1.28 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 154 HIS 0.007 0.001 HIS I 35 PHE 0.013 0.001 PHE B 237 TYR 0.016 0.002 TYR B 457 ARG 0.003 0.000 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 MET cc_start: 0.8431 (tpt) cc_final: 0.8111 (tpt) REVERT: H 171 GLN cc_start: 0.7104 (mt0) cc_final: 0.6827 (mt0) REVERT: N 26 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8751 (p) REVERT: N 51 ASP cc_start: 0.7528 (m-30) cc_final: 0.7293 (m-30) outliers start: 25 outliers final: 14 residues processed: 214 average time/residue: 2.5555 time to fit residues: 629.4921 Evaluate side-chains 193 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 178 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 207 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 29 ASN Chi-restraints excluded: chain N residue 137 ILE Chi-restraints excluded: chain J residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 237 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 80 optimal weight: 0.0970 chunk 190 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 HIS ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20595 Z= 0.257 Angle : 0.611 7.241 27987 Z= 0.321 Chirality : 0.046 0.150 3261 Planarity : 0.004 0.048 3555 Dihedral : 5.123 59.466 2822 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.46 % Allowed : 9.60 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2625 helix: 0.86 (0.26), residues: 462 sheet: 0.72 (0.18), residues: 819 loop : -1.30 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 314 HIS 0.009 0.002 HIS J 100B PHE 0.012 0.002 PHE J 100E TYR 0.020 0.002 TYR B 457 ARG 0.006 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 3.309 Fit side-chains revert: symmetry clash REVERT: A 289 MET cc_start: 0.8391 (tpt) cc_final: 0.8041 (tpt) REVERT: B 262 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7819 (t0) REVERT: C 204 LEU cc_start: 0.8081 (mp) cc_final: 0.7835 (mm) REVERT: H 171 GLN cc_start: 0.7028 (mt0) cc_final: 0.6755 (mt0) REVERT: N 26 SER cc_start: 0.9036 (OUTLIER) cc_final: 0.8744 (p) outliers start: 34 outliers final: 19 residues processed: 213 average time/residue: 2.5849 time to fit residues: 634.7751 Evaluate side-chains 197 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 176 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 500 ASN Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 207 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 29 ASN Chi-restraints excluded: chain N residue 137 ILE Chi-restraints excluded: chain J residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 238 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 chunk 124 optimal weight: 0.4980 chunk 225 optimal weight: 0.0770 chunk 67 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20595 Z= 0.146 Angle : 0.517 7.130 27987 Z= 0.266 Chirality : 0.044 0.148 3261 Planarity : 0.003 0.040 3555 Dihedral : 4.662 58.917 2822 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.03 % Allowed : 11.15 % Favored : 87.81 % 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 (0.16), residues: 2625 helix: 1.11 (0.26), residues: 462 sheet: 0.93 (0.18), residues: 786 loop : -1.23 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 314 HIS 0.003 0.001 HIS J 35 PHE 0.016 0.001 PHE A 488 TYR 0.011 0.001 TYR A 457 ARG 0.002 0.000 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 3.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8353 (tpt) cc_final: 0.7942 (tpt) REVERT: B 216 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7308 (p0) REVERT: B 289 MET cc_start: 0.8529 (tpt) cc_final: 0.8264 (tpt) REVERT: C 204 LEU cc_start: 0.8059 (mp) cc_final: 0.7845 (mm) REVERT: C 274 MET cc_start: 0.8817 (mtp) cc_final: 0.8543 (mtp) REVERT: H 171 GLN cc_start: 0.6988 (mt0) cc_final: 0.6717 (mt0) REVERT: N 26 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8658 (p) outliers start: 24 outliers final: 16 residues processed: 205 average time/residue: 2.6292 time to fit residues: 619.3005 Evaluate side-chains 192 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 207 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 29 ASN Chi-restraints excluded: chain N residue 137 ILE Chi-restraints excluded: chain J residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 20.0000 chunk 143 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 GLN ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 HIS ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20595 Z= 0.271 Angle : 0.612 6.997 27987 Z= 0.321 Chirality : 0.046 0.151 3261 Planarity : 0.004 0.049 3555 Dihedral : 4.972 56.736 2822 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.51 % Allowed : 12.23 % Favored : 86.26 % 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: -0.26 (0.16), residues: 2625 helix: 0.96 (0.26), residues: 462 sheet: 0.88 (0.18), residues: 813 loop : -1.29 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 100D HIS 0.006 0.001 HIS I 35 PHE 0.014 0.002 PHE I 100E TYR 0.021 0.002 TYR B 457 ARG 0.006 0.001 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 3.371 Fit side-chains revert: symmetry clash REVERT: A 289 MET cc_start: 0.8454 (tpt) cc_final: 0.8022 (tpt) REVERT: B 262 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7812 (t0) REVERT: C 497 GLU cc_start: 0.6828 (pt0) cc_final: 0.6521 (pt0) REVERT: H 171 GLN cc_start: 0.7002 (mt0) cc_final: 0.6720 (mt0) REVERT: N 26 SER cc_start: 0.9048 (OUTLIER) cc_final: 0.8755 (p) outliers start: 35 outliers final: 21 residues processed: 209 average time/residue: 2.5269 time to fit residues: 610.7705 Evaluate side-chains 190 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 3.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 207 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 29 ASN Chi-restraints excluded: chain N residue 137 ILE Chi-restraints excluded: chain J residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 0.6980 chunk 227 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 148 optimal weight: 0.0270 chunk 62 optimal weight: 0.4980 chunk 252 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 GLN ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20595 Z= 0.141 Angle : 0.506 6.991 27987 Z= 0.260 Chirality : 0.043 0.142 3261 Planarity : 0.003 0.041 3555 Dihedral : 4.519 55.148 2822 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.38 % Allowed : 12.53 % Favored : 86.09 % 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: -0.12 (0.17), residues: 2625 helix: 1.23 (0.26), residues: 462 sheet: 0.94 (0.18), residues: 795 loop : -1.21 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.003 0.001 HIS J 35 PHE 0.012 0.001 PHE B 505 TYR 0.011 0.001 TYR A 457 ARG 0.002 0.000 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 3.459 Fit side-chains revert: symmetry clash REVERT: A 289 MET cc_start: 0.8427 (tpt) cc_final: 0.7918 (tpt) REVERT: C 369 THR cc_start: 0.8700 (m) cc_final: 0.8423 (t) REVERT: C 497 GLU cc_start: 0.6805 (pt0) cc_final: 0.6518 (pt0) REVERT: H 171 GLN cc_start: 0.6925 (mt0) cc_final: 0.6647 (mt0) REVERT: N 26 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8613 (p) REVERT: J 100 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8426 (m-80) outliers start: 32 outliers final: 20 residues processed: 203 average time/residue: 2.5715 time to fit residues: 600.5126 Evaluate side-chains 198 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 207 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 29 ASN Chi-restraints excluded: chain N residue 137 ILE Chi-restraints excluded: chain J residue 98 THR Chi-restraints excluded: chain J residue 100 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 184 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 212 optimal weight: 0.0270 chunk 141 optimal weight: 0.7980 chunk 251 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN C 501 GLN ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20595 Z= 0.173 Angle : 0.531 7.172 27987 Z= 0.276 Chirality : 0.044 0.147 3261 Planarity : 0.003 0.043 3555 Dihedral : 4.546 53.553 2822 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.38 % Allowed : 12.79 % Favored : 85.83 % 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: -0.08 (0.17), residues: 2625 helix: 1.31 (0.26), residues: 462 sheet: 0.94 (0.18), residues: 795 loop : -1.19 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 314 HIS 0.004 0.001 HIS I 35 PHE 0.019 0.001 PHE A 488 TYR 0.015 0.001 TYR B 457 ARG 0.004 0.000 ARG M 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 3.266 Fit side-chains revert: symmetry clash REVERT: A 289 MET cc_start: 0.8446 (tpt) cc_final: 0.7983 (tpt) REVERT: B 216 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7324 (p0) REVERT: C 297 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8465 (tp) REVERT: C 497 GLU cc_start: 0.6823 (pt0) cc_final: 0.6487 (pt0) REVERT: H 171 GLN cc_start: 0.6927 (mt0) cc_final: 0.6644 (mt0) REVERT: N 26 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8665 (p) REVERT: J 100 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8544 (m-80) outliers start: 32 outliers final: 20 residues processed: 202 average time/residue: 2.5232 time to fit residues: 588.2794 Evaluate side-chains 195 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 207 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 29 ASN Chi-restraints excluded: chain N residue 137 ILE Chi-restraints excluded: chain J residue 98 THR Chi-restraints excluded: chain J residue 100 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 75 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 GLN ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20595 Z= 0.214 Angle : 0.561 7.042 27987 Z= 0.293 Chirality : 0.045 0.147 3261 Planarity : 0.004 0.045 3555 Dihedral : 4.682 51.343 2822 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.55 % Allowed : 12.96 % Favored : 85.49 % 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 (0.17), residues: 2625 helix: 1.19 (0.26), residues: 462 sheet: 0.85 (0.18), residues: 801 loop : -1.23 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 314 HIS 0.005 0.001 HIS A 317 PHE 0.029 0.001 PHE A 505 TYR 0.018 0.002 TYR B 457 ARG 0.003 0.000 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 3.368 Fit side-chains REVERT: A 289 MET cc_start: 0.8496 (tpt) cc_final: 0.7989 (tpt) REVERT: B 289 MET cc_start: 0.8487 (tpt) cc_final: 0.8185 (tpt) REVERT: C 297 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8624 (tp) REVERT: C 497 GLU cc_start: 0.6852 (pt0) cc_final: 0.6547 (pt0) REVERT: H 171 GLN cc_start: 0.6924 (mt0) cc_final: 0.6653 (mt0) REVERT: N 26 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8710 (p) outliers start: 36 outliers final: 25 residues processed: 207 average time/residue: 2.5434 time to fit residues: 606.2225 Evaluate side-chains 198 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 207 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 29 ASN Chi-restraints excluded: chain N residue 137 ILE Chi-restraints excluded: chain J residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 2.9990 chunk 241 optimal weight: 0.3980 chunk 219 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 240 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 GLN ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20595 Z= 0.157 Angle : 0.516 9.629 27987 Z= 0.266 Chirality : 0.043 0.143 3261 Planarity : 0.003 0.043 3555 Dihedral : 4.442 49.572 2822 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.25 % Allowed : 13.44 % Favored : 85.31 % 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: -0.07 (0.17), residues: 2625 helix: 1.32 (0.26), residues: 462 sheet: 0.94 (0.18), residues: 795 loop : -1.19 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 314 HIS 0.003 0.001 HIS J 35 PHE 0.022 0.001 PHE A 488 TYR 0.013 0.001 TYR A 457 ARG 0.002 0.000 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8468 (tpt) cc_final: 0.7958 (tpt) REVERT: C 297 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8512 (tp) REVERT: C 497 GLU cc_start: 0.6824 (pt0) cc_final: 0.6525 (pt0) REVERT: H 171 GLN cc_start: 0.6889 (mt0) cc_final: 0.6624 (mt0) REVERT: N 26 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8638 (p) outliers start: 29 outliers final: 21 residues processed: 196 average time/residue: 2.6182 time to fit residues: 601.1308 Evaluate side-chains 192 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 3.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 207 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 29 ASN Chi-restraints excluded: chain N residue 137 ILE Chi-restraints excluded: chain J residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 172 optimal weight: 30.0000 chunk 260 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 GLN ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20595 Z= 0.344 Angle : 0.660 7.186 27987 Z= 0.347 Chirality : 0.048 0.161 3261 Planarity : 0.005 0.050 3555 Dihedral : 5.011 47.790 2822 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.42 % Allowed : 13.35 % Favored : 85.23 % 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: -0.35 (0.16), residues: 2625 helix: 0.95 (0.26), residues: 462 sheet: 0.72 (0.17), residues: 831 loop : -1.33 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 100D HIS 0.006 0.001 HIS B 317 PHE 0.017 0.002 PHE I 100E TYR 0.023 0.002 TYR B 457 ARG 0.005 0.001 ARG I 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 3.292 Fit side-chains REVERT: A 289 MET cc_start: 0.8523 (tpt) cc_final: 0.8011 (tpt) REVERT: C 297 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8604 (tp) REVERT: C 497 GLU cc_start: 0.6864 (pt0) cc_final: 0.6541 (pt0) REVERT: H 171 GLN cc_start: 0.6958 (mt0) cc_final: 0.6697 (mt0) REVERT: N 26 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8705 (p) outliers start: 33 outliers final: 25 residues processed: 209 average time/residue: 2.4287 time to fit residues: 587.1430 Evaluate side-chains 202 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 207 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 29 ASN Chi-restraints excluded: chain N residue 137 ILE Chi-restraints excluded: chain J residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 ASN ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 ASN J 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.171610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.101689 restraints weight = 59095.316| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.97 r_work: 0.2910 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20595 Z= 0.271 Angle : 0.600 7.623 27987 Z= 0.316 Chirality : 0.046 0.145 3261 Planarity : 0.005 0.055 3555 Dihedral : 4.903 46.389 2822 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.38 % Allowed : 13.78 % Favored : 84.84 % 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: -0.42 (0.16), residues: 2625 helix: 0.94 (0.26), residues: 462 sheet: 0.70 (0.18), residues: 801 loop : -1.37 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 314 HIS 0.005 0.001 HIS A 317 PHE 0.027 0.002 PHE A 505 TYR 0.019 0.002 TYR B 457 ARG 0.005 0.001 ARG I 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12726.82 seconds wall clock time: 223 minutes 44.98 seconds (13424.98 seconds total)