Starting phenix.real_space_refine on Mon Sep 30 06:31:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t22_25609/09_2024/7t22_25609.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t22_25609/09_2024/7t22_25609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t22_25609/09_2024/7t22_25609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t22_25609/09_2024/7t22_25609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t22_25609/09_2024/7t22_25609.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t22_25609/09_2024/7t22_25609.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians Al 5 5.89 5 P 23 5.49 5 Mg 5 5.21 5 S 99 5.16 5 C 15138 2.51 5 N 4323 2.21 5 O 4923 1.98 5 F 20 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24536 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "B" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "C" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "D" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "E" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "F" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "G" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "H" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "I" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "M" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 260 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 17.84, per 1000 atoms: 0.73 Number of scatterers: 24536 At special positions: 0 Unit cell: (161.68, 155.1, 152.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 99 16.00 P 23 15.00 Al 5 13.00 Mg 5 11.99 F 20 9.00 O 4923 8.00 N 4323 7.00 C 15138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS G 568 " distance=2.04 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS H 568 " distance=2.04 Simple disulfide: pdb=" SG CYS F 103 " - pdb=" SG CYS I 568 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.18 Conformation dependent library (CDL) restraints added in 3.2 seconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5790 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 7 sheets defined 66.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.540A pdb=" N ARG A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 79 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 97 through 100 Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.586A pdb=" N THR A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 Processing helix chain 'A' and resid 153 through 172 removed outlier: 3.528A pdb=" N LEU A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 removed outlier: 3.561A pdb=" N GLN A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 Processing helix chain 'A' and resid 236 through 251 removed outlier: 3.725A pdb=" N ALA A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 290 through 308 Processing helix chain 'A' and resid 319 through 335 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 356 through 376 Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.504A pdb=" N LEU A 389 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.776A pdb=" N TYR A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.705A pdb=" N ARG B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 96 through 101 Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.596A pdb=" N TYR B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 Processing helix chain 'B' and resid 153 through 177 removed outlier: 3.585A pdb=" N ILE B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B 176 " --> pdb=" O ARG B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 236 through 251 Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 290 through 308 Processing helix chain 'B' and resid 319 through 335 Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 356 through 376 Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'B' and resid 404 through 412 removed outlier: 4.700A pdb=" N ILE B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 removed outlier: 3.735A pdb=" N TYR B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 79 Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.580A pdb=" N GLY C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.691A pdb=" N TYR C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 Processing helix chain 'C' and resid 153 through 172 Processing helix chain 'C' and resid 182 through 199 removed outlier: 3.702A pdb=" N GLN C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 236 through 251 Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'C' and resid 290 through 308 Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 350 through 354 Processing helix chain 'C' and resid 356 through 376 Processing helix chain 'C' and resid 386 through 392 Processing helix chain 'C' and resid 398 through 402 removed outlier: 3.638A pdb=" N LEU C 402 " --> pdb=" O ASN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 412 removed outlier: 4.576A pdb=" N ILE C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLN C 410 " --> pdb=" O GLY C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 425 removed outlier: 3.704A pdb=" N TYR C 424 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 78 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.935A pdb=" N THR D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 Processing helix chain 'D' and resid 153 through 172 removed outlier: 3.810A pdb=" N ARG D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 182 through 199 Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'D' and resid 236 through 251 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'D' and resid 290 through 308 Processing helix chain 'D' and resid 319 through 335 Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 350 through 354 Processing helix chain 'D' and resid 356 through 376 Processing helix chain 'D' and resid 386 through 392 Processing helix chain 'D' and resid 398 through 402 removed outlier: 3.557A pdb=" N LEU D 402 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 412 removed outlier: 4.324A pdb=" N ILE D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 410 " --> pdb=" O GLY D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 425 removed outlier: 3.912A pdb=" N TYR D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 44 Processing helix chain 'E' and resid 47 through 53 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 78 Processing helix chain 'E' and resid 83 through 94 Processing helix chain 'E' and resid 97 through 100 Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.622A pdb=" N TYR E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 148 Processing helix chain 'E' and resid 153 through 172 removed outlier: 3.646A pdb=" N ARG E 172 " --> pdb=" O ILE E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 199 removed outlier: 4.182A pdb=" N VAL E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 219 Processing helix chain 'E' and resid 236 through 252 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'E' and resid 290 through 308 Processing helix chain 'E' and resid 319 through 335 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 350 through 354 Processing helix chain 'E' and resid 356 through 376 Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 398 through 402 removed outlier: 3.697A pdb=" N LEU E 402 " --> pdb=" O ASN E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 412 removed outlier: 4.377A pdb=" N ILE E 408 " --> pdb=" O GLU E 404 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN E 410 " --> pdb=" O GLY E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 425 removed outlier: 3.895A pdb=" N TYR E 424 " --> pdb=" O ARG E 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 44 Processing helix chain 'F' and resid 47 through 55 removed outlier: 3.926A pdb=" N ARG F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 79 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 96 through 101 Processing helix chain 'F' and resid 101 through 112 removed outlier: 3.689A pdb=" N TYR F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 117 No H-bonds generated for 'chain 'F' and resid 115 through 117' Processing helix chain 'F' and resid 118 through 148 Processing helix chain 'F' and resid 153 through 169 removed outlier: 3.968A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 172 No H-bonds generated for 'chain 'F' and resid 170 through 172' Processing helix chain 'F' and resid 182 through 198 removed outlier: 4.310A pdb=" N PHE F 197 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 219 Processing helix chain 'F' and resid 236 through 251 Processing helix chain 'F' and resid 264 through 278 Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'F' and resid 290 through 308 Processing helix chain 'F' and resid 319 through 335 Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 350 through 354 Processing helix chain 'F' and resid 356 through 376 Processing helix chain 'F' and resid 387 through 392 removed outlier: 3.706A pdb=" N GLN F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG F 392 " --> pdb=" O SER F 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 387 through 392' Processing helix chain 'F' and resid 398 through 402 Processing helix chain 'F' and resid 404 through 412 removed outlier: 3.645A pdb=" N ILE F 408 " --> pdb=" O GLU F 404 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN F 410 " --> pdb=" O GLY F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 425 removed outlier: 3.737A pdb=" N TYR F 424 " --> pdb=" O ARG F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 461 Processing helix chain 'G' and resid 462 through 468 removed outlier: 3.603A pdb=" N THR G 466 " --> pdb=" O GLU G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 495 removed outlier: 3.780A pdb=" N GLN G 495 " --> pdb=" O THR G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 505 Processing helix chain 'G' and resid 506 through 511 removed outlier: 4.599A pdb=" N GLY G 509 " --> pdb=" O HIS G 506 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASN G 511 " --> pdb=" O ARG G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 522 removed outlier: 3.646A pdb=" N MET G 521 " --> pdb=" O GLU G 517 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP G 522 " --> pdb=" O LYS G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 528 through 559 removed outlier: 3.601A pdb=" N GLU G 532 " --> pdb=" O LYS G 528 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN G 533 " --> pdb=" O ASN G 529 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR G 534 " --> pdb=" O ILE G 530 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU G 553 " --> pdb=" O LEU G 549 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG G 559 " --> pdb=" O ILE G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 564 through 580 removed outlier: 3.587A pdb=" N LEU G 574 " --> pdb=" O GLU G 570 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN G 575 " --> pdb=" O LEU G 571 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN G 576 " --> pdb=" O TRP G 572 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU G 577 " --> pdb=" O THR G 573 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU G 578 " --> pdb=" O LEU G 574 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 461 Processing helix chain 'H' and resid 462 through 468 removed outlier: 3.821A pdb=" N THR H 466 " --> pdb=" O GLU H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 481 through 493 removed outlier: 4.381A pdb=" N PHE H 485 " --> pdb=" O GLY H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 505 Processing helix chain 'H' and resid 506 through 508 No H-bonds generated for 'chain 'H' and resid 506 through 508' Processing helix chain 'H' and resid 512 through 522 removed outlier: 3.759A pdb=" N MET H 521 " --> pdb=" O GLU H 517 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP H 522 " --> pdb=" O LYS H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 530 through 562 removed outlier: 3.815A pdb=" N THR H 534 " --> pdb=" O ILE H 530 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU H 546 " --> pdb=" O MET H 542 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU H 547 " --> pdb=" O PHE H 543 " (cutoff:3.500A) Processing helix chain 'H' and resid 564 through 580 removed outlier: 3.589A pdb=" N LEU H 578 " --> pdb=" O LEU H 574 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS H 580 " --> pdb=" O GLN H 576 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 461 Processing helix chain 'I' and resid 462 through 468 Processing helix chain 'I' and resid 481 through 495 removed outlier: 4.395A pdb=" N PHE I 485 " --> pdb=" O GLY I 481 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN I 495 " --> pdb=" O THR I 491 " (cutoff:3.500A) Processing helix chain 'I' and resid 499 through 505 Processing helix chain 'I' and resid 506 through 511 removed outlier: 4.575A pdb=" N GLY I 509 " --> pdb=" O HIS I 506 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASN I 511 " --> pdb=" O ARG I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 522 removed outlier: 3.632A pdb=" N MET I 521 " --> pdb=" O GLU I 517 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP I 522 " --> pdb=" O LYS I 518 " (cutoff:3.500A) Processing helix chain 'I' and resid 528 through 562 removed outlier: 3.850A pdb=" N GLU I 532 " --> pdb=" O LYS I 528 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN I 533 " --> pdb=" O ASN I 529 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR I 534 " --> pdb=" O ILE I 530 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER I 545 " --> pdb=" O HIS I 541 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU I 546 " --> pdb=" O MET I 542 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU I 547 " --> pdb=" O PHE I 543 " (cutoff:3.500A) Processing helix chain 'I' and resid 564 through 580 removed outlier: 3.642A pdb=" N GLU I 577 " --> pdb=" O THR I 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I 578 " --> pdb=" O LEU I 574 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA I 579 " --> pdb=" O ASN I 575 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS I 580 " --> pdb=" O GLN I 576 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.420A pdb=" N LEU B 257 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASP B 343 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE B 259 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE B 340 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU B 382 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE B 342 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N GLN B 384 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE B 227 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER B 383 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 229 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE B 415 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 462 removed outlier: 6.059A pdb=" N ILE A 415 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 414 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 227 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER A 383 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 229 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 340 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU A 382 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 342 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N GLN A 384 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 256 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ASP A 313 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 258 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 180 through 181 removed outlier: 6.358A pdb=" N VAL C 256 " --> pdb=" O TYR C 311 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ASP C 313 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 258 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU C 257 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASP C 343 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE C 259 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 340 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU C 382 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE C 342 " --> pdb=" O LEU C 382 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 227 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER C 383 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 229 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU C 226 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N MET C 416 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE C 228 " --> pdb=" O MET C 416 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE C 418 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA C 230 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE C 415 " --> pdb=" O GLY C 439 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 180 through 181 removed outlier: 6.599A pdb=" N LEU D 257 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASP D 343 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE D 259 " --> pdb=" O ASP D 343 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE D 340 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU D 382 " --> pdb=" O ILE D 340 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE D 342 " --> pdb=" O LEU D 382 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE D 227 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER D 383 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL D 229 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE D 415 " --> pdb=" O GLY D 439 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 180 through 181 removed outlier: 6.246A pdb=" N VAL E 256 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ASP E 313 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE E 258 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 257 " --> pdb=" O MET E 341 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASP E 343 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE E 259 " --> pdb=" O ASP E 343 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE E 340 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE E 227 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER E 383 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL E 229 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 180 through 181 removed outlier: 6.246A pdb=" N VAL E 256 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ASP E 313 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE E 258 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 257 " --> pdb=" O MET E 341 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASP E 343 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE E 259 " --> pdb=" O ASP E 343 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE E 340 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE E 227 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU E 226 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N MET E 416 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE E 228 " --> pdb=" O MET E 416 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE E 418 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA E 230 " --> pdb=" O ILE E 418 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE E 415 " --> pdb=" O GLY E 439 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 310 through 313 removed outlier: 6.418A pdb=" N VAL F 256 " --> pdb=" O TYR F 311 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ASP F 313 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE F 258 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE F 340 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU F 382 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE F 342 " --> pdb=" O LEU F 382 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL F 229 " --> pdb=" O ALA F 381 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA F 231 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE F 415 " --> pdb=" O GLY F 439 " (cutoff:3.500A) 1468 hydrogen bonds defined for protein. 4128 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: 8.64 Time building geometry restraints manager: 8.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8476 1.34 - 1.46: 4408 1.46 - 1.58: 11770 1.58 - 1.70: 40 1.70 - 1.82: 206 Bond restraints: 24900 Sorted by residual: bond pdb=" F1 ALF F1002 " pdb="AL ALF F1002 " ideal model delta sigma weight residual 1.684 1.805 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" F1 ALF D1002 " pdb="AL ALF D1002 " ideal model delta sigma weight residual 1.684 1.803 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" F1 ALF B1002 " pdb="AL ALF B1002 " ideal model delta sigma weight residual 1.684 1.803 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" F1 ALF E1002 " pdb="AL ALF E1002 " ideal model delta sigma weight residual 1.684 1.803 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" F4 ALF C1002 " pdb="AL ALF C1002 " ideal model delta sigma weight residual 1.686 1.804 -0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 24895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.09: 33747 14.09 - 28.19: 20 28.19 - 42.28: 0 42.28 - 56.37: 0 56.37 - 70.46: 10 Bond angle restraints: 33777 Sorted by residual: angle pdb=" F1 ALF E1002 " pdb="AL ALF E1002 " pdb=" F2 ALF E1002 " ideal model delta sigma weight residual 108.68 179.14 -70.46 3.00e+00 1.11e-01 5.52e+02 angle pdb=" F1 ALF C1002 " pdb="AL ALF C1002 " pdb=" F2 ALF C1002 " ideal model delta sigma weight residual 108.68 179.11 -70.43 3.00e+00 1.11e-01 5.51e+02 angle pdb=" F1 ALF D1002 " pdb="AL ALF D1002 " pdb=" F2 ALF D1002 " ideal model delta sigma weight residual 108.68 179.08 -70.40 3.00e+00 1.11e-01 5.51e+02 angle pdb=" F1 ALF B1002 " pdb="AL ALF B1002 " pdb=" F2 ALF B1002 " ideal model delta sigma weight residual 108.68 179.03 -70.35 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F1 ALF F1002 " pdb="AL ALF F1002 " pdb=" F2 ALF F1002 " ideal model delta sigma weight residual 108.68 178.95 -70.27 3.00e+00 1.11e-01 5.49e+02 ... (remaining 33772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.03: 15164 30.03 - 60.06: 166 60.06 - 90.09: 6 90.09 - 120.12: 7 120.12 - 150.15: 1 Dihedral angle restraints: 15344 sinusoidal: 6416 harmonic: 8928 Sorted by residual: dihedral pdb=" CA GLU D 404 " pdb=" C GLU D 404 " pdb=" N SER D 405 " pdb=" CA SER D 405 " ideal model delta harmonic sigma weight residual 180.00 -142.98 -37.02 0 5.00e+00 4.00e-02 5.48e+01 dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 90.15 -150.15 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" CA GLU E 404 " pdb=" C GLU E 404 " pdb=" N SER E 405 " pdb=" CA SER E 405 " ideal model delta harmonic sigma weight residual -180.00 -147.90 -32.10 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 15341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2718 0.029 - 0.058: 718 0.058 - 0.088: 219 0.088 - 0.117: 147 0.117 - 0.146: 50 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA VAL C 449 " pdb=" N VAL C 449 " pdb=" C VAL C 449 " pdb=" CB VAL C 449 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA VAL E 449 " pdb=" N VAL E 449 " pdb=" C VAL E 449 " pdb=" CB VAL E 449 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA VAL D 449 " pdb=" N VAL D 449 " pdb=" C VAL D 449 " pdb=" CB VAL D 449 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 3849 not shown) Planarity restraints: 4422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 199 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO F 200 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 200 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 200 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 199 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO B 200 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 468 " 0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO G 469 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO G 469 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 469 " 0.015 5.00e-02 4.00e+02 ... (remaining 4419 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 327 2.57 - 3.15: 21509 3.15 - 3.74: 40104 3.74 - 4.32: 53707 4.32 - 4.90: 90437 Nonbonded interactions: 206084 Sorted by model distance: nonbonded pdb=" F4 ALF F1002 " pdb="MG MG F1003 " model vdw 1.992 2.120 nonbonded pdb=" F4 ALF B1002 " pdb="MG MG B1003 " model vdw 1.993 2.120 nonbonded pdb=" F1 ALF B1002 " pdb="MG MG B1003 " model vdw 1.993 2.120 nonbonded pdb=" F4 ALF D1002 " pdb="MG MG D1003 " model vdw 1.993 2.120 nonbonded pdb=" F1 ALF F1002 " pdb="MG MG F1003 " model vdw 1.994 2.120 ... (remaining 206079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 24 through 471) selection = (chain 'C' and resid 24 through 471) selection = (chain 'D' and resid 24 through 471) selection = (chain 'E' and resid 24 through 471) selection = (chain 'F' and resid 24 through 471) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.150 Check model and map are aligned: 0.200 Set scattering table: 0.200 Process input model: 59.940 Find NCS groups from input model: 1.250 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 24900 Z= 0.288 Angle : 1.412 70.464 33777 Z= 0.532 Chirality : 0.037 0.146 3852 Planarity : 0.003 0.038 4422 Dihedral : 10.318 150.151 9545 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.18 % Allowed : 3.45 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.16), residues: 3066 helix: 2.89 (0.13), residues: 1717 sheet: -0.92 (0.26), residues: 319 loop : 0.48 (0.21), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 48 HIS 0.003 0.001 HIS E 334 PHE 0.006 0.001 PHE D 166 TYR 0.008 0.001 TYR B 344 ARG 0.006 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 659 time to evaluate : 2.922 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8368 (tt0) cc_final: 0.8072 (pp20) REVERT: A 58 ASP cc_start: 0.9083 (m-30) cc_final: 0.8654 (p0) REVERT: A 135 MET cc_start: 0.9057 (ttm) cc_final: 0.8515 (ppp) REVERT: A 291 ASP cc_start: 0.8674 (m-30) cc_final: 0.8095 (p0) REVERT: A 345 LEU cc_start: 0.8307 (mt) cc_final: 0.7830 (mt) REVERT: B 72 MET cc_start: 0.8897 (mtt) cc_final: 0.8637 (mtt) REVERT: B 226 LEU cc_start: 0.8288 (tp) cc_final: 0.7775 (mm) REVERT: B 240 PHE cc_start: 0.9322 (t80) cc_final: 0.9079 (t80) REVERT: B 263 MET cc_start: 0.6032 (mtp) cc_final: 0.5786 (mtt) REVERT: B 269 MET cc_start: 0.8878 (tpp) cc_final: 0.8591 (tpp) REVERT: B 291 ASP cc_start: 0.8979 (m-30) cc_final: 0.8735 (p0) REVERT: B 324 ARG cc_start: 0.9166 (ttm170) cc_final: 0.8898 (ttm-80) REVERT: B 348 MET cc_start: 0.7184 (mtp) cc_final: 0.6966 (ttm) REVERT: B 414 LEU cc_start: 0.9277 (tp) cc_final: 0.8938 (tp) REVERT: C 60 PHE cc_start: 0.9225 (m-80) cc_final: 0.8922 (m-10) REVERT: C 61 TYR cc_start: 0.8669 (t80) cc_final: 0.8430 (t80) REVERT: C 240 PHE cc_start: 0.8919 (t80) cc_final: 0.8480 (t80) REVERT: C 259 PHE cc_start: 0.9023 (m-80) cc_final: 0.8749 (m-80) REVERT: C 263 MET cc_start: 0.7866 (mtp) cc_final: 0.7514 (ttm) REVERT: C 269 MET cc_start: 0.8870 (tpp) cc_final: 0.8559 (ttt) REVERT: C 270 MET cc_start: 0.9052 (mtm) cc_final: 0.8236 (mtp) REVERT: C 382 LEU cc_start: 0.8828 (mt) cc_final: 0.8326 (mt) REVERT: D 50 ASP cc_start: 0.8181 (m-30) cc_final: 0.7810 (p0) REVERT: D 58 ASP cc_start: 0.9006 (m-30) cc_final: 0.8762 (p0) REVERT: D 87 LEU cc_start: 0.8533 (tp) cc_final: 0.7932 (pp) REVERT: D 118 ASN cc_start: 0.9391 (m-40) cc_final: 0.9089 (m-40) REVERT: D 160 LEU cc_start: 0.9159 (tp) cc_final: 0.8873 (tt) REVERT: D 228 ILE cc_start: 0.8273 (mm) cc_final: 0.8045 (mm) REVERT: D 237 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8189 (ptpt) REVERT: D 263 MET cc_start: 0.8062 (mtp) cc_final: 0.7790 (mtt) REVERT: D 337 ILE cc_start: 0.8701 (mt) cc_final: 0.8411 (mm) REVERT: D 341 MET cc_start: 0.7657 (tmt) cc_final: 0.7042 (tmm) REVERT: D 363 GLU cc_start: 0.7849 (tp30) cc_final: 0.7256 (tm-30) REVERT: D 426 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7601 (tp30) REVERT: E 60 PHE cc_start: 0.8983 (m-80) cc_final: 0.8285 (m-80) REVERT: E 92 GLU cc_start: 0.8879 (tt0) cc_final: 0.8484 (tm-30) REVERT: E 135 MET cc_start: 0.9300 (ttm) cc_final: 0.8934 (tmm) REVERT: E 235 MET cc_start: 0.8937 (mmt) cc_final: 0.8143 (mmm) REVERT: E 270 MET cc_start: 0.8963 (mtm) cc_final: 0.8354 (ppp) REVERT: E 301 MET cc_start: 0.9056 (mtp) cc_final: 0.8105 (tpp) REVERT: E 310 ILE cc_start: 0.9285 (mt) cc_final: 0.8954 (mm) REVERT: E 320 PRO cc_start: 0.8637 (Cg_exo) cc_final: 0.7891 (Cg_endo) REVERT: E 363 GLU cc_start: 0.9103 (tp30) cc_final: 0.8898 (tp30) REVERT: E 443 ASN cc_start: 0.8521 (m-40) cc_final: 0.7423 (t0) REVERT: F 282 THR cc_start: 0.9096 (m) cc_final: 0.8803 (p) REVERT: F 361 ILE cc_start: 0.9135 (mm) cc_final: 0.8910 (mm) REVERT: F 414 LEU cc_start: 0.9094 (tp) cc_final: 0.8892 (tp) REVERT: G 471 LEU cc_start: 0.7256 (pp) cc_final: 0.6464 (mp) REVERT: G 521 MET cc_start: 0.9210 (ppp) cc_final: 0.9009 (ppp) REVERT: G 553 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8743 (pm20) REVERT: G 568 CYS cc_start: 0.8504 (m) cc_final: 0.8111 (t) REVERT: H 498 LEU cc_start: 0.0378 (pt) cc_final: -0.0328 (pt) REVERT: H 550 ARG cc_start: 0.8960 (mmp80) cc_final: 0.8648 (mmm160) REVERT: I 530 ILE cc_start: 0.8998 (tt) cc_final: 0.8670 (pt) outliers start: 31 outliers final: 4 residues processed: 683 average time/residue: 0.4294 time to fit residues: 432.0306 Evaluate side-chains 377 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 372 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 238 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 76 GLN A 410 GLN B 45 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 ASN F 441 GLN G 541 HIS I 502 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24900 Z= 0.253 Angle : 1.048 30.989 33777 Z= 0.428 Chirality : 0.042 0.244 3852 Planarity : 0.005 0.118 4422 Dihedral : 7.557 121.779 3554 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.30 % Allowed : 2.01 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.15), residues: 3066 helix: 2.21 (0.12), residues: 1785 sheet: -0.59 (0.27), residues: 322 loop : 0.40 (0.22), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 48 HIS 0.008 0.002 HIS A 334 PHE 0.022 0.002 PHE F 240 TYR 0.026 0.002 TYR F 122 ARG 0.015 0.001 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 448 time to evaluate : 2.936 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.9151 (m-30) cc_final: 0.8695 (p0) REVERT: A 135 MET cc_start: 0.8918 (ttm) cc_final: 0.8571 (ppp) REVERT: A 291 ASP cc_start: 0.8714 (m-30) cc_final: 0.8151 (p0) REVERT: A 345 LEU cc_start: 0.8047 (mt) cc_final: 0.7777 (mt) REVERT: B 72 MET cc_start: 0.8624 (mtt) cc_final: 0.8376 (mtt) REVERT: B 226 LEU cc_start: 0.8468 (tp) cc_final: 0.8182 (mm) REVERT: B 235 MET cc_start: 0.8932 (mmt) cc_final: 0.8505 (mmm) REVERT: B 240 PHE cc_start: 0.9274 (t80) cc_final: 0.9017 (t80) REVERT: B 269 MET cc_start: 0.8940 (tpp) cc_final: 0.8539 (tpp) REVERT: B 291 ASP cc_start: 0.8948 (m-30) cc_final: 0.8702 (p0) REVERT: B 297 ILE cc_start: 0.9535 (mm) cc_final: 0.9295 (pt) REVERT: B 301 MET cc_start: 0.9045 (tmm) cc_final: 0.8845 (tmm) REVERT: B 324 ARG cc_start: 0.9184 (ttm170) cc_final: 0.8700 (ttt180) REVERT: B 348 MET cc_start: 0.7215 (mtp) cc_final: 0.6716 (mpp) REVERT: B 414 LEU cc_start: 0.9136 (tp) cc_final: 0.8860 (tp) REVERT: C 235 MET cc_start: 0.9121 (mmp) cc_final: 0.8776 (mmm) REVERT: C 259 PHE cc_start: 0.9169 (m-80) cc_final: 0.8760 (m-80) REVERT: C 263 MET cc_start: 0.8349 (mtp) cc_final: 0.8143 (ttm) REVERT: C 312 ILE cc_start: 0.9375 (mp) cc_final: 0.8973 (tt) REVERT: C 382 LEU cc_start: 0.8867 (mt) cc_final: 0.8612 (mt) REVERT: C 427 ASN cc_start: 0.8023 (p0) cc_final: 0.7683 (p0) REVERT: D 34 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8757 (mt-10) REVERT: D 58 ASP cc_start: 0.9027 (m-30) cc_final: 0.8771 (p0) REVERT: D 118 ASN cc_start: 0.9460 (m-40) cc_final: 0.9180 (m-40) REVERT: D 160 LEU cc_start: 0.9205 (tp) cc_final: 0.8916 (tt) REVERT: D 237 LYS cc_start: 0.8650 (ttpt) cc_final: 0.8414 (ptpt) REVERT: D 269 MET cc_start: 0.8547 (ttm) cc_final: 0.8139 (ttm) REVERT: D 301 MET cc_start: 0.8831 (mtm) cc_final: 0.8527 (mtt) REVERT: D 337 ILE cc_start: 0.8619 (mt) cc_final: 0.8385 (mm) REVERT: E 60 PHE cc_start: 0.9120 (m-80) cc_final: 0.8908 (m-80) REVERT: E 85 ILE cc_start: 0.9491 (pt) cc_final: 0.9286 (mp) REVERT: E 92 GLU cc_start: 0.8799 (tt0) cc_final: 0.8538 (tm-30) REVERT: E 135 MET cc_start: 0.9366 (ttm) cc_final: 0.9083 (tmm) REVERT: E 235 MET cc_start: 0.8862 (mmt) cc_final: 0.8292 (mmm) REVERT: E 267 GLN cc_start: 0.9169 (mp10) cc_final: 0.8950 (mp10) REVERT: E 363 GLU cc_start: 0.9128 (tp30) cc_final: 0.8812 (tp30) REVERT: F 98 ASP cc_start: 0.7670 (t0) cc_final: 0.7470 (p0) REVERT: F 235 MET cc_start: 0.7315 (mtt) cc_final: 0.6430 (mtp) REVERT: F 263 MET cc_start: 0.7020 (mpp) cc_final: 0.6734 (mpp) REVERT: F 282 THR cc_start: 0.9190 (m) cc_final: 0.8859 (p) REVERT: F 318 LEU cc_start: 0.8351 (mp) cc_final: 0.8069 (mp) REVERT: G 468 VAL cc_start: 0.7217 (t) cc_final: 0.6952 (t) REVERT: G 568 CYS cc_start: 0.8139 (m) cc_final: 0.7715 (t) REVERT: H 550 ARG cc_start: 0.8981 (mmp80) cc_final: 0.8671 (mmm160) REVERT: I 530 ILE cc_start: 0.8895 (tt) cc_final: 0.8611 (pt) outliers start: 8 outliers final: 1 residues processed: 452 average time/residue: 0.3883 time to fit residues: 264.5857 Evaluate side-chains 322 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 321 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 5.9990 chunk 85 optimal weight: 0.2980 chunk 229 optimal weight: 9.9990 chunk 187 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 276 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 chunk 246 optimal weight: 5.9990 chunk 274 optimal weight: 0.0040 chunk 94 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 overall best weight: 2.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS F 96 GLN G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24900 Z= 0.194 Angle : 1.013 30.505 33777 Z= 0.406 Chirality : 0.041 0.224 3852 Planarity : 0.005 0.085 4422 Dihedral : 7.311 124.549 3554 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.08 % Allowed : 2.28 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.15), residues: 3066 helix: 2.05 (0.12), residues: 1780 sheet: -0.63 (0.27), residues: 331 loop : 0.49 (0.22), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 48 HIS 0.011 0.001 HIS D 65 PHE 0.018 0.002 PHE F 240 TYR 0.024 0.001 TYR B 122 ARG 0.010 0.001 ARG C 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 425 time to evaluate : 3.345 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 58 ASP cc_start: 0.9140 (m-30) cc_final: 0.8661 (p0) REVERT: A 72 MET cc_start: 0.8424 (mmp) cc_final: 0.8211 (mmp) REVERT: A 194 GLU cc_start: 0.9224 (mt-10) cc_final: 0.9002 (tp30) REVERT: A 242 MET cc_start: 0.8925 (ppp) cc_final: 0.8666 (ppp) REVERT: A 291 ASP cc_start: 0.8697 (m-30) cc_final: 0.8131 (p0) REVERT: A 345 LEU cc_start: 0.7956 (mt) cc_final: 0.7640 (mt) REVERT: A 348 MET cc_start: 0.9110 (ttm) cc_final: 0.8538 (ttm) REVERT: B 72 MET cc_start: 0.8647 (mtt) cc_final: 0.8416 (mtt) REVERT: B 226 LEU cc_start: 0.8207 (tp) cc_final: 0.7703 (mm) REVERT: B 240 PHE cc_start: 0.9206 (t80) cc_final: 0.8953 (t80) REVERT: B 269 MET cc_start: 0.9013 (tpp) cc_final: 0.8644 (tpp) REVERT: B 291 ASP cc_start: 0.8941 (m-30) cc_final: 0.8686 (p0) REVERT: B 301 MET cc_start: 0.9126 (tmm) cc_final: 0.8692 (ppp) REVERT: B 324 ARG cc_start: 0.9172 (ttm170) cc_final: 0.8726 (ttt180) REVERT: B 348 MET cc_start: 0.7318 (mtp) cc_final: 0.6826 (mpp) REVERT: C 235 MET cc_start: 0.8998 (mmp) cc_final: 0.8663 (mmm) REVERT: C 259 PHE cc_start: 0.9085 (m-80) cc_final: 0.8730 (m-80) REVERT: C 263 MET cc_start: 0.8498 (mtp) cc_final: 0.8177 (ttm) REVERT: C 322 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8152 (mt-10) REVERT: C 382 LEU cc_start: 0.8806 (mt) cc_final: 0.8315 (mt) REVERT: C 419 TYR cc_start: 0.7756 (t80) cc_final: 0.7502 (t80) REVERT: C 427 ASN cc_start: 0.8035 (p0) cc_final: 0.7750 (p0) REVERT: D 58 ASP cc_start: 0.9030 (m-30) cc_final: 0.8735 (p0) REVERT: D 118 ASN cc_start: 0.9443 (m-40) cc_final: 0.9134 (m-40) REVERT: D 160 LEU cc_start: 0.9245 (tp) cc_final: 0.8955 (tt) REVERT: D 284 ILE cc_start: 0.9167 (mt) cc_final: 0.8926 (mt) REVERT: D 301 MET cc_start: 0.8816 (mtm) cc_final: 0.8515 (mtt) REVERT: D 337 ILE cc_start: 0.8581 (mt) cc_final: 0.8358 (mm) REVERT: E 42 MET cc_start: 0.8337 (mtm) cc_final: 0.8064 (ptp) REVERT: E 85 ILE cc_start: 0.9521 (pt) cc_final: 0.9233 (mp) REVERT: E 92 GLU cc_start: 0.8811 (tt0) cc_final: 0.8523 (tm-30) REVERT: E 135 MET cc_start: 0.9368 (ttm) cc_final: 0.9021 (tmm) REVERT: E 235 MET cc_start: 0.8817 (mmt) cc_final: 0.8189 (mmm) REVERT: E 363 GLU cc_start: 0.9133 (tp30) cc_final: 0.8804 (tp30) REVERT: F 98 ASP cc_start: 0.7654 (t0) cc_final: 0.7442 (p0) REVERT: F 235 MET cc_start: 0.7414 (mtt) cc_final: 0.6632 (mtp) REVERT: F 270 MET cc_start: 0.8076 (ttt) cc_final: 0.7802 (ttt) REVERT: F 282 THR cc_start: 0.9127 (m) cc_final: 0.8767 (p) REVERT: G 537 ASP cc_start: 0.8746 (t0) cc_final: 0.8403 (t0) REVERT: G 568 CYS cc_start: 0.7916 (m) cc_final: 0.7540 (t) REVERT: H 550 ARG cc_start: 0.8984 (mmp80) cc_final: 0.8670 (mmm160) REVERT: I 530 ILE cc_start: 0.8883 (tt) cc_final: 0.8593 (pt) outliers start: 2 outliers final: 1 residues processed: 427 average time/residue: 0.3821 time to fit residues: 248.8334 Evaluate side-chains 313 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 312 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 143 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 185 optimal weight: 20.0000 chunk 277 optimal weight: 40.0000 chunk 293 optimal weight: 40.0000 chunk 145 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN D 45 ASN D 198 GLN E 222 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24900 Z= 0.334 Angle : 1.097 33.158 33777 Z= 0.459 Chirality : 0.043 0.182 3852 Planarity : 0.005 0.068 4422 Dihedral : 7.512 131.600 3554 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.19 % Allowed : 2.85 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3066 helix: 1.47 (0.12), residues: 1786 sheet: -0.78 (0.27), residues: 328 loop : 0.16 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 48 HIS 0.007 0.002 HIS G 541 PHE 0.027 0.002 PHE B 60 TYR 0.029 0.002 TYR D 122 ARG 0.008 0.001 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 376 time to evaluate : 3.009 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: A 58 ASP cc_start: 0.9237 (m-30) cc_final: 0.8726 (p0) REVERT: A 194 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8951 (tp30) REVERT: A 242 MET cc_start: 0.9023 (ppp) cc_final: 0.8683 (ppp) REVERT: A 291 ASP cc_start: 0.8736 (m-30) cc_final: 0.8090 (p0) REVERT: A 345 LEU cc_start: 0.7962 (mt) cc_final: 0.7605 (mt) REVERT: B 72 MET cc_start: 0.8805 (mtt) cc_final: 0.8566 (mtt) REVERT: B 240 PHE cc_start: 0.9219 (t80) cc_final: 0.8971 (t80) REVERT: B 269 MET cc_start: 0.9019 (tpp) cc_final: 0.8631 (tpp) REVERT: B 291 ASP cc_start: 0.9040 (m-30) cc_final: 0.8767 (p0) REVERT: B 301 MET cc_start: 0.9159 (tmm) cc_final: 0.8854 (tmm) REVERT: B 348 MET cc_start: 0.7785 (mtp) cc_final: 0.7249 (ttm) REVERT: B 414 LEU cc_start: 0.9308 (tp) cc_final: 0.9078 (tp) REVERT: B 416 MET cc_start: 0.8820 (pmm) cc_final: 0.8581 (pmm) REVERT: C 235 MET cc_start: 0.9097 (mmp) cc_final: 0.8773 (mmp) REVERT: C 270 MET cc_start: 0.9008 (mtp) cc_final: 0.7974 (ttt) REVERT: C 322 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8096 (mt-10) REVERT: C 382 LEU cc_start: 0.9049 (mt) cc_final: 0.8772 (mt) REVERT: C 419 TYR cc_start: 0.7693 (t80) cc_final: 0.7218 (t80) REVERT: C 427 ASN cc_start: 0.8237 (p0) cc_final: 0.7992 (p0) REVERT: D 118 ASN cc_start: 0.9551 (m-40) cc_final: 0.9307 (m-40) REVERT: D 160 LEU cc_start: 0.9242 (tp) cc_final: 0.8953 (tt) REVERT: D 235 MET cc_start: 0.9180 (mmp) cc_final: 0.8848 (mmp) REVERT: D 269 MET cc_start: 0.8878 (mtp) cc_final: 0.8530 (mtp) REVERT: D 301 MET cc_start: 0.8933 (mtm) cc_final: 0.8560 (mtt) REVERT: D 337 ILE cc_start: 0.8693 (mt) cc_final: 0.8477 (mm) REVERT: D 399 ASN cc_start: 0.8840 (m-40) cc_final: 0.8614 (p0) REVERT: E 42 MET cc_start: 0.8397 (mtm) cc_final: 0.8044 (ptm) REVERT: E 92 GLU cc_start: 0.8833 (tt0) cc_final: 0.8494 (tm-30) REVERT: E 135 MET cc_start: 0.9398 (ttm) cc_final: 0.9175 (tmm) REVERT: E 235 MET cc_start: 0.8970 (mmt) cc_final: 0.8750 (mmm) REVERT: E 301 MET cc_start: 0.9181 (mtm) cc_final: 0.8882 (mtp) REVERT: E 348 MET cc_start: 0.8485 (mmp) cc_final: 0.8102 (mmp) REVERT: E 363 GLU cc_start: 0.9134 (tp30) cc_final: 0.8809 (tp30) REVERT: F 263 MET cc_start: 0.7270 (mpp) cc_final: 0.6998 (mpp) REVERT: F 341 MET cc_start: 0.8859 (tpt) cc_final: 0.8526 (tpp) REVERT: F 391 GLN cc_start: 0.9428 (mt0) cc_final: 0.9172 (mt0) REVERT: G 537 ASP cc_start: 0.8817 (t0) cc_final: 0.8472 (t0) REVERT: G 568 CYS cc_start: 0.8169 (m) cc_final: 0.7767 (t) REVERT: I 530 ILE cc_start: 0.8969 (tt) cc_final: 0.8661 (pt) outliers start: 5 outliers final: 1 residues processed: 381 average time/residue: 0.3729 time to fit residues: 218.9801 Evaluate side-chains 277 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 150 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN B 281 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN D 29 HIS F 45 ASN F 252 GLN G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24900 Z= 0.246 Angle : 1.033 30.772 33777 Z= 0.419 Chirality : 0.041 0.179 3852 Planarity : 0.004 0.074 4422 Dihedral : 7.278 131.371 3554 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.15), residues: 3066 helix: 1.59 (0.12), residues: 1781 sheet: -0.71 (0.27), residues: 321 loop : 0.21 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 48 HIS 0.006 0.001 HIS A 334 PHE 0.018 0.002 PHE B 60 TYR 0.025 0.002 TYR D 122 ARG 0.005 0.001 ARG C 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 3.079 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: A 58 ASP cc_start: 0.9203 (m-30) cc_final: 0.8660 (p0) REVERT: A 194 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8936 (tp30) REVERT: A 269 MET cc_start: 0.7397 (tpt) cc_final: 0.6725 (tpt) REVERT: A 291 ASP cc_start: 0.8732 (m-30) cc_final: 0.8087 (p0) REVERT: B 187 ASP cc_start: 0.9176 (m-30) cc_final: 0.8963 (m-30) REVERT: B 225 ASP cc_start: 0.7659 (m-30) cc_final: 0.7397 (m-30) REVERT: B 240 PHE cc_start: 0.9188 (t80) cc_final: 0.8919 (t80) REVERT: B 291 ASP cc_start: 0.9032 (m-30) cc_final: 0.8752 (p0) REVERT: B 301 MET cc_start: 0.9220 (tmm) cc_final: 0.8911 (tmm) REVERT: B 348 MET cc_start: 0.7736 (mtp) cc_final: 0.7215 (ttm) REVERT: B 414 LEU cc_start: 0.9328 (tp) cc_final: 0.8997 (tp) REVERT: C 235 MET cc_start: 0.9067 (mmp) cc_final: 0.8764 (mmm) REVERT: C 270 MET cc_start: 0.9002 (mtp) cc_final: 0.8021 (ttt) REVERT: C 322 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8067 (mt-10) REVERT: C 382 LEU cc_start: 0.8970 (mt) cc_final: 0.8720 (mt) REVERT: C 419 TYR cc_start: 0.7620 (t80) cc_final: 0.7075 (t80) REVERT: C 427 ASN cc_start: 0.8307 (p0) cc_final: 0.8078 (p0) REVERT: D 50 ASP cc_start: 0.8473 (m-30) cc_final: 0.7853 (p0) REVERT: D 118 ASN cc_start: 0.9518 (m-40) cc_final: 0.9254 (m-40) REVERT: D 160 LEU cc_start: 0.9254 (tp) cc_final: 0.8985 (tt) REVERT: D 235 MET cc_start: 0.9044 (mmp) cc_final: 0.8779 (mmp) REVERT: D 269 MET cc_start: 0.8877 (mtp) cc_final: 0.8629 (ttm) REVERT: D 270 MET cc_start: 0.9012 (ttm) cc_final: 0.8491 (tpp) REVERT: D 284 ILE cc_start: 0.9260 (mt) cc_final: 0.9054 (mt) REVERT: D 301 MET cc_start: 0.8924 (mtm) cc_final: 0.8524 (mtt) REVERT: E 92 GLU cc_start: 0.8822 (tt0) cc_final: 0.8466 (tm-30) REVERT: E 135 MET cc_start: 0.9367 (ttm) cc_final: 0.8997 (tmm) REVERT: E 187 ASP cc_start: 0.8591 (m-30) cc_final: 0.8317 (p0) REVERT: E 235 MET cc_start: 0.8901 (mmt) cc_final: 0.8316 (mmm) REVERT: E 301 MET cc_start: 0.9105 (mtm) cc_final: 0.8806 (mtp) REVERT: E 339 LEU cc_start: 0.8903 (tt) cc_final: 0.8117 (mt) REVERT: E 348 MET cc_start: 0.8495 (mmp) cc_final: 0.7995 (mmp) REVERT: E 363 GLU cc_start: 0.9096 (tp30) cc_final: 0.8817 (tp30) REVERT: E 399 ASN cc_start: 0.8847 (p0) cc_final: 0.8505 (t0) REVERT: F 98 ASP cc_start: 0.7553 (t0) cc_final: 0.7325 (p0) REVERT: F 235 MET cc_start: 0.7431 (mtt) cc_final: 0.6541 (mtp) REVERT: F 270 MET cc_start: 0.8644 (ttt) cc_final: 0.8296 (ttt) REVERT: F 391 GLN cc_start: 0.9416 (mt0) cc_final: 0.9086 (mt0) REVERT: G 537 ASP cc_start: 0.8777 (t0) cc_final: 0.8410 (t0) REVERT: G 568 CYS cc_start: 0.8091 (m) cc_final: 0.7709 (t) REVERT: H 550 ARG cc_start: 0.9062 (mmp80) cc_final: 0.8684 (mmm160) REVERT: I 530 ILE cc_start: 0.8949 (tt) cc_final: 0.8637 (pt) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.3808 time to fit residues: 219.8714 Evaluate side-chains 280 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 4.9990 chunk 264 optimal weight: 30.0000 chunk 58 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 294 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN G 541 HIS H 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24900 Z= 0.306 Angle : 1.076 32.064 33777 Z= 0.446 Chirality : 0.043 0.187 3852 Planarity : 0.005 0.100 4422 Dihedral : 7.408 132.721 3554 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.08 % Allowed : 1.67 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.93 (0.15), residues: 3066 helix: 1.31 (0.12), residues: 1789 sheet: -0.80 (0.28), residues: 310 loop : -0.04 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 457 HIS 0.006 0.002 HIS A 334 PHE 0.025 0.002 PHE C 147 TYR 0.027 0.002 TYR D 122 ARG 0.013 0.001 ARG F 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 362 time to evaluate : 3.239 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: A 58 ASP cc_start: 0.9260 (m-30) cc_final: 0.8625 (p0) REVERT: A 72 MET cc_start: 0.8606 (mmp) cc_final: 0.8374 (mmp) REVERT: A 194 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8934 (tp30) REVERT: A 242 MET cc_start: 0.8834 (ppp) cc_final: 0.8628 (ppp) REVERT: B 187 ASP cc_start: 0.9184 (m-30) cc_final: 0.8976 (m-30) REVERT: B 291 ASP cc_start: 0.9038 (m-30) cc_final: 0.8747 (p0) REVERT: B 301 MET cc_start: 0.9241 (tmm) cc_final: 0.8932 (tmm) REVERT: B 348 MET cc_start: 0.7749 (mtp) cc_final: 0.7201 (mpp) REVERT: B 414 LEU cc_start: 0.9293 (tp) cc_final: 0.9032 (tt) REVERT: C 235 MET cc_start: 0.9076 (mmp) cc_final: 0.8779 (mmm) REVERT: C 250 MET cc_start: 0.8730 (tmm) cc_final: 0.8492 (tmm) REVERT: C 270 MET cc_start: 0.9055 (mtp) cc_final: 0.8131 (ttt) REVERT: C 322 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8056 (mt-10) REVERT: C 382 LEU cc_start: 0.9073 (mt) cc_final: 0.8821 (mt) REVERT: C 419 TYR cc_start: 0.7492 (t80) cc_final: 0.6971 (t80) REVERT: C 427 ASN cc_start: 0.8263 (p0) cc_final: 0.8055 (p0) REVERT: D 50 ASP cc_start: 0.8462 (m-30) cc_final: 0.7804 (p0) REVERT: D 118 ASN cc_start: 0.9579 (m-40) cc_final: 0.9319 (m-40) REVERT: D 301 MET cc_start: 0.8964 (mtm) cc_final: 0.8607 (mtt) REVERT: E 42 MET cc_start: 0.8669 (ptp) cc_final: 0.8401 (ptp) REVERT: E 92 GLU cc_start: 0.8845 (tt0) cc_final: 0.8441 (tm-30) REVERT: E 135 MET cc_start: 0.9338 (ttm) cc_final: 0.9023 (tmm) REVERT: E 235 MET cc_start: 0.8854 (mmt) cc_final: 0.8368 (mmm) REVERT: E 348 MET cc_start: 0.8598 (mmp) cc_final: 0.8105 (mmp) REVERT: E 363 GLU cc_start: 0.9124 (tp30) cc_final: 0.8853 (tp30) REVERT: E 399 ASN cc_start: 0.8865 (p0) cc_final: 0.8434 (t0) REVERT: F 192 ARG cc_start: 0.8046 (ttt90) cc_final: 0.7814 (tpp-160) REVERT: F 235 MET cc_start: 0.7446 (mtt) cc_final: 0.6565 (mtt) REVERT: F 263 MET cc_start: 0.7207 (mpp) cc_final: 0.6966 (mpp) REVERT: F 270 MET cc_start: 0.8733 (ttt) cc_final: 0.8499 (ttt) REVERT: F 391 GLN cc_start: 0.9396 (mt0) cc_final: 0.9104 (mt0) REVERT: F 418 ILE cc_start: 0.8190 (mp) cc_final: 0.7782 (mp) REVERT: G 537 ASP cc_start: 0.8811 (t0) cc_final: 0.8457 (t0) REVERT: G 568 CYS cc_start: 0.8257 (m) cc_final: 0.7874 (t) REVERT: H 541 HIS cc_start: 0.9181 (m-70) cc_final: 0.8959 (m170) REVERT: H 550 ARG cc_start: 0.9055 (mmp80) cc_final: 0.8670 (mmm160) REVERT: I 530 ILE cc_start: 0.8939 (tt) cc_final: 0.8613 (pt) outliers start: 2 outliers final: 1 residues processed: 363 average time/residue: 0.3864 time to fit residues: 217.3405 Evaluate side-chains 272 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 214 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 293 optimal weight: 50.0000 chunk 183 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN B 243 ASN B 252 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN F 252 GLN G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24900 Z= 0.215 Angle : 1.035 30.550 33777 Z= 0.419 Chirality : 0.042 0.275 3852 Planarity : 0.004 0.083 4422 Dihedral : 7.255 131.394 3554 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.15), residues: 3066 helix: 1.41 (0.12), residues: 1802 sheet: -0.78 (0.28), residues: 321 loop : 0.04 (0.22), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 48 HIS 0.006 0.001 HIS A 67 PHE 0.016 0.002 PHE B 240 TYR 0.037 0.002 TYR B 122 ARG 0.010 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.826 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: A 58 ASP cc_start: 0.9200 (m-30) cc_final: 0.8558 (p0) REVERT: A 194 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8934 (tp30) REVERT: B 82 ILE cc_start: 0.8464 (mt) cc_final: 0.8201 (mp) REVERT: B 187 ASP cc_start: 0.9114 (m-30) cc_final: 0.8892 (m-30) REVERT: B 291 ASP cc_start: 0.8970 (m-30) cc_final: 0.8683 (p0) REVERT: B 301 MET cc_start: 0.9248 (tmm) cc_final: 0.8971 (tmm) REVERT: C 235 MET cc_start: 0.9030 (mmp) cc_final: 0.8723 (mmm) REVERT: C 250 MET cc_start: 0.8761 (tmm) cc_final: 0.8512 (tmm) REVERT: C 270 MET cc_start: 0.8991 (mtp) cc_final: 0.7940 (mtp) REVERT: C 312 ILE cc_start: 0.9443 (mp) cc_final: 0.9045 (tt) REVERT: C 322 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8027 (mt-10) REVERT: C 382 LEU cc_start: 0.9023 (mt) cc_final: 0.8796 (mt) REVERT: C 419 TYR cc_start: 0.7472 (t80) cc_final: 0.6925 (t80) REVERT: D 50 ASP cc_start: 0.8481 (m-30) cc_final: 0.7806 (p0) REVERT: D 118 ASN cc_start: 0.9521 (m-40) cc_final: 0.9231 (m-40) REVERT: D 270 MET cc_start: 0.9024 (ttm) cc_final: 0.8822 (tpp) REVERT: D 301 MET cc_start: 0.8908 (mtm) cc_final: 0.8535 (mtt) REVERT: D 348 MET cc_start: 0.8508 (tpp) cc_final: 0.8250 (tpp) REVERT: E 92 GLU cc_start: 0.8777 (tt0) cc_final: 0.8383 (tm-30) REVERT: E 135 MET cc_start: 0.9331 (ttm) cc_final: 0.8977 (tmm) REVERT: E 167 LYS cc_start: 0.9237 (pttp) cc_final: 0.8987 (pttt) REVERT: E 187 ASP cc_start: 0.8576 (m-30) cc_final: 0.8292 (p0) REVERT: E 235 MET cc_start: 0.8786 (mmt) cc_final: 0.8415 (mmm) REVERT: E 301 MET cc_start: 0.9002 (mtm) cc_final: 0.8795 (mtp) REVERT: E 342 ILE cc_start: 0.9403 (mm) cc_final: 0.9162 (mp) REVERT: E 348 MET cc_start: 0.8548 (mmp) cc_final: 0.8021 (mmp) REVERT: E 399 ASN cc_start: 0.8809 (p0) cc_final: 0.8398 (t0) REVERT: F 72 MET cc_start: 0.9001 (ptt) cc_final: 0.8736 (ptt) REVERT: F 98 ASP cc_start: 0.7636 (t0) cc_final: 0.7403 (p0) REVERT: F 235 MET cc_start: 0.7347 (mtt) cc_final: 0.6425 (mtp) REVERT: F 263 MET cc_start: 0.7326 (mpp) cc_final: 0.7071 (mpp) REVERT: F 270 MET cc_start: 0.8644 (ttt) cc_final: 0.8382 (ttt) REVERT: F 391 GLN cc_start: 0.9394 (mt0) cc_final: 0.9043 (mt0) REVERT: G 537 ASP cc_start: 0.8775 (t0) cc_final: 0.8418 (t0) REVERT: G 568 CYS cc_start: 0.8252 (m) cc_final: 0.7849 (t) REVERT: H 541 HIS cc_start: 0.9120 (m-70) cc_final: 0.8878 (m170) REVERT: H 550 ARG cc_start: 0.9059 (mmp80) cc_final: 0.8646 (mmm160) REVERT: I 530 ILE cc_start: 0.8918 (tt) cc_final: 0.8600 (pt) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.3738 time to fit residues: 209.7071 Evaluate side-chains 275 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 174 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 199 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 490 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24900 Z= 0.216 Angle : 1.040 30.684 33777 Z= 0.420 Chirality : 0.042 0.210 3852 Planarity : 0.004 0.071 4422 Dihedral : 7.177 131.095 3554 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3066 helix: 1.48 (0.12), residues: 1799 sheet: -0.72 (0.28), residues: 317 loop : 0.06 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 457 HIS 0.007 0.001 HIS A 67 PHE 0.029 0.002 PHE A 147 TYR 0.027 0.002 TYR B 122 ARG 0.015 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 3.090 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: A 58 ASP cc_start: 0.9215 (m-30) cc_final: 0.8573 (p0) REVERT: A 194 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8908 (tp30) REVERT: A 291 ASP cc_start: 0.8779 (m-30) cc_final: 0.8117 (p0) REVERT: B 187 ASP cc_start: 0.9098 (m-30) cc_final: 0.8873 (m-30) REVERT: B 291 ASP cc_start: 0.8977 (m-30) cc_final: 0.8681 (p0) REVERT: B 301 MET cc_start: 0.9260 (tmm) cc_final: 0.8988 (tmm) REVERT: B 348 MET cc_start: 0.7247 (mtp) cc_final: 0.6941 (ttm) REVERT: B 414 LEU cc_start: 0.9283 (tp) cc_final: 0.8892 (tt) REVERT: C 235 MET cc_start: 0.9013 (mmp) cc_final: 0.8721 (mmm) REVERT: C 250 MET cc_start: 0.8766 (tmm) cc_final: 0.8517 (tmm) REVERT: C 312 ILE cc_start: 0.9410 (mp) cc_final: 0.8997 (tt) REVERT: C 322 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8106 (mt-10) REVERT: C 337 ILE cc_start: 0.8882 (tt) cc_final: 0.8367 (mt) REVERT: C 382 LEU cc_start: 0.9056 (mt) cc_final: 0.8822 (mt) REVERT: C 419 TYR cc_start: 0.7581 (t80) cc_final: 0.7068 (t80) REVERT: C 427 ASN cc_start: 0.8413 (p0) cc_final: 0.8120 (p0) REVERT: D 50 ASP cc_start: 0.8519 (m-30) cc_final: 0.7825 (p0) REVERT: D 118 ASN cc_start: 0.9572 (m-40) cc_final: 0.9265 (m-40) REVERT: D 135 MET cc_start: 0.8949 (ppp) cc_final: 0.8485 (ppp) REVERT: D 301 MET cc_start: 0.8908 (mtm) cc_final: 0.8537 (mtt) REVERT: D 348 MET cc_start: 0.8570 (tpp) cc_final: 0.8341 (tpp) REVERT: E 92 GLU cc_start: 0.8764 (tt0) cc_final: 0.8384 (tm-30) REVERT: E 135 MET cc_start: 0.9338 (ttm) cc_final: 0.9036 (tmm) REVERT: E 235 MET cc_start: 0.8756 (mmt) cc_final: 0.8362 (mmm) REVERT: E 339 LEU cc_start: 0.9009 (tt) cc_final: 0.8147 (mt) REVERT: E 348 MET cc_start: 0.8576 (mmp) cc_final: 0.8037 (mmp) REVERT: E 399 ASN cc_start: 0.8840 (p0) cc_final: 0.8383 (t0) REVERT: F 72 MET cc_start: 0.9039 (ptt) cc_final: 0.8767 (ptt) REVERT: F 98 ASP cc_start: 0.7549 (t0) cc_final: 0.7341 (p0) REVERT: F 235 MET cc_start: 0.7376 (mtt) cc_final: 0.6479 (mtt) REVERT: F 263 MET cc_start: 0.7037 (mpp) cc_final: 0.6726 (mpp) REVERT: F 284 ILE cc_start: 0.9079 (mt) cc_final: 0.8670 (mt) REVERT: F 391 GLN cc_start: 0.9371 (mt0) cc_final: 0.9044 (mt0) REVERT: F 418 ILE cc_start: 0.8101 (mp) cc_final: 0.7674 (mp) REVERT: G 537 ASP cc_start: 0.8739 (t0) cc_final: 0.8390 (t0) REVERT: G 568 CYS cc_start: 0.8133 (m) cc_final: 0.7799 (t) REVERT: H 550 ARG cc_start: 0.9050 (mmp80) cc_final: 0.8631 (mmm160) REVERT: I 530 ILE cc_start: 0.8908 (tt) cc_final: 0.8592 (pt) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.3802 time to fit residues: 207.2296 Evaluate side-chains 266 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 256 optimal weight: 20.0000 chunk 273 optimal weight: 20.0000 chunk 164 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 246 optimal weight: 0.8980 chunk 258 optimal weight: 8.9990 chunk 272 optimal weight: 0.0000 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24900 Z= 0.180 Angle : 1.032 30.604 33777 Z= 0.414 Chirality : 0.042 0.224 3852 Planarity : 0.004 0.070 4422 Dihedral : 7.021 128.908 3554 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.15), residues: 3066 helix: 1.54 (0.12), residues: 1802 sheet: -0.65 (0.28), residues: 313 loop : 0.13 (0.22), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 48 HIS 0.008 0.001 HIS H 541 PHE 0.025 0.001 PHE B 240 TYR 0.030 0.002 TYR F 105 ARG 0.023 0.001 ARG F 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 2.976 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 58 ASP cc_start: 0.9186 (m-30) cc_final: 0.8609 (p0) REVERT: A 84 LEU cc_start: 0.9392 (pp) cc_final: 0.9000 (mp) REVERT: A 291 ASP cc_start: 0.8814 (m-30) cc_final: 0.8180 (p0) REVERT: A 451 LEU cc_start: 0.8812 (mt) cc_final: 0.8599 (mt) REVERT: B 187 ASP cc_start: 0.9098 (m-30) cc_final: 0.8866 (m-30) REVERT: B 240 PHE cc_start: 0.9205 (t80) cc_final: 0.8925 (t80) REVERT: B 244 LEU cc_start: 0.9601 (mt) cc_final: 0.9319 (mt) REVERT: B 269 MET cc_start: 0.8811 (tpt) cc_final: 0.8057 (tpp) REVERT: B 291 ASP cc_start: 0.8936 (m-30) cc_final: 0.8656 (p0) REVERT: B 301 MET cc_start: 0.9260 (tmm) cc_final: 0.8786 (ppp) REVERT: B 348 MET cc_start: 0.7154 (mtp) cc_final: 0.6943 (ttm) REVERT: C 235 MET cc_start: 0.8937 (mmp) cc_final: 0.8633 (mmm) REVERT: C 250 MET cc_start: 0.8775 (tmm) cc_final: 0.8496 (tmm) REVERT: C 312 ILE cc_start: 0.9330 (mp) cc_final: 0.8890 (tt) REVERT: C 322 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7999 (mt-10) REVERT: C 337 ILE cc_start: 0.8741 (tt) cc_final: 0.8259 (mt) REVERT: C 427 ASN cc_start: 0.8421 (p0) cc_final: 0.8162 (p0) REVERT: D 50 ASP cc_start: 0.8471 (m-30) cc_final: 0.7784 (p0) REVERT: D 118 ASN cc_start: 0.9528 (m-40) cc_final: 0.9180 (m-40) REVERT: D 135 MET cc_start: 0.8952 (ppp) cc_final: 0.8535 (ppp) REVERT: D 160 LEU cc_start: 0.9284 (tp) cc_final: 0.9037 (tt) REVERT: D 301 MET cc_start: 0.8882 (mtm) cc_final: 0.8542 (mtt) REVERT: D 348 MET cc_start: 0.8572 (tpp) cc_final: 0.8303 (tpp) REVERT: E 42 MET cc_start: 0.8510 (ptp) cc_final: 0.7877 (ppp) REVERT: E 72 MET cc_start: 0.8015 (mtt) cc_final: 0.7735 (mtm) REVERT: E 92 GLU cc_start: 0.8711 (tt0) cc_final: 0.8362 (tm-30) REVERT: E 135 MET cc_start: 0.9309 (ttm) cc_final: 0.9027 (tmm) REVERT: E 235 MET cc_start: 0.8695 (mmt) cc_final: 0.8298 (mmm) REVERT: E 339 LEU cc_start: 0.8976 (tt) cc_final: 0.8133 (mt) REVERT: E 348 MET cc_start: 0.8544 (mmp) cc_final: 0.7979 (mmp) REVERT: E 373 LYS cc_start: 0.9559 (mmmt) cc_final: 0.9354 (mmmm) REVERT: E 399 ASN cc_start: 0.8758 (p0) cc_final: 0.8341 (t0) REVERT: F 72 MET cc_start: 0.8996 (ptt) cc_final: 0.8692 (ptt) REVERT: F 98 ASP cc_start: 0.7595 (t0) cc_final: 0.7385 (p0) REVERT: F 235 MET cc_start: 0.7297 (mtt) cc_final: 0.6391 (mtp) REVERT: F 391 GLN cc_start: 0.9378 (mt0) cc_final: 0.9063 (mt0) REVERT: G 537 ASP cc_start: 0.8726 (t0) cc_final: 0.8378 (t0) REVERT: G 568 CYS cc_start: 0.7976 (m) cc_final: 0.7691 (t) REVERT: H 541 HIS cc_start: 0.9072 (m-70) cc_final: 0.8826 (m170) REVERT: H 550 ARG cc_start: 0.9062 (mmp80) cc_final: 0.8643 (mmm160) REVERT: I 521 MET cc_start: 0.7050 (ppp) cc_final: 0.6800 (pmm) REVERT: I 530 ILE cc_start: 0.8903 (tt) cc_final: 0.8595 (pt) REVERT: I 537 ASP cc_start: 0.9090 (t70) cc_final: 0.8728 (p0) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.3699 time to fit residues: 204.0935 Evaluate side-chains 276 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 6.9990 chunk 288 optimal weight: 0.8980 chunk 176 optimal weight: 0.2980 chunk 136 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 chunk 241 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS H 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24900 Z= 0.197 Angle : 1.037 30.592 33777 Z= 0.416 Chirality : 0.042 0.249 3852 Planarity : 0.004 0.082 4422 Dihedral : 6.979 129.620 3554 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.15), residues: 3066 helix: 1.54 (0.12), residues: 1808 sheet: -0.68 (0.28), residues: 319 loop : 0.13 (0.22), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 48 HIS 0.007 0.001 HIS H 541 PHE 0.028 0.002 PHE A 147 TYR 0.024 0.001 TYR D 122 ARG 0.011 0.001 ARG F 285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 2.733 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 38 LEU cc_start: 0.8798 (pp) cc_final: 0.8569 (pp) REVERT: A 58 ASP cc_start: 0.9197 (m-30) cc_final: 0.8613 (p0) REVERT: A 84 LEU cc_start: 0.9382 (pp) cc_final: 0.9000 (mp) REVERT: A 291 ASP cc_start: 0.8817 (m-30) cc_final: 0.8191 (p0) REVERT: A 451 LEU cc_start: 0.8824 (mt) cc_final: 0.8614 (mt) REVERT: B 42 MET cc_start: 0.8248 (mtp) cc_final: 0.7758 (ttm) REVERT: B 72 MET cc_start: 0.8821 (mtt) cc_final: 0.8474 (mmm) REVERT: B 187 ASP cc_start: 0.9113 (m-30) cc_final: 0.8871 (m-30) REVERT: B 240 PHE cc_start: 0.9197 (t80) cc_final: 0.8943 (t80) REVERT: B 244 LEU cc_start: 0.9606 (mt) cc_final: 0.9287 (mt) REVERT: B 269 MET cc_start: 0.8824 (tpt) cc_final: 0.8083 (tpp) REVERT: B 291 ASP cc_start: 0.8936 (m-30) cc_final: 0.8601 (p0) REVERT: B 301 MET cc_start: 0.9249 (tmm) cc_final: 0.8981 (tmm) REVERT: B 348 MET cc_start: 0.7175 (mtp) cc_final: 0.6952 (ttm) REVERT: C 235 MET cc_start: 0.8871 (mmp) cc_final: 0.8576 (mmm) REVERT: C 250 MET cc_start: 0.8810 (tmm) cc_final: 0.8517 (tmm) REVERT: C 312 ILE cc_start: 0.9359 (mp) cc_final: 0.8909 (tt) REVERT: C 322 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7995 (mt-10) REVERT: C 337 ILE cc_start: 0.8721 (tt) cc_final: 0.8239 (mt) REVERT: C 427 ASN cc_start: 0.8396 (p0) cc_final: 0.8134 (p0) REVERT: D 38 LEU cc_start: 0.9059 (mt) cc_final: 0.8775 (mt) REVERT: D 50 ASP cc_start: 0.8435 (m-30) cc_final: 0.7778 (p0) REVERT: D 118 ASN cc_start: 0.9515 (m-40) cc_final: 0.9176 (m-40) REVERT: D 135 MET cc_start: 0.8948 (ppp) cc_final: 0.8541 (ppp) REVERT: D 160 LEU cc_start: 0.9299 (tp) cc_final: 0.9035 (tt) REVERT: D 269 MET cc_start: 0.8720 (ptm) cc_final: 0.8237 (ppp) REVERT: D 301 MET cc_start: 0.8901 (mtm) cc_final: 0.8515 (mtt) REVERT: E 42 MET cc_start: 0.8479 (ptp) cc_final: 0.7811 (ppp) REVERT: E 92 GLU cc_start: 0.8718 (tt0) cc_final: 0.8360 (tm-30) REVERT: E 135 MET cc_start: 0.9312 (ttm) cc_final: 0.9031 (tmm) REVERT: E 235 MET cc_start: 0.8676 (mmt) cc_final: 0.8293 (mmm) REVERT: E 242 MET cc_start: 0.8827 (mmp) cc_final: 0.8359 (mmm) REVERT: E 269 MET cc_start: 0.9287 (ttp) cc_final: 0.9080 (ttm) REVERT: E 339 LEU cc_start: 0.9009 (tt) cc_final: 0.8206 (mt) REVERT: E 348 MET cc_start: 0.8546 (mmp) cc_final: 0.7992 (mmp) REVERT: E 363 GLU cc_start: 0.9139 (tp30) cc_final: 0.8874 (tp30) REVERT: E 399 ASN cc_start: 0.8791 (p0) cc_final: 0.8359 (t0) REVERT: F 38 LEU cc_start: 0.8420 (mt) cc_final: 0.7582 (mt) REVERT: F 72 MET cc_start: 0.8964 (ptt) cc_final: 0.8693 (ptt) REVERT: F 235 MET cc_start: 0.7293 (mtt) cc_final: 0.6356 (mtp) REVERT: F 347 LEU cc_start: 0.8524 (mt) cc_final: 0.8265 (mt) REVERT: F 391 GLN cc_start: 0.9383 (mt0) cc_final: 0.9079 (mt0) REVERT: G 537 ASP cc_start: 0.8745 (t0) cc_final: 0.8408 (t0) REVERT: G 568 CYS cc_start: 0.7985 (m) cc_final: 0.7681 (t) REVERT: H 541 HIS cc_start: 0.8844 (m90) cc_final: 0.8596 (m170) REVERT: H 550 ARG cc_start: 0.9054 (mmp80) cc_final: 0.8644 (mmm160) REVERT: I 521 MET cc_start: 0.7050 (ppp) cc_final: 0.6801 (pmm) REVERT: I 530 ILE cc_start: 0.8888 (tt) cc_final: 0.8580 (pt) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.3664 time to fit residues: 197.9080 Evaluate side-chains 269 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 73 optimal weight: 0.0050 chunk 222 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 0.0040 overall best weight: 2.0012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.075353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.058794 restraints weight = 173823.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.060228 restraints weight = 123551.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.061244 restraints weight = 94929.410| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24900 Z= 0.183 Angle : 1.035 30.494 33777 Z= 0.415 Chirality : 0.042 0.243 3852 Planarity : 0.004 0.068 4422 Dihedral : 6.902 129.548 3554 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.16), residues: 3066 helix: 1.58 (0.12), residues: 1800 sheet: -0.66 (0.28), residues: 313 loop : 0.22 (0.22), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 48 HIS 0.004 0.001 HIS A 334 PHE 0.024 0.001 PHE B 240 TYR 0.023 0.001 TYR D 122 ARG 0.008 0.001 ARG C 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5267.04 seconds wall clock time: 94 minutes 52.27 seconds (5692.27 seconds total)