Starting phenix.real_space_refine on Sun Jul 21 08:30:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlh_22244/07_2024/6xlh_22244_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlh_22244/07_2024/6xlh_22244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlh_22244/07_2024/6xlh_22244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlh_22244/07_2024/6xlh_22244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlh_22244/07_2024/6xlh_22244_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlh_22244/07_2024/6xlh_22244_neut.cif" } resolution = 2.83 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= 0.004 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 5 5.49 5 Mg 2 5.21 5 S 26 5.16 5 C 8696 2.51 5 N 2240 2.21 5 O 2637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B ARG 595": "NH1" <-> "NH2" Residue "B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13608 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4906 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 20, 'TRANS': 586} Chain breaks: 3 Chain: "B" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4906 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 20, 'TRANS': 586} Chain breaks: 3 Chain: "C" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2544 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain breaks: 1 Chain: "D" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1190 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.00, per 1000 atoms: 0.59 Number of scatterers: 13608 At special positions: 0 Unit cell: (104.394, 113.436, 132.342, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 26 16.00 P 5 15.00 Mg 2 11.99 O 2637 8.00 N 2240 7.00 C 8696 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: 4.83 Conformation dependent library (CDL) restraints added in 2.7 seconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 16 sheets defined 40.9% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 11 through 21 removed outlier: 4.457A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 50 removed outlier: 4.083A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 85 through 92 removed outlier: 3.695A pdb=" N ILE A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'A' and resid 123 through 129 removed outlier: 3.642A pdb=" N SER A 126 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.825A pdb=" N TYR A 184 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 197 Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.578A pdb=" N TYR A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 405 Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.569A pdb=" N PHE A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 428 removed outlier: 3.678A pdb=" N VAL A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.590A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 459 Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.566A pdb=" N VAL A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 removed outlier: 4.372A pdb=" N LEU A 487 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 510 removed outlier: 4.456A pdb=" N TYR A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 510 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 543 Processing helix chain 'A' and resid 543 through 555 Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 615 through 627 Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.523A pdb=" N LEU A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 removed outlier: 3.965A pdb=" N PHE A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 4.787A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 50 removed outlier: 4.143A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 removed outlier: 3.659A pdb=" N GLU B 57 " --> pdb=" O LYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 removed outlier: 3.717A pdb=" N ILE B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.780A pdb=" N LEU B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 removed outlier: 3.528A pdb=" N SER B 126 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.755A pdb=" N TYR B 184 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 195 removed outlier: 3.763A pdb=" N ILE B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.628A pdb=" N TYR B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 406 removed outlier: 3.908A pdb=" N ASP B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.603A pdb=" N ASP B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 428 removed outlier: 3.622A pdb=" N VAL B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 437 removed outlier: 3.652A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 459 Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.509A pdb=" N VAL B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 490 removed outlier: 4.427A pdb=" N LEU B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.952A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 510 " --> pdb=" O PHE B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 543 Processing helix chain 'B' and resid 543 through 555 Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 582 through 590 removed outlier: 3.580A pdb=" N ARG B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 627 Processing helix chain 'B' and resid 632 through 651 removed outlier: 3.664A pdb=" N LEU B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 removed outlier: 3.789A pdb=" N PHE B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.675A pdb=" N TRP C 9 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 28 Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.569A pdb=" N SER C 121 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.510A pdb=" N ILE C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 150 removed outlier: 3.827A pdb=" N GLY C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.619A pdb=" N ASN C 169 " --> pdb=" O TYR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.682A pdb=" N GLU C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 removed outlier: 3.855A pdb=" N ALA C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.666A pdb=" N GLU C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 344 removed outlier: 3.765A pdb=" N ILE C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.731A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 244 removed outlier: 3.955A pdb=" N ALA D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 336 through 344 removed outlier: 3.682A pdb=" N ILE D 340 " --> pdb=" O TYR D 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.523A pdb=" N GLU A 4 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG B 133 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 174 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 64 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU B 208 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE B 66 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 6.599A pdb=" N GLN A 9 " --> pdb=" O ILE B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 265 removed outlier: 6.102A pdb=" N ILE A 64 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU A 208 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE A 66 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG A 133 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 307 removed outlier: 3.727A pdb=" N ALA A 315 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 307 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU A 339 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 451 through 452 removed outlier: 4.033A pdb=" N ASN A 442 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N LEU A 495 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR A 468 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU A 497 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 470 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE A 467 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 560 through 563 removed outlier: 6.431A pdb=" N LYS A 560 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A 611 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 562 " --> pdb=" O ILE A 611 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 307 removed outlier: 7.286A pdb=" N LEU B 339 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 451 through 452 removed outlier: 3.890A pdb=" N ASN B 442 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N LEU B 495 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR B 468 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU B 497 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 470 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE B 467 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 560 through 563 removed outlier: 6.550A pdb=" N LYS B 560 " --> pdb=" O PHE B 609 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE B 611 " --> pdb=" O LYS B 560 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 562 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 12 through 15 removed outlier: 3.616A pdb=" N VAL C 12 " --> pdb=" O GLN C 58 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN C 58 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 32 through 34 removed outlier: 8.176A pdb=" N LYS C 43 " --> pdb=" O HIS C 78 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N HIS C 78 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS C 45 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLU C 76 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL C 47 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU C 74 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 77 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 213 through 218 removed outlier: 6.854A pdb=" N ILE C 216 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N THR C 318 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU C 218 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS C 316 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 221 through 222 removed outlier: 3.706A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 213 through 218 removed outlier: 6.937A pdb=" N ILE D 216 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR D 318 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU D 218 " --> pdb=" O LYS D 316 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYS D 316 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 274 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS D 284 " --> pdb=" O LEU D 272 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU D 272 " --> pdb=" O HIS D 284 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS D 286 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER D 270 " --> pdb=" O LYS D 286 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 259 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 221 through 222 596 hydrogen bonds defined for protein. 1650 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: 4.76 Time building geometry restraints manager: 5.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 4495 1.37 - 1.52: 4085 1.52 - 1.66: 5235 1.66 - 1.81: 42 1.81 - 1.95: 5 Bond restraints: 13862 Sorted by residual: bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.472 0.018 2.00e-02 2.50e+03 8.34e-01 bond pdb=" C ALA C 292 " pdb=" N PRO C 293 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.66e-01 bond pdb=" C VAL A 23 " pdb=" O VAL A 23 " ideal model delta sigma weight residual 1.245 1.235 0.010 1.41e-02 5.03e+03 5.11e-01 bond pdb=" C GLU B 655 " pdb=" N GLU B 656 " ideal model delta sigma weight residual 1.331 1.343 -0.012 2.07e-02 2.33e+03 3.60e-01 bond pdb=" N ILE C 320 " pdb=" CA ILE C 320 " ideal model delta sigma weight residual 1.461 1.468 -0.007 1.23e-02 6.61e+03 2.86e-01 ... (remaining 13857 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.47: 392 107.47 - 114.60: 8296 114.60 - 121.73: 6856 121.73 - 128.86: 3091 128.86 - 135.99: 69 Bond angle restraints: 18704 Sorted by residual: angle pdb=" N VAL A 23 " pdb=" CA VAL A 23 " pdb=" C VAL A 23 " ideal model delta sigma weight residual 113.71 108.38 5.33 9.50e-01 1.11e+00 3.15e+01 angle pdb=" N ILE B 384 " pdb=" CA ILE B 384 " pdb=" C ILE B 384 " ideal model delta sigma weight residual 113.53 108.18 5.35 9.80e-01 1.04e+00 2.98e+01 angle pdb=" N ILE A 384 " pdb=" CA ILE A 384 " pdb=" C ILE A 384 " ideal model delta sigma weight residual 113.53 108.69 4.84 9.80e-01 1.04e+00 2.44e+01 angle pdb=" CA ILE B 384 " pdb=" C ILE B 384 " pdb=" N MET B 385 " ideal model delta sigma weight residual 119.31 116.30 3.01 1.15e+00 7.56e-01 6.83e+00 angle pdb=" CA ILE A 384 " pdb=" C ILE A 384 " pdb=" N MET A 385 " ideal model delta sigma weight residual 119.31 116.51 2.80 1.15e+00 7.56e-01 5.94e+00 ... (remaining 18699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.51: 8413 33.51 - 67.01: 30 67.01 - 100.52: 0 100.52 - 134.03: 2 134.03 - 167.53: 1 Dihedral angle restraints: 8446 sinusoidal: 3542 harmonic: 4904 Sorted by residual: dihedral pdb=" O2A ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PA ADP B 801 " pdb=" PB ADP B 801 " ideal model delta sinusoidal sigma weight residual 300.00 132.47 167.53 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1B AGS A 801 " pdb=" O3B AGS A 801 " pdb=" PB AGS A 801 " pdb=" PG AGS A 801 " ideal model delta sinusoidal sigma weight residual 68.91 -44.98 113.89 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" O1A AGS A 801 " pdb=" O3A AGS A 801 " pdb=" PA AGS A 801 " pdb=" PB AGS A 801 " ideal model delta sinusoidal sigma weight residual -67.73 -173.26 105.53 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 8443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1362 0.030 - 0.059: 500 0.059 - 0.089: 102 0.089 - 0.118: 106 0.118 - 0.148: 17 Chirality restraints: 2087 Sorted by residual: chirality pdb=" CA ILE C 154 " pdb=" N ILE C 154 " pdb=" C ILE C 154 " pdb=" CB ILE C 154 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE C 320 " pdb=" N ILE C 320 " pdb=" C ILE C 320 " pdb=" CB ILE C 320 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA VAL C 95 " pdb=" N VAL C 95 " pdb=" C VAL C 95 " pdb=" CB VAL C 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 2084 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 355 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 320 " 0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO C 321 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 321 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 321 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 354 " 0.016 5.00e-02 4.00e+02 2.50e-02 9.99e-01 pdb=" N PRO B 355 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 355 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 355 " 0.014 5.00e-02 4.00e+02 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.70: 320 2.70 - 3.31: 14840 3.31 - 3.92: 26511 3.92 - 4.53: 35564 4.53 - 5.14: 56834 Nonbonded interactions: 134069 Sorted by model distance: nonbonded pdb=" O2G AGS A 801 " pdb="MG MG A 802 " model vdw 2.093 2.170 nonbonded pdb=" OD1 ASN A 37 " pdb="MG MG A 802 " model vdw 2.093 2.170 nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.134 2.170 nonbonded pdb=" OH TYR A 301 " pdb=" OE1 GLU A 402 " model vdw 2.253 2.440 nonbonded pdb=" O LYS A 480 " pdb=" OG1 THR B 658 " model vdw 2.256 2.440 ... (remaining 134064 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 3 through 675 or resid 802 through 803)) selection = (chain 'B' and (resid 3 through 675 or resid 802 through 803)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 39.080 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.001 0.020 13862 Z= 0.077 Angle : 0.388 6.793 18704 Z= 0.223 Chirality : 0.039 0.148 2087 Planarity : 0.002 0.032 2388 Dihedral : 7.607 167.535 5254 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.13 % Allowed : 2.73 % Favored : 97.13 % 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: -3.84 (0.16), residues: 1653 helix: -3.18 (0.12), residues: 613 sheet: -1.62 (0.25), residues: 362 loop : -2.23 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 273 HIS 0.001 0.000 HIS B 304 PHE 0.004 0.000 PHE A 609 TYR 0.008 0.000 TYR A 24 ARG 0.001 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 474 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 LYS cc_start: 0.7729 (mtpp) cc_final: 0.7516 (mtpp) REVERT: C 301 THR cc_start: 0.8435 (m) cc_final: 0.8193 (m) REVERT: C 325 GLU cc_start: 0.7229 (pt0) cc_final: 0.6989 (pm20) outliers start: 2 outliers final: 0 residues processed: 475 average time/residue: 1.5033 time to fit residues: 767.8796 Evaluate side-chains 193 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 135 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN A 336 ASN A 380 GLN A 381 GLN A 409 GLN A 592 GLN B 14 GLN B 26 ASN B 55 GLN B 91 ASN B 335 ASN B 463 HIS C 4 ASN C 57 ASN C 94 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 306 GLN D 207 GLN D 314 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13862 Z= 0.309 Angle : 0.612 7.123 18704 Z= 0.317 Chirality : 0.046 0.208 2087 Planarity : 0.004 0.040 2388 Dihedral : 6.848 151.703 1813 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.73 % Allowed : 14.60 % Favored : 80.67 % 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: -1.97 (0.19), residues: 1653 helix: -0.90 (0.18), residues: 624 sheet: -1.31 (0.25), residues: 382 loop : -1.49 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 581 HIS 0.005 0.001 HIS A 463 PHE 0.016 0.002 PHE A 104 TYR 0.012 0.002 TYR C 23 ARG 0.005 0.001 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 194 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8161 (mp) REVERT: A 78 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7693 (tpt-90) REVERT: A 165 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: A 339 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8816 (tt) REVERT: A 623 LYS cc_start: 0.8110 (mtpt) cc_final: 0.7697 (ttmt) REVERT: B 149 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: B 427 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: B 559 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6941 (tm-30) REVERT: C 288 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8153 (ttpp) REVERT: C 301 THR cc_start: 0.8425 (m) cc_final: 0.8211 (m) outliers start: 71 outliers final: 23 residues processed: 246 average time/residue: 1.3028 time to fit residues: 348.7802 Evaluate side-chains 153 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 381 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 HIS A 584 ASN B 14 GLN B 335 ASN B 382 ASN B 409 GLN B 463 HIS ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN D 212 ASN D 314 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13862 Z= 0.276 Angle : 0.564 7.383 18704 Z= 0.290 Chirality : 0.044 0.149 2087 Planarity : 0.004 0.044 2388 Dihedral : 6.972 140.162 1813 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.67 % Allowed : 15.80 % Favored : 79.53 % 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: -1.22 (0.20), residues: 1653 helix: 0.01 (0.20), residues: 627 sheet: -1.14 (0.26), residues: 386 loop : -1.26 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 581 HIS 0.006 0.001 HIS C 78 PHE 0.017 0.002 PHE A 104 TYR 0.019 0.002 TYR B 504 ARG 0.004 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 137 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 165 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: A 166 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.6214 (tpm-80) REVERT: A 188 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8163 (ttpt) REVERT: A 339 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8759 (tt) REVERT: B 149 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: B 377 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7758 (pt0) REVERT: B 509 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8893 (tt) REVERT: C 68 ASP cc_start: 0.7761 (t0) cc_final: 0.7457 (t0) REVERT: C 288 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8192 (ttpp) REVERT: D 306 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7243 (pm20) outliers start: 70 outliers final: 32 residues processed: 195 average time/residue: 1.2601 time to fit residues: 269.3670 Evaluate side-chains 165 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 124 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 0.0070 chunk 78 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 381 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS B 631 GLN ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN D 303 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13862 Z= 0.250 Angle : 0.542 6.492 18704 Z= 0.280 Chirality : 0.044 0.158 2087 Planarity : 0.004 0.038 2388 Dihedral : 7.011 137.215 1813 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.27 % Allowed : 17.53 % Favored : 78.20 % 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: -0.94 (0.20), residues: 1653 helix: 0.36 (0.21), residues: 627 sheet: -1.10 (0.26), residues: 382 loop : -1.15 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 148 HIS 0.004 0.001 HIS A 463 PHE 0.017 0.001 PHE A 104 TYR 0.016 0.001 TYR B 504 ARG 0.003 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 137 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8213 (mp) REVERT: A 78 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7758 (tpt-90) REVERT: A 90 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8550 (mm) REVERT: A 165 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: A 188 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8142 (ttpt) REVERT: A 339 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8726 (tt) REVERT: B 149 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: B 427 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: B 509 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8973 (tt) REVERT: B 559 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: C 68 ASP cc_start: 0.7629 (t0) cc_final: 0.7313 (t0) REVERT: C 97 GLU cc_start: 0.6964 (tp30) cc_final: 0.6663 (tp30) REVERT: C 144 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.7936 (mmtt) REVERT: C 279 LYS cc_start: 0.8132 (mmmt) cc_final: 0.7921 (tppt) REVERT: C 288 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8069 (ttpp) REVERT: D 306 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7278 (pm20) outliers start: 64 outliers final: 31 residues processed: 187 average time/residue: 1.2823 time to fit residues: 262.4686 Evaluate side-chains 154 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 111 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.0570 chunk 90 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 0.0050 chunk 136 optimal weight: 0.2980 chunk 110 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.2512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 381 GLN B 14 GLN B 380 GLN B 381 GLN B 463 HIS B 631 GLN C 78 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13862 Z= 0.124 Angle : 0.487 7.743 18704 Z= 0.249 Chirality : 0.041 0.160 2087 Planarity : 0.003 0.038 2388 Dihedral : 6.697 129.645 1813 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.40 % Allowed : 18.60 % Favored : 78.00 % 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: -0.56 (0.21), residues: 1653 helix: 0.72 (0.21), residues: 631 sheet: -0.97 (0.26), residues: 372 loop : -0.95 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 242 HIS 0.003 0.001 HIS B 463 PHE 0.016 0.001 PHE A 104 TYR 0.013 0.001 TYR B 504 ARG 0.003 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 145 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8636 (t) REVERT: A 29 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8136 (mp) REVERT: A 188 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8151 (ttpt) REVERT: A 339 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8661 (tt) REVERT: A 430 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6833 (pm20) REVERT: B 427 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: B 503 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7018 (tp30) REVERT: B 559 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6987 (tm-30) REVERT: C 108 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6249 (mm-40) REVERT: C 293 PRO cc_start: 0.7040 (Cg_endo) cc_final: 0.6568 (Cg_exo) outliers start: 51 outliers final: 14 residues processed: 182 average time/residue: 1.3660 time to fit residues: 271.7599 Evaluate side-chains 137 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 159 optimal weight: 0.1980 chunk 132 optimal weight: 0.2980 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 381 GLN B 14 GLN B 381 GLN B 382 ASN B 463 HIS B 631 GLN D 212 ASN D 284 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13862 Z= 0.155 Angle : 0.493 8.333 18704 Z= 0.252 Chirality : 0.042 0.158 2087 Planarity : 0.003 0.037 2388 Dihedral : 6.697 130.700 1813 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.00 % Allowed : 20.07 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1653 helix: 0.87 (0.21), residues: 634 sheet: -0.82 (0.27), residues: 372 loop : -0.86 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 148 HIS 0.003 0.001 HIS C 309 PHE 0.014 0.001 PHE A 104 TYR 0.021 0.001 TYR C 23 ARG 0.002 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 134 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8181 (mp) REVERT: A 339 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8695 (tt) REVERT: A 430 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6885 (pm20) REVERT: B 427 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: B 544 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7459 (tm-30) REVERT: B 559 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: C 68 ASP cc_start: 0.7573 (t0) cc_final: 0.7321 (t0) REVERT: C 108 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6160 (mm-40) outliers start: 45 outliers final: 22 residues processed: 165 average time/residue: 1.2814 time to fit residues: 232.0849 Evaluate side-chains 147 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 0.0270 chunk 116 optimal weight: 0.0370 chunk 134 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN A 381 GLN B 14 GLN B 381 GLN B 382 ASN B 463 HIS B 631 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13862 Z= 0.137 Angle : 0.491 10.003 18704 Z= 0.252 Chirality : 0.041 0.153 2087 Planarity : 0.003 0.038 2388 Dihedral : 6.656 129.586 1813 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.93 % Allowed : 20.20 % Favored : 76.87 % 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: -0.24 (0.21), residues: 1653 helix: 0.94 (0.21), residues: 635 sheet: -0.73 (0.27), residues: 372 loop : -0.79 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 9 HIS 0.003 0.001 HIS C 309 PHE 0.014 0.001 PHE A 104 TYR 0.017 0.001 TYR C 23 ARG 0.002 0.000 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 1.802 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8166 (mp) REVERT: A 165 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7143 (tt0) REVERT: A 339 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8677 (tt) REVERT: A 430 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6856 (pm20) REVERT: B 559 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: C 108 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6194 (mm-40) outliers start: 44 outliers final: 22 residues processed: 160 average time/residue: 1.1524 time to fit residues: 203.6410 Evaluate side-chains 145 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 14 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN A 381 GLN B 381 GLN B 463 HIS B 631 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13862 Z= 0.156 Angle : 0.504 11.065 18704 Z= 0.258 Chirality : 0.042 0.165 2087 Planarity : 0.003 0.040 2388 Dihedral : 6.689 130.271 1813 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.60 % Allowed : 20.53 % Favored : 76.87 % 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: -0.17 (0.21), residues: 1653 helix: 0.97 (0.22), residues: 635 sheet: -0.69 (0.27), residues: 372 loop : -0.72 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 9 HIS 0.003 0.001 HIS C 309 PHE 0.013 0.001 PHE A 104 TYR 0.016 0.001 TYR C 23 ARG 0.002 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 1.667 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8170 (mp) REVERT: A 165 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: A 339 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8688 (tt) REVERT: A 430 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: B 559 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: C 108 GLN cc_start: 0.6814 (OUTLIER) cc_final: 0.6196 (mm-40) outliers start: 39 outliers final: 19 residues processed: 160 average time/residue: 1.1496 time to fit residues: 203.8087 Evaluate side-chains 140 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 148 optimal weight: 0.4980 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 97 optimal weight: 0.0010 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN A 381 GLN B 381 GLN B 382 ASN B 463 HIS B 631 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13862 Z= 0.138 Angle : 0.501 10.845 18704 Z= 0.256 Chirality : 0.042 0.173 2087 Planarity : 0.003 0.038 2388 Dihedral : 6.660 129.089 1813 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.53 % Allowed : 21.00 % Favored : 76.47 % 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: -0.11 (0.21), residues: 1653 helix: 0.99 (0.22), residues: 637 sheet: -0.64 (0.27), residues: 369 loop : -0.67 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 9 HIS 0.003 0.001 HIS B 463 PHE 0.012 0.001 PHE A 104 TYR 0.016 0.001 TYR C 23 ARG 0.002 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 1.798 Fit side-chains REVERT: A 29 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8159 (mp) REVERT: A 314 ARG cc_start: 0.8002 (mpp80) cc_final: 0.7635 (mpp-170) REVERT: A 339 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8662 (tt) REVERT: A 352 ASP cc_start: 0.7151 (t0) cc_final: 0.6879 (t0) REVERT: A 430 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6928 (pm20) REVERT: B 559 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6950 (tm-30) REVERT: C 68 ASP cc_start: 0.7431 (t0) cc_final: 0.7163 (t0) REVERT: C 108 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6166 (mm-40) REVERT: C 144 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.7909 (mmtt) outliers start: 38 outliers final: 23 residues processed: 156 average time/residue: 1.1780 time to fit residues: 203.7407 Evaluate side-chains 150 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN B 463 HIS B 631 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13862 Z= 0.272 Angle : 0.573 10.614 18704 Z= 0.291 Chirality : 0.044 0.170 2087 Planarity : 0.004 0.041 2388 Dihedral : 7.007 135.467 1813 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.20 % Allowed : 21.47 % Favored : 76.33 % 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: -0.19 (0.21), residues: 1653 helix: 0.90 (0.22), residues: 633 sheet: -0.64 (0.27), residues: 372 loop : -0.71 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 9 HIS 0.004 0.001 HIS A 463 PHE 0.016 0.002 PHE D 261 TYR 0.022 0.002 TYR C 23 ARG 0.004 0.000 ARG B 343 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 1.668 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8200 (mp) REVERT: A 192 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6672 (tp30) REVERT: A 314 ARG cc_start: 0.8030 (mpp80) cc_final: 0.7762 (mpp-170) REVERT: A 339 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8761 (tt) REVERT: C 68 ASP cc_start: 0.7540 (t0) cc_final: 0.7258 (t0) REVERT: C 144 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.7972 (mmtt) outliers start: 33 outliers final: 21 residues processed: 145 average time/residue: 1.0964 time to fit residues: 177.2457 Evaluate side-chains 131 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN B 382 ASN B 463 HIS B 631 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104839 restraints weight = 21605.529| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.79 r_work: 0.3242 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13862 Z= 0.189 Angle : 0.540 10.617 18704 Z= 0.275 Chirality : 0.043 0.168 2087 Planarity : 0.003 0.040 2388 Dihedral : 6.933 132.447 1813 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.27 % Allowed : 21.67 % Favored : 76.07 % 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: -0.14 (0.21), residues: 1653 helix: 0.92 (0.21), residues: 634 sheet: -0.61 (0.27), residues: 372 loop : -0.66 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 9 HIS 0.003 0.001 HIS B 463 PHE 0.014 0.001 PHE D 261 TYR 0.022 0.001 TYR C 23 ARG 0.003 0.000 ARG B 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5257.95 seconds wall clock time: 93 minutes 6.14 seconds (5586.14 seconds total)