Starting phenix.real_space_refine on Mon Mar 18 14:30:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0b_13743/03_2024/7q0b_13743_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0b_13743/03_2024/7q0b_13743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0b_13743/03_2024/7q0b_13743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0b_13743/03_2024/7q0b_13743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0b_13743/03_2024/7q0b_13743_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0b_13743/03_2024/7q0b_13743_updated.pdb" } resolution = 3.0 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 104 5.16 5 C 13542 2.51 5 N 3634 2.21 5 O 3886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A ASP 594": "OD1" <-> "OD2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 594": "OD1" <-> "OD2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 594": "OD1" <-> "OD2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 594": "OD1" <-> "OD2" Residue "F GLU 326": "OE1" <-> "OE2" Residue "G TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21168 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5002 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 5026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5026 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 28, 'TRANS': 594} Chain breaks: 2 Chain: "C" Number of atoms: 5026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5026 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 28, 'TRANS': 594} Chain breaks: 2 Chain: "D" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5002 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain breaks: 2 Chain: "E" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "F" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "G" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "H" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Time building chain proxies: 9.44, per 1000 atoms: 0.45 Number of scatterers: 21168 At special positions: 0 Unit cell: (124.89, 111.858, 137.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 2 15.00 O 3886 8.00 N 3634 7.00 C 13542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.18 Conformation dependent library (CDL) restraints added in 3.5 seconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4908 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 12 sheets defined 47.8% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.38 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 removed outlier: 4.727A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 76 Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 126 through 137 removed outlier: 3.749A pdb=" N GLY A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 167 Processing helix chain 'A' and resid 182 through 193 removed outlier: 5.283A pdb=" N VAL A 186 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 removed outlier: 4.151A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 284 through 287 No H-bonds generated for 'chain 'A' and resid 284 through 287' Processing helix chain 'A' and resid 294 through 311 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 377 through 409 Processing helix chain 'A' and resid 422 through 435 removed outlier: 3.556A pdb=" N THR A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 463 Processing helix chain 'A' and resid 493 through 499 removed outlier: 3.788A pdb=" N GLY A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 533 through 541 Processing helix chain 'A' and resid 545 through 548 Processing helix chain 'A' and resid 560 through 575 Processing helix chain 'A' and resid 579 through 596 removed outlier: 4.063A pdb=" N LEU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER A 593 " --> pdb=" O THR A 589 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP A 594 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 601 No H-bonds generated for 'chain 'A' and resid 598 through 601' Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'B' and resid 43 through 58 removed outlier: 4.726A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 76 Processing helix chain 'B' and resid 85 through 96 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.764A pdb=" N GLY B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 167 Processing helix chain 'B' and resid 182 through 193 removed outlier: 5.291A pdb=" N VAL B 186 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 214 removed outlier: 4.151A pdb=" N TYR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 235 Processing helix chain 'B' and resid 239 through 250 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 284 through 287 No H-bonds generated for 'chain 'B' and resid 284 through 287' Processing helix chain 'B' and resid 294 through 311 Processing helix chain 'B' and resid 339 through 355 Processing helix chain 'B' and resid 377 through 409 Processing helix chain 'B' and resid 422 through 434 Processing helix chain 'B' and resid 455 through 463 Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.969A pdb=" N GLY B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 521 Processing helix chain 'B' and resid 533 through 541 Processing helix chain 'B' and resid 545 through 548 Processing helix chain 'B' and resid 560 through 575 Processing helix chain 'B' and resid 579 through 596 removed outlier: 3.513A pdb=" N ARG B 591 " --> pdb=" O ASN B 587 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N SER B 593 " --> pdb=" O THR B 589 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP B 594 " --> pdb=" O GLU B 590 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 601 No H-bonds generated for 'chain 'B' and resid 598 through 601' Processing helix chain 'B' and resid 603 through 616 Processing helix chain 'C' and resid 43 through 58 removed outlier: 4.728A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 76 Processing helix chain 'C' and resid 85 through 96 Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 123 through 137 removed outlier: 4.314A pdb=" N GLU C 127 " --> pdb=" O TRP C 124 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS C 130 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 133 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N CYS C 137 " --> pdb=" O TRP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 167 Processing helix chain 'C' and resid 182 through 193 removed outlier: 5.304A pdb=" N VAL C 186 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 187 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 removed outlier: 4.150A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 235 Processing helix chain 'C' and resid 239 through 250 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 284 through 287 No H-bonds generated for 'chain 'C' and resid 284 through 287' Processing helix chain 'C' and resid 294 through 311 Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 377 through 409 Processing helix chain 'C' and resid 422 through 434 Processing helix chain 'C' and resid 455 through 463 Processing helix chain 'C' and resid 493 through 499 removed outlier: 3.763A pdb=" N GLY C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 521 Processing helix chain 'C' and resid 533 through 541 Processing helix chain 'C' and resid 545 through 548 Processing helix chain 'C' and resid 560 through 575 Processing helix chain 'C' and resid 579 through 596 removed outlier: 4.063A pdb=" N LEU C 592 " --> pdb=" O ARG C 588 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N SER C 593 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP C 594 " --> pdb=" O GLU C 590 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 601 No H-bonds generated for 'chain 'C' and resid 598 through 601' Processing helix chain 'C' and resid 603 through 616 Processing helix chain 'D' and resid 43 through 58 removed outlier: 4.727A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 123 through 137 removed outlier: 4.311A pdb=" N GLU D 127 " --> pdb=" O TRP D 124 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS D 130 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU D 133 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS D 137 " --> pdb=" O TRP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 167 Processing helix chain 'D' and resid 182 through 193 removed outlier: 5.304A pdb=" N VAL D 186 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D 187 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 214 removed outlier: 4.150A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 235 Processing helix chain 'D' and resid 239 through 250 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 284 through 287 No H-bonds generated for 'chain 'D' and resid 284 through 287' Processing helix chain 'D' and resid 294 through 311 Processing helix chain 'D' and resid 339 through 355 Processing helix chain 'D' and resid 377 through 409 Processing helix chain 'D' and resid 422 through 434 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 493 through 499 removed outlier: 3.760A pdb=" N GLY D 499 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 521 Processing helix chain 'D' and resid 533 through 541 Processing helix chain 'D' and resid 545 through 548 Processing helix chain 'D' and resid 560 through 575 Processing helix chain 'D' and resid 579 through 596 removed outlier: 4.078A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER D 593 " --> pdb=" O THR D 589 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASP D 594 " --> pdb=" O GLU D 590 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU D 595 " --> pdb=" O ARG D 591 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 601 No H-bonds generated for 'chain 'D' and resid 598 through 601' Processing helix chain 'D' and resid 603 through 616 Processing helix chain 'E' and resid 319 through 327 Processing helix chain 'E' and resid 338 through 347 removed outlier: 4.218A pdb=" N THR E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 327 Processing helix chain 'F' and resid 338 through 347 removed outlier: 4.220A pdb=" N THR F 347 " --> pdb=" O ARG F 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 327 Processing helix chain 'G' and resid 338 through 347 removed outlier: 4.235A pdb=" N THR G 347 " --> pdb=" O ARG G 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 327 Processing helix chain 'H' and resid 338 through 347 removed outlier: 4.237A pdb=" N THR H 347 " --> pdb=" O ARG H 343 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.931A pdb=" N LEU A 113 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N PHE A 63 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 29 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL A 65 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N HIS A 174 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE A 30 " --> pdb=" O HIS A 174 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 176 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 32 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N HIS A 178 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 254 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N THR A 204 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR A 256 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 323 through 329 removed outlier: 6.615A pdb=" N THR A 361 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE A 326 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 363 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE A 328 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE A 365 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 526 through 529 Processing sheet with id= D, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.955A pdb=" N LEU B 113 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N PHE B 63 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU B 29 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL B 65 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU B 31 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N HIS B 174 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE B 30 " --> pdb=" O HIS B 174 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B 176 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL B 32 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N HIS B 178 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 254 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N THR B 204 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR B 256 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 323 through 329 removed outlier: 6.614A pdb=" N THR B 361 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE B 326 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 363 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE B 328 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE B 365 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 526 through 529 Processing sheet with id= G, first strand: chain 'C' and resid 77 through 79 removed outlier: 3.949A pdb=" N LEU C 113 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N PHE C 63 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU C 29 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL C 65 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N HIS C 174 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE C 30 " --> pdb=" O HIS C 174 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 176 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C 32 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N HIS C 178 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 254 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N THR C 204 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR C 256 " --> pdb=" O THR C 204 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 323 through 329 removed outlier: 6.613A pdb=" N THR C 361 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE C 326 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 363 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ILE C 328 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE C 365 " --> pdb=" O ILE C 328 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 526 through 529 Processing sheet with id= J, first strand: chain 'D' and resid 77 through 79 removed outlier: 3.949A pdb=" N LEU D 113 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N PHE D 63 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU D 29 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL D 65 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU D 31 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS D 174 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N PHE D 30 " --> pdb=" O HIS D 174 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL D 176 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL D 32 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N HIS D 178 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL D 254 " --> pdb=" O PHE D 202 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N THR D 204 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR D 256 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 323 through 329 removed outlier: 6.611A pdb=" N THR D 361 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE D 326 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL D 363 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE D 328 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE D 365 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 526 through 529 862 hydrogen bonds defined for protein. 2439 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: 6.10 Time building geometry restraints manager: 8.77 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: 6906 1.34 - 1.46: 3823 1.46 - 1.57: 10827 1.57 - 1.69: 8 1.69 - 1.80: 156 Bond restraints: 21720 Sorted by residual: bond pdb=" CA ASP D 135 " pdb=" C ASP D 135 " ideal model delta sigma weight residual 1.523 1.505 0.017 1.41e-02 5.03e+03 1.48e+00 bond pdb=" C ARG B 638 " pdb=" N PRO B 639 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.16e+00 bond pdb=" CA VAL C 642 " pdb=" C VAL C 642 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.10e-02 2.27e+03 7.12e-01 bond pdb=" CA PRO D 639 " pdb=" C PRO D 639 " ideal model delta sigma weight residual 1.527 1.516 0.011 1.35e-02 5.49e+03 6.68e-01 bond pdb=" CB PRO D 639 " pdb=" CG PRO D 639 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.24e-01 ... (remaining 21715 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.03: 432 106.03 - 113.03: 11323 113.03 - 120.03: 7807 120.03 - 127.03: 9573 127.03 - 134.03: 291 Bond angle restraints: 29426 Sorted by residual: angle pdb=" N ARG B 638 " pdb=" CA ARG B 638 " pdb=" C ARG B 638 " ideal model delta sigma weight residual 109.81 116.74 -6.93 2.21e+00 2.05e-01 9.85e+00 angle pdb=" C SER A 641 " pdb=" N VAL A 642 " pdb=" CA VAL A 642 " ideal model delta sigma weight residual 121.70 125.93 -4.23 1.80e+00 3.09e-01 5.52e+00 angle pdb=" C ARG D 638 " pdb=" N PRO D 639 " pdb=" CA PRO D 639 " ideal model delta sigma weight residual 121.65 119.44 2.21 1.01e+00 9.80e-01 4.77e+00 angle pdb=" CA LEU B 488 " pdb=" CB LEU B 488 " pdb=" CG LEU B 488 " ideal model delta sigma weight residual 116.30 123.55 -7.25 3.50e+00 8.16e-02 4.29e+00 angle pdb=" CA LEU A 488 " pdb=" CB LEU A 488 " pdb=" CG LEU A 488 " ideal model delta sigma weight residual 116.30 123.50 -7.20 3.50e+00 8.16e-02 4.23e+00 ... (remaining 29421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 11412 17.85 - 35.71: 1090 35.71 - 53.56: 203 53.56 - 71.41: 47 71.41 - 89.26: 40 Dihedral angle restraints: 12792 sinusoidal: 5174 harmonic: 7618 Sorted by residual: dihedral pdb=" CA ARG B 638 " pdb=" C ARG B 638 " pdb=" N PRO B 639 " pdb=" CA PRO B 639 " ideal model delta harmonic sigma weight residual -180.00 -153.40 -26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA LEU C 488 " pdb=" C LEU C 488 " pdb=" N LEU C 489 " pdb=" CA LEU C 489 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA LEU D 488 " pdb=" C LEU D 488 " pdb=" N LEU D 489 " pdb=" CA LEU D 489 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 12789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1957 0.033 - 0.065: 833 0.065 - 0.098: 219 0.098 - 0.130: 97 0.130 - 0.163: 20 Chirality restraints: 3126 Sorted by residual: chirality pdb=" CA THR C 515 " pdb=" N THR C 515 " pdb=" C THR C 515 " pdb=" CB THR C 515 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA THR D 515 " pdb=" N THR D 515 " pdb=" C THR D 515 " pdb=" CB THR D 515 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA THR A 515 " pdb=" N THR A 515 " pdb=" C THR A 515 " pdb=" CB THR A 515 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 3123 not shown) Planarity restraints: 3802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 638 " -0.043 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO B 639 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 639 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 639 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 303 " -0.127 9.50e-02 1.11e+02 5.70e-02 2.33e+00 pdb=" NE ARG C 303 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 303 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 303 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 303 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 303 " 0.126 9.50e-02 1.11e+02 5.66e-02 2.28e+00 pdb=" NE ARG D 303 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG D 303 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 303 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 303 " 0.001 2.00e-02 2.50e+03 ... (remaining 3799 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4782 2.78 - 3.31: 19294 3.31 - 3.84: 34787 3.84 - 4.37: 42086 4.37 - 4.90: 73987 Nonbonded interactions: 174936 Sorted by model distance: nonbonded pdb=" OE2 GLU D 31 " pdb=" NE2 HIS D 180 " model vdw 2.254 2.520 nonbonded pdb=" OE2 GLU C 31 " pdb=" NE2 HIS C 180 " model vdw 2.255 2.520 nonbonded pdb=" OE2 GLU B 31 " pdb=" NE2 HIS B 180 " model vdw 2.255 2.520 nonbonded pdb=" OE2 GLU A 31 " pdb=" NE2 HIS A 180 " model vdw 2.261 2.520 nonbonded pdb=" OE2 GLU C 35 " pdb=" N GLY C 41 " model vdw 2.263 2.520 ... (remaining 174931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 640 or resid 642)) selection = (chain 'B' and (resid 13 through 640 or resid 642)) selection = (chain 'C' and (resid 13 through 640 or resid 642)) selection = (chain 'D' and (resid 13 through 640 or resid 642)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.380 Check model and map are aligned: 0.280 Set scattering table: 0.150 Process input model: 51.050 Find NCS groups from input model: 1.450 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: 0.000 Load rotamer database and sin/cos tables:10.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 0.039 21720 Z= 0.248 Angle : 0.542 7.249 29426 Z= 0.276 Chirality : 0.041 0.163 3126 Planarity : 0.004 0.066 3802 Dihedral : 15.106 89.265 7884 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.13 % Allowed : 0.22 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2580 helix: 1.36 (0.15), residues: 1326 sheet: -0.39 (0.29), residues: 342 loop : -0.55 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 134 HIS 0.003 0.001 HIS A 240 PHE 0.014 0.002 PHE A 22 TYR 0.010 0.001 TYR A 623 ARG 0.010 0.001 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 263 time to evaluate : 2.364 Fit side-chains REVERT: A 237 GLN cc_start: 0.7732 (mp10) cc_final: 0.7424 (mp10) REVERT: A 448 MET cc_start: 0.8162 (mmp) cc_final: 0.7961 (mmp) REVERT: B 237 GLN cc_start: 0.7729 (mp10) cc_final: 0.7421 (mp10) REVERT: B 448 MET cc_start: 0.8198 (mmp) cc_final: 0.7943 (mmp) REVERT: C 237 GLN cc_start: 0.7738 (mp10) cc_final: 0.7427 (mp10) REVERT: C 448 MET cc_start: 0.8197 (mmp) cc_final: 0.7635 (mmp) REVERT: D 237 GLN cc_start: 0.7685 (mp10) cc_final: 0.7388 (mp10) REVERT: D 293 PHE cc_start: 0.7623 (m-80) cc_final: 0.7232 (m-80) REVERT: D 448 MET cc_start: 0.8193 (mmp) cc_final: 0.7944 (mmp) REVERT: E 336 ASP cc_start: 0.8142 (m-30) cc_final: 0.7934 (m-30) REVERT: F 336 ASP cc_start: 0.8154 (m-30) cc_final: 0.7921 (m-30) REVERT: G 336 ASP cc_start: 0.8179 (m-30) cc_final: 0.7948 (m-30) REVERT: H 336 ASP cc_start: 0.8156 (m-30) cc_final: 0.7929 (m-30) outliers start: 3 outliers final: 0 residues processed: 265 average time/residue: 1.8654 time to fit residues: 542.9216 Evaluate side-chains 202 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 109 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 236 optimal weight: 0.1980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN B 360 GLN C 360 GLN D 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21720 Z= 0.256 Angle : 0.503 6.881 29426 Z= 0.259 Chirality : 0.041 0.155 3126 Planarity : 0.004 0.051 3802 Dihedral : 4.036 28.014 2884 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.42 % Allowed : 7.77 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2580 helix: 1.38 (0.14), residues: 1324 sheet: -0.53 (0.28), residues: 352 loop : -0.55 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 325 HIS 0.003 0.001 HIS A 205 PHE 0.014 0.002 PHE A 22 TYR 0.010 0.001 TYR A 623 ARG 0.006 0.000 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 217 time to evaluate : 2.469 Fit side-chains REVERT: A 282 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8760 (pp) REVERT: A 448 MET cc_start: 0.8184 (mmp) cc_final: 0.7902 (mmp) REVERT: A 489 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6535 (mm) REVERT: B 70 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6482 (tm-30) REVERT: B 282 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8742 (pp) REVERT: B 448 MET cc_start: 0.8214 (mmp) cc_final: 0.7866 (mmp) REVERT: B 489 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6487 (mm) REVERT: C 282 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8736 (pp) REVERT: C 489 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6501 (mm) REVERT: D 237 GLN cc_start: 0.7698 (mp10) cc_final: 0.7475 (mp10) REVERT: D 282 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8759 (pp) REVERT: D 293 PHE cc_start: 0.7667 (m-80) cc_final: 0.7294 (m-80) REVERT: D 418 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7765 (ptmt) REVERT: D 448 MET cc_start: 0.8223 (mmp) cc_final: 0.7876 (mmp) REVERT: D 489 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6502 (mm) REVERT: E 336 ASP cc_start: 0.8177 (m-30) cc_final: 0.7939 (m-30) REVERT: F 336 ASP cc_start: 0.8177 (m-30) cc_final: 0.7927 (m-30) REVERT: G 336 ASP cc_start: 0.8195 (m-30) cc_final: 0.7951 (m-30) REVERT: H 326 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7401 (mm-30) REVERT: H 336 ASP cc_start: 0.8182 (m-30) cc_final: 0.7940 (m-30) outliers start: 32 outliers final: 12 residues processed: 234 average time/residue: 1.8132 time to fit residues: 467.6831 Evaluate side-chains 222 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 200 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN D 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 21720 Z= 0.548 Angle : 0.683 8.636 29426 Z= 0.348 Chirality : 0.049 0.209 3126 Planarity : 0.005 0.052 3802 Dihedral : 4.488 28.506 2884 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.49 % Allowed : 11.37 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2580 helix: 0.79 (0.14), residues: 1336 sheet: -0.59 (0.29), residues: 352 loop : -0.71 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 325 HIS 0.005 0.002 HIS D 268 PHE 0.023 0.003 PHE C 22 TYR 0.014 0.002 TYR H 332 ARG 0.006 0.001 ARG D 638 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 213 time to evaluate : 2.302 Fit side-chains REVERT: A 70 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6708 (tm-30) REVERT: A 282 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8914 (pp) REVERT: A 489 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7076 (mt) REVERT: B 70 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6717 (tm-30) REVERT: B 282 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8899 (pp) REVERT: B 489 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7036 (mt) REVERT: C 70 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6725 (tm-30) REVERT: C 128 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7209 (ttm-80) REVERT: C 282 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8899 (pp) REVERT: C 293 PHE cc_start: 0.7586 (m-80) cc_final: 0.7175 (m-80) REVERT: C 421 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7741 (p0) REVERT: C 489 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6995 (mt) REVERT: D 70 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: D 128 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7209 (ttm-80) REVERT: D 282 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8920 (pp) REVERT: D 489 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7003 (mt) REVERT: E 322 LYS cc_start: 0.7324 (tttm) cc_final: 0.7116 (ttpp) REVERT: E 336 ASP cc_start: 0.8392 (m-30) cc_final: 0.8126 (m-30) REVERT: F 336 ASP cc_start: 0.8363 (m-30) cc_final: 0.8082 (m-30) REVERT: G 336 ASP cc_start: 0.8399 (m-30) cc_final: 0.8123 (m-30) REVERT: H 326 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7357 (mm-30) REVERT: H 336 ASP cc_start: 0.8352 (m-30) cc_final: 0.8100 (m-30) outliers start: 56 outliers final: 14 residues processed: 248 average time/residue: 1.7638 time to fit residues: 482.4501 Evaluate side-chains 224 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 122 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 237 optimal weight: 0.5980 chunk 251 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 224 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN B 360 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN D 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21720 Z= 0.179 Angle : 0.468 7.043 29426 Z= 0.245 Chirality : 0.039 0.147 3126 Planarity : 0.003 0.049 3802 Dihedral : 4.035 26.944 2884 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.00 % Allowed : 12.88 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2580 helix: 1.23 (0.14), residues: 1330 sheet: -0.59 (0.28), residues: 352 loop : -0.57 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 325 HIS 0.003 0.001 HIS C 205 PHE 0.011 0.001 PHE A 22 TYR 0.011 0.001 TYR A 623 ARG 0.006 0.000 ARG D 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 211 time to evaluate : 1.768 Fit side-chains REVERT: A 70 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: A 237 GLN cc_start: 0.7631 (mp10) cc_final: 0.7403 (mp10) REVERT: A 294 GLN cc_start: 0.6379 (OUTLIER) cc_final: 0.6127 (mt0) REVERT: A 448 MET cc_start: 0.8163 (mmp) cc_final: 0.7716 (mmp) REVERT: A 489 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6901 (mm) REVERT: B 70 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: B 237 GLN cc_start: 0.7635 (mp10) cc_final: 0.7408 (mp10) REVERT: B 448 MET cc_start: 0.8189 (mmp) cc_final: 0.7681 (mmp) REVERT: B 489 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6796 (mm) REVERT: C 70 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6885 (tm-30) REVERT: C 128 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7170 (ttm-80) REVERT: C 237 GLN cc_start: 0.7643 (mp10) cc_final: 0.7408 (mp10) REVERT: C 293 PHE cc_start: 0.7539 (m-80) cc_final: 0.7182 (m-80) REVERT: C 294 GLN cc_start: 0.6296 (OUTLIER) cc_final: 0.6011 (mt0) REVERT: C 489 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6780 (mm) REVERT: D 70 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6877 (tm-30) REVERT: D 128 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7175 (ttm-80) REVERT: D 448 MET cc_start: 0.8196 (mmp) cc_final: 0.7684 (mmp) REVERT: D 489 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6788 (mm) REVERT: E 322 LYS cc_start: 0.7244 (tttm) cc_final: 0.7040 (ttpp) REVERT: E 336 ASP cc_start: 0.8246 (m-30) cc_final: 0.8002 (m-30) REVERT: F 336 ASP cc_start: 0.8223 (m-30) cc_final: 0.7953 (m-30) REVERT: G 336 ASP cc_start: 0.8226 (m-30) cc_final: 0.7976 (m-30) REVERT: H 326 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7323 (mm-30) REVERT: H 336 ASP cc_start: 0.8226 (m-30) cc_final: 0.7975 (m-30) outliers start: 45 outliers final: 13 residues processed: 243 average time/residue: 1.7250 time to fit residues: 462.0047 Evaluate side-chains 217 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 187 optimal weight: 0.0050 chunk 103 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 0.5980 chunk 225 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN B 360 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN D 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21720 Z= 0.215 Angle : 0.485 8.245 29426 Z= 0.248 Chirality : 0.040 0.149 3126 Planarity : 0.004 0.056 3802 Dihedral : 3.981 26.831 2884 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.75 % Allowed : 13.94 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2580 helix: 1.32 (0.14), residues: 1334 sheet: -0.54 (0.28), residues: 352 loop : -0.49 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 325 HIS 0.004 0.001 HIS C 205 PHE 0.012 0.001 PHE A 537 TYR 0.009 0.001 TYR D 623 ARG 0.008 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 204 time to evaluate : 2.347 Fit side-chains REVERT: A 70 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: A 264 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8829 (mp) REVERT: A 294 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.6147 (mt0) REVERT: A 448 MET cc_start: 0.8171 (mmp) cc_final: 0.7929 (mmp) REVERT: A 489 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6924 (mt) REVERT: B 70 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: B 264 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8833 (mp) REVERT: B 418 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7738 (ptmt) REVERT: B 448 MET cc_start: 0.8167 (mmp) cc_final: 0.7870 (mmp) REVERT: B 489 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6892 (mt) REVERT: C 70 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: C 128 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7177 (ttm-80) REVERT: C 264 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8834 (mp) REVERT: C 293 PHE cc_start: 0.7558 (m-80) cc_final: 0.7266 (m-80) REVERT: C 294 GLN cc_start: 0.6286 (OUTLIER) cc_final: 0.6037 (mt0) REVERT: C 418 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7705 (ptmt) REVERT: C 489 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6884 (mt) REVERT: D 70 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: D 128 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7173 (ttm-80) REVERT: D 264 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8831 (mp) REVERT: D 448 MET cc_start: 0.8193 (mmp) cc_final: 0.7905 (mmp) REVERT: D 489 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6888 (mt) REVERT: E 322 LYS cc_start: 0.7262 (tttm) cc_final: 0.7061 (ttpp) REVERT: E 336 ASP cc_start: 0.8237 (m-30) cc_final: 0.8007 (m-30) REVERT: F 336 ASP cc_start: 0.8236 (m-30) cc_final: 0.7991 (m-30) REVERT: G 336 ASP cc_start: 0.8251 (m-30) cc_final: 0.8019 (m-30) REVERT: H 336 ASP cc_start: 0.8217 (m-30) cc_final: 0.7981 (m-30) outliers start: 62 outliers final: 24 residues processed: 253 average time/residue: 1.6888 time to fit residues: 473.1813 Evaluate side-chains 240 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 198 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 418 LYS Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 4.9990 chunk 226 optimal weight: 0.0570 chunk 49 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN B 360 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN D 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21720 Z= 0.248 Angle : 0.508 7.907 29426 Z= 0.259 Chirality : 0.041 0.148 3126 Planarity : 0.004 0.070 3802 Dihedral : 4.002 28.018 2884 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.58 % Allowed : 14.21 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2580 helix: 1.29 (0.14), residues: 1334 sheet: -0.54 (0.28), residues: 352 loop : -0.48 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 325 HIS 0.003 0.001 HIS C 205 PHE 0.014 0.001 PHE A 537 TYR 0.009 0.001 TYR D 44 ARG 0.010 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 206 time to evaluate : 2.179 Fit side-chains REVERT: A 70 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6891 (tm-30) REVERT: A 264 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8836 (mp) REVERT: A 294 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.6170 (mt0) REVERT: A 448 MET cc_start: 0.8161 (mmp) cc_final: 0.7948 (mmp) REVERT: A 489 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6890 (mt) REVERT: B 70 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: B 264 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8818 (mp) REVERT: B 418 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7720 (ptmt) REVERT: B 448 MET cc_start: 0.8183 (mmp) cc_final: 0.7926 (mmp) REVERT: C 70 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: C 128 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7152 (ttm-80) REVERT: C 264 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8841 (mp) REVERT: C 293 PHE cc_start: 0.7556 (m-80) cc_final: 0.7263 (m-80) REVERT: C 294 GLN cc_start: 0.6314 (OUTLIER) cc_final: 0.6035 (mt0) REVERT: C 418 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7685 (ptmt) REVERT: C 489 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6852 (mt) REVERT: D 70 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: D 128 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7179 (ttm-80) REVERT: D 264 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8835 (mp) REVERT: D 448 MET cc_start: 0.8187 (mmp) cc_final: 0.7926 (mmp) REVERT: D 489 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6866 (mt) REVERT: E 322 LYS cc_start: 0.7275 (tttm) cc_final: 0.7073 (ttpp) REVERT: E 336 ASP cc_start: 0.8244 (m-30) cc_final: 0.8015 (m-30) REVERT: F 336 ASP cc_start: 0.8249 (m-30) cc_final: 0.7998 (m-30) REVERT: G 336 ASP cc_start: 0.8258 (m-30) cc_final: 0.8025 (m-30) REVERT: H 336 ASP cc_start: 0.8260 (m-30) cc_final: 0.8028 (m-30) outliers start: 58 outliers final: 28 residues processed: 249 average time/residue: 1.7138 time to fit residues: 471.2580 Evaluate side-chains 243 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 198 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 418 LYS Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 250 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN B 360 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN C 374 ASN D 360 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21720 Z= 0.200 Angle : 0.482 7.341 29426 Z= 0.246 Chirality : 0.040 0.147 3126 Planarity : 0.004 0.064 3802 Dihedral : 3.924 30.519 2884 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.75 % Allowed : 14.65 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.17), residues: 2580 helix: 1.48 (0.14), residues: 1312 sheet: -0.54 (0.28), residues: 352 loop : -0.37 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 134 HIS 0.003 0.001 HIS D 205 PHE 0.011 0.001 PHE D 537 TYR 0.010 0.001 TYR D 623 ARG 0.011 0.000 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 212 time to evaluate : 2.638 Fit side-chains REVERT: A 70 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6920 (tm-30) REVERT: A 264 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 294 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.6178 (mt0) REVERT: B 70 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: B 264 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8742 (mp) REVERT: B 418 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7683 (ptmt) REVERT: B 448 MET cc_start: 0.8128 (mmp) cc_final: 0.7899 (mmp) REVERT: C 70 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6924 (tm-30) REVERT: C 128 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7152 (ttm-80) REVERT: C 264 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8755 (mp) REVERT: C 293 PHE cc_start: 0.7551 (m-80) cc_final: 0.7268 (m-80) REVERT: C 294 GLN cc_start: 0.6255 (OUTLIER) cc_final: 0.6017 (mt0) REVERT: C 418 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7653 (ptmt) REVERT: D 70 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6921 (tm-30) REVERT: D 128 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7200 (ttm-80) REVERT: D 264 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8752 (mp) REVERT: D 448 MET cc_start: 0.8133 (mmp) cc_final: 0.7912 (mmp) REVERT: E 322 LYS cc_start: 0.7274 (tttm) cc_final: 0.7071 (ttpp) REVERT: E 336 ASP cc_start: 0.8187 (m-30) cc_final: 0.7983 (m-30) REVERT: F 336 ASP cc_start: 0.8187 (m-30) cc_final: 0.7972 (m-30) REVERT: G 336 ASP cc_start: 0.8206 (m-30) cc_final: 0.7994 (m-30) REVERT: H 336 ASP cc_start: 0.8228 (m-30) cc_final: 0.8015 (m-30) outliers start: 62 outliers final: 26 residues processed: 256 average time/residue: 1.6922 time to fit residues: 483.1073 Evaluate side-chains 242 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 202 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 418 LYS Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 49 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 159 optimal weight: 0.0010 chunk 170 optimal weight: 0.7980 chunk 123 optimal weight: 0.0270 chunk 23 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN B 360 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN D 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21720 Z= 0.139 Angle : 0.452 9.196 29426 Z= 0.232 Chirality : 0.039 0.148 3126 Planarity : 0.003 0.046 3802 Dihedral : 3.738 33.899 2884 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.13 % Allowed : 15.32 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2580 helix: 1.69 (0.15), residues: 1312 sheet: -0.46 (0.28), residues: 352 loop : -0.29 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 134 HIS 0.001 0.000 HIS B 205 PHE 0.006 0.001 PHE B 537 TYR 0.007 0.001 TYR A 44 ARG 0.013 0.000 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 239 time to evaluate : 2.404 Fit side-chains REVERT: A 70 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: A 264 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8536 (mp) REVERT: B 264 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8542 (mp) REVERT: B 448 MET cc_start: 0.8022 (mmp) cc_final: 0.7615 (mmp) REVERT: C 70 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: C 128 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.7164 (ttm-80) REVERT: C 264 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8527 (mp) REVERT: C 293 PHE cc_start: 0.7444 (m-80) cc_final: 0.7084 (m-80) REVERT: D 70 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: D 128 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7143 (ttm-80) REVERT: D 264 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8527 (mp) REVERT: D 448 MET cc_start: 0.8040 (mmp) cc_final: 0.7559 (mmp) outliers start: 48 outliers final: 17 residues processed: 267 average time/residue: 1.5958 time to fit residues: 474.1608 Evaluate side-chains 234 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.6980 chunk 240 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 233 optimal weight: 0.0070 chunk 140 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 360 GLN B 360 GLN C 360 GLN D 360 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21720 Z= 0.309 Angle : 0.560 10.360 29426 Z= 0.281 Chirality : 0.043 0.168 3126 Planarity : 0.004 0.086 3802 Dihedral : 4.007 33.530 2884 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.00 % Allowed : 16.03 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2580 helix: 1.43 (0.14), residues: 1310 sheet: -0.51 (0.28), residues: 352 loop : -0.40 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 134 HIS 0.003 0.001 HIS C 240 PHE 0.015 0.002 PHE A 537 TYR 0.010 0.001 TYR B 44 ARG 0.016 0.001 ARG D 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 207 time to evaluate : 2.214 Fit side-chains REVERT: A 70 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6930 (tm-30) REVERT: A 264 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8723 (mp) REVERT: B 70 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: B 264 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8725 (mp) REVERT: C 70 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6991 (tm-30) REVERT: C 128 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7183 (ttm-80) REVERT: C 264 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8709 (mp) REVERT: C 293 PHE cc_start: 0.7647 (m-80) cc_final: 0.7332 (m-80) REVERT: D 70 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: D 128 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7170 (ttm-80) REVERT: D 264 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8707 (mp) REVERT: D 293 PHE cc_start: 0.7650 (m-80) cc_final: 0.7367 (m-80) REVERT: D 418 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7443 (ptmt) outliers start: 45 outliers final: 21 residues processed: 240 average time/residue: 1.7449 time to fit residues: 461.7922 Evaluate side-chains 235 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 203 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 259 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN B 360 GLN C 360 GLN D 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21720 Z= 0.234 Angle : 0.531 10.564 29426 Z= 0.266 Chirality : 0.041 0.156 3126 Planarity : 0.004 0.082 3802 Dihedral : 4.009 33.800 2884 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.82 % Allowed : 16.61 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2580 helix: 1.43 (0.14), residues: 1310 sheet: -0.53 (0.28), residues: 352 loop : -0.42 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 134 HIS 0.003 0.001 HIS B 205 PHE 0.012 0.001 PHE A 537 TYR 0.009 0.001 TYR D 44 ARG 0.016 0.001 ARG D 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 2.357 Fit side-chains REVERT: A 70 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6977 (tm-30) REVERT: A 264 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8710 (mp) REVERT: B 70 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: B 264 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8698 (mp) REVERT: C 70 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: C 128 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7153 (ttm-80) REVERT: C 264 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8678 (mp) REVERT: C 293 PHE cc_start: 0.7641 (m-80) cc_final: 0.7345 (m-80) REVERT: D 70 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: D 128 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7168 (ttm-80) REVERT: D 264 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8675 (mp) REVERT: D 293 PHE cc_start: 0.7682 (m-80) cc_final: 0.7387 (m-80) REVERT: D 418 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7499 (ptmt) outliers start: 41 outliers final: 23 residues processed: 240 average time/residue: 1.8741 time to fit residues: 496.3909 Evaluate side-chains 233 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 199 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.7980 chunk 219 optimal weight: 2.9990 chunk 63 optimal weight: 0.0070 chunk 190 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN B 360 GLN C 360 GLN D 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114611 restraints weight = 25771.205| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.64 r_work: 0.3134 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21720 Z= 0.170 Angle : 0.488 10.668 29426 Z= 0.246 Chirality : 0.040 0.162 3126 Planarity : 0.004 0.069 3802 Dihedral : 3.872 34.471 2884 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.51 % Allowed : 16.83 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.17), residues: 2580 helix: 1.58 (0.14), residues: 1312 sheet: -0.50 (0.28), residues: 352 loop : -0.33 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 134 HIS 0.003 0.001 HIS D 205 PHE 0.009 0.001 PHE A 537 TYR 0.008 0.001 TYR D 623 ARG 0.012 0.000 ARG D 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7525.69 seconds wall clock time: 135 minutes 52.17 seconds (8152.17 seconds total)