Starting phenix.real_space_refine on Mon Mar 18 20:06:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6p_35202/03_2024/8i6p_35202.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6p_35202/03_2024/8i6p_35202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6p_35202/03_2024/8i6p_35202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6p_35202/03_2024/8i6p_35202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6p_35202/03_2024/8i6p_35202.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6p_35202/03_2024/8i6p_35202.pdb" } resolution = 3.5 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: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 13968 2.51 5 N 3776 2.21 5 O 4132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 85": "OD1" <-> "OD2" Residue "B ASP 119": "OD1" <-> "OD2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ASP 344": "OD1" <-> "OD2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B ASP 493": "OD1" <-> "OD2" Residue "B ASP 549": "OD1" <-> "OD2" Residue "B PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 605": "OE1" <-> "OE2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B GLU 623": "OE1" <-> "OE2" Residue "B GLU 643": "OE1" <-> "OE2" Residue "B GLU 672": "OE1" <-> "OE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B GLU 695": "OE1" <-> "OE2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B ASP 711": "OD1" <-> "OD2" Residue "B GLU 713": "OE1" <-> "OE2" Residue "B ARG 719": "NH1" <-> "NH2" Residue "B TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 759": "OD1" <-> "OD2" Residue "B PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C ASP 119": "OD1" <-> "OD2" Residue "C ASP 192": "OD1" <-> "OD2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C ASP 258": "OD1" <-> "OD2" Residue "C PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C ASP 344": "OD1" <-> "OD2" Residue "C TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 384": "OD1" <-> "OD2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 463": "OE1" <-> "OE2" Residue "C ASP 493": "OD1" <-> "OD2" Residue "C ASP 549": "OD1" <-> "OD2" Residue "C PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 567": "OE1" <-> "OE2" Residue "C ARG 570": "NH1" <-> "NH2" Residue "C PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 605": "OE1" <-> "OE2" Residue "C GLU 606": "OE1" <-> "OE2" Residue "C GLU 623": "OE1" <-> "OE2" Residue "C GLU 643": "OE1" <-> "OE2" Residue "C GLU 672": "OE1" <-> "OE2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C GLU 695": "OE1" <-> "OE2" Residue "C GLU 698": "OE1" <-> "OE2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C ASP 711": "OD1" <-> "OD2" Residue "C GLU 713": "OE1" <-> "OE2" Residue "C ARG 719": "NH1" <-> "NH2" Residue "C TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 759": "OD1" <-> "OD2" Residue "C PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D ASP 119": "OD1" <-> "OD2" Residue "D ASP 192": "OD1" <-> "OD2" Residue "D ASP 240": "OD1" <-> "OD2" Residue "D ASP 258": "OD1" <-> "OD2" Residue "D PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 290": "OD1" <-> "OD2" Residue "D GLU 295": "OE1" <-> "OE2" Residue "D TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ASP 344": "OD1" <-> "OD2" Residue "D TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 384": "OD1" <-> "OD2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 463": "OE1" <-> "OE2" Residue "D ASP 493": "OD1" <-> "OD2" Residue "D ASP 549": "OD1" <-> "OD2" Residue "D PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 567": "OE1" <-> "OE2" Residue "D ARG 570": "NH1" <-> "NH2" Residue "D PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 605": "OE1" <-> "OE2" Residue "D GLU 606": "OE1" <-> "OE2" Residue "D GLU 623": "OE1" <-> "OE2" Residue "D GLU 643": "OE1" <-> "OE2" Residue "D GLU 672": "OE1" <-> "OE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D GLU 695": "OE1" <-> "OE2" Residue "D GLU 698": "OE1" <-> "OE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D GLU 705": "OE1" <-> "OE2" Residue "D ASP 711": "OD1" <-> "OD2" Residue "D GLU 713": "OE1" <-> "OE2" Residue "D ARG 719": "NH1" <-> "NH2" Residue "D TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 759": "OD1" <-> "OD2" Residue "D PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A ASP 119": "OD1" <-> "OD2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 344": "OD1" <-> "OD2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A ASP 493": "OD1" <-> "OD2" Residue "A ASP 549": "OD1" <-> "OD2" Residue "A PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A GLU 672": "OE1" <-> "OE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A GLU 695": "OE1" <-> "OE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A ASP 711": "OD1" <-> "OD2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A ARG 719": "NH1" <-> "NH2" Residue "A TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 759": "OD1" <-> "OD2" Residue "A PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22016 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "C" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "D" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "A" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Time building chain proxies: 10.68, per 1000 atoms: 0.49 Number of scatterers: 22016 At special positions: 0 Unit cell: (180.83, 131.61, 141.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 4132 8.00 N 3776 7.00 C 13968 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: 8.81 Conformation dependent library (CDL) restraints added in 4.0 seconds 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5144 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 69.4% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'B' and resid 80 through 93 removed outlier: 4.148A pdb=" N ILE B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 112 removed outlier: 3.504A pdb=" N LEU B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 147 through 165 removed outlier: 3.814A pdb=" N MET B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 183 removed outlier: 3.805A pdb=" N CYS B 172 " --> pdb=" O HIS B 168 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 removed outlier: 3.527A pdb=" N ALA B 187 " --> pdb=" O TRP B 184 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 189 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 213 Proline residue: B 203 - end of helix removed outlier: 3.709A pdb=" N ASP B 211 " --> pdb=" O ASP B 207 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 212 " --> pdb=" O MET B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 237 Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 277 through 286 removed outlier: 3.562A pdb=" N THR B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 303 removed outlier: 3.546A pdb=" N PHE B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 329 removed outlier: 3.579A pdb=" N VAL B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 325 " --> pdb=" O TRP B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 349 Processing helix chain 'B' and resid 365 through 378 removed outlier: 3.899A pdb=" N THR B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 4.166A pdb=" N VAL B 387 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 419 removed outlier: 4.502A pdb=" N MET B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 446 removed outlier: 3.828A pdb=" N ASP B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY B 446 " --> pdb=" O GLN B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 470 removed outlier: 4.330A pdb=" N GLU B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 509 through 540 removed outlier: 3.601A pdb=" N LYS B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 531 " --> pdb=" O ARG B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 549 through 565 removed outlier: 3.986A pdb=" N THR B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 570 through 595 Processing helix chain 'B' and resid 596 through 600 Processing helix chain 'B' and resid 603 through 611 removed outlier: 4.441A pdb=" N ILE B 608 " --> pdb=" O GLU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 635 removed outlier: 4.024A pdb=" N LEU B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 659 Processing helix chain 'B' and resid 666 through 696 removed outlier: 3.759A pdb=" N LEU B 670 " --> pdb=" O GLN B 666 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 722 removed outlier: 3.765A pdb=" N VAL B 703 " --> pdb=" O SER B 699 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 747 removed outlier: 4.219A pdb=" N PHE B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 763 removed outlier: 4.036A pdb=" N SER B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.503A pdb=" N SER C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.504A pdb=" N LEU C 108 " --> pdb=" O TYR C 104 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 133 Processing helix chain 'C' and resid 147 through 165 removed outlier: 3.813A pdb=" N MET C 153 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.805A pdb=" N CYS C 172 " --> pdb=" O HIS C 168 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.526A pdb=" N ALA C 187 " --> pdb=" O TRP C 184 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU C 189 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 213 Proline residue: C 203 - end of helix removed outlier: 3.709A pdb=" N ASP C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU C 212 " --> pdb=" O MET C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 237 Processing helix chain 'C' and resid 239 through 245 Processing helix chain 'C' and resid 247 through 252 Processing helix chain 'C' and resid 277 through 286 removed outlier: 3.562A pdb=" N THR C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 303 removed outlier: 3.547A pdb=" N PHE C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 296 " --> pdb=" O LYS C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 329 removed outlier: 3.578A pdb=" N VAL C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG C 325 " --> pdb=" O TRP C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 349 Processing helix chain 'C' and resid 365 through 378 removed outlier: 3.899A pdb=" N THR C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 4.166A pdb=" N VAL C 387 " --> pdb=" O ASP C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 419 removed outlier: 4.503A pdb=" N MET C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 446 removed outlier: 3.828A pdb=" N ASP C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG C 444 " --> pdb=" O PHE C 440 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY C 446 " --> pdb=" O GLN C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 470 removed outlier: 4.330A pdb=" N GLU C 463 " --> pdb=" O ASP C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 475 Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 509 through 540 removed outlier: 3.601A pdb=" N LYS C 513 " --> pdb=" O ASP C 509 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 531 " --> pdb=" O ARG C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 549 through 565 removed outlier: 3.986A pdb=" N THR C 553 " --> pdb=" O ASP C 549 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 569 No H-bonds generated for 'chain 'C' and resid 567 through 569' Processing helix chain 'C' and resid 570 through 595 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 603 through 611 removed outlier: 4.441A pdb=" N ILE C 608 " --> pdb=" O GLU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 635 removed outlier: 4.025A pdb=" N LEU C 621 " --> pdb=" O TYR C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 659 Processing helix chain 'C' and resid 666 through 696 removed outlier: 3.760A pdb=" N LEU C 670 " --> pdb=" O GLN C 666 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN C 696 " --> pdb=" O LEU C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 722 removed outlier: 3.765A pdb=" N VAL C 703 " --> pdb=" O SER C 699 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 713 " --> pdb=" O GLN C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 747 removed outlier: 4.219A pdb=" N PHE C 736 " --> pdb=" O THR C 732 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 737 " --> pdb=" O ARG C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 763 removed outlier: 4.035A pdb=" N SER C 756 " --> pdb=" O GLU C 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.504A pdb=" N SER D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 112 removed outlier: 3.505A pdb=" N LEU D 108 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.813A pdb=" N MET D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.806A pdb=" N CYS D 172 " --> pdb=" O HIS D 168 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 removed outlier: 3.526A pdb=" N ALA D 187 " --> pdb=" O TRP D 184 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU D 189 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 213 Proline residue: D 203 - end of helix removed outlier: 3.708A pdb=" N ASP D 211 " --> pdb=" O ASP D 207 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 212 " --> pdb=" O MET D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 237 Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'D' and resid 277 through 286 removed outlier: 3.562A pdb=" N THR D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 303 removed outlier: 3.547A pdb=" N PHE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR D 296 " --> pdb=" O LYS D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 329 removed outlier: 3.579A pdb=" N VAL D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG D 325 " --> pdb=" O TRP D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 349 Processing helix chain 'D' and resid 365 through 378 removed outlier: 3.899A pdb=" N THR D 369 " --> pdb=" O ASP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 4.165A pdb=" N VAL D 387 " --> pdb=" O ASP D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 419 removed outlier: 4.502A pdb=" N MET D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 446 removed outlier: 3.828A pdb=" N ASP D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG D 444 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY D 446 " --> pdb=" O GLN D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 4.329A pdb=" N GLU D 463 " --> pdb=" O ASP D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 475 Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 509 through 540 removed outlier: 3.601A pdb=" N LYS D 513 " --> pdb=" O ASP D 509 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 549 through 565 removed outlier: 3.987A pdb=" N THR D 553 " --> pdb=" O ASP D 549 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 569 No H-bonds generated for 'chain 'D' and resid 567 through 569' Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 596 through 600 Processing helix chain 'D' and resid 603 through 611 removed outlier: 4.442A pdb=" N ILE D 608 " --> pdb=" O GLU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 635 removed outlier: 4.024A pdb=" N LEU D 621 " --> pdb=" O TYR D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 659 Processing helix chain 'D' and resid 666 through 696 removed outlier: 3.760A pdb=" N LEU D 670 " --> pdb=" O GLN D 666 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN D 696 " --> pdb=" O LEU D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 722 removed outlier: 3.764A pdb=" N VAL D 703 " --> pdb=" O SER D 699 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 713 " --> pdb=" O GLN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 747 removed outlier: 4.218A pdb=" N PHE D 736 " --> pdb=" O THR D 732 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D 737 " --> pdb=" O ARG D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 763 removed outlier: 4.034A pdb=" N SER D 756 " --> pdb=" O GLU D 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.504A pdb=" N SER A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.505A pdb=" N LEU A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.813A pdb=" N MET A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 183 removed outlier: 3.805A pdb=" N CYS A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.526A pdb=" N ALA A 187 " --> pdb=" O TRP A 184 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 213 Proline residue: A 203 - end of helix removed outlier: 3.709A pdb=" N ASP A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 237 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.561A pdb=" N THR A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 303 removed outlier: 3.547A pdb=" N PHE A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 296 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 removed outlier: 3.579A pdb=" N VAL A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 325 " --> pdb=" O TRP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 349 Processing helix chain 'A' and resid 365 through 378 removed outlier: 3.900A pdb=" N THR A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 4.165A pdb=" N VAL A 387 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 419 removed outlier: 4.503A pdb=" N MET A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 removed outlier: 3.828A pdb=" N ASP A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 470 removed outlier: 4.329A pdb=" N GLU A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 509 through 540 removed outlier: 3.602A pdb=" N LYS A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 549 through 565 removed outlier: 3.986A pdb=" N THR A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 595 Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 603 through 611 removed outlier: 4.441A pdb=" N ILE A 608 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 635 removed outlier: 4.025A pdb=" N LEU A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 659 Processing helix chain 'A' and resid 666 through 696 removed outlier: 3.760A pdb=" N LEU A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 722 removed outlier: 3.765A pdb=" N VAL A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 747 removed outlier: 4.219A pdb=" N PHE A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 removed outlier: 4.035A pdb=" N SER A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 392 through 393 Processing sheet with id=AA2, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AA3, first strand: chain 'C' and resid 392 through 393 Processing sheet with id=AA4, first strand: chain 'C' and resid 455 through 456 Processing sheet with id=AA5, first strand: chain 'D' and resid 392 through 393 Processing sheet with id=AA6, first strand: chain 'D' and resid 455 through 456 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 393 Processing sheet with id=AA8, first strand: chain 'A' and resid 455 through 456 1252 hydrogen bonds defined for protein. 3504 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: 6.77 Time building geometry restraints manager: 9.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7271 1.35 - 1.47: 5371 1.47 - 1.59: 9658 1.59 - 1.71: 0 1.71 - 1.83: 208 Bond restraints: 22508 Sorted by residual: bond pdb=" C LYS D 422 " pdb=" N PHE D 423 " ideal model delta sigma weight residual 1.331 1.244 0.087 2.07e-02 2.33e+03 1.75e+01 bond pdb=" C LYS C 422 " pdb=" N PHE C 423 " ideal model delta sigma weight residual 1.331 1.245 0.086 2.07e-02 2.33e+03 1.73e+01 bond pdb=" C LYS B 422 " pdb=" N PHE B 423 " ideal model delta sigma weight residual 1.331 1.245 0.086 2.07e-02 2.33e+03 1.72e+01 bond pdb=" C LYS A 422 " pdb=" N PHE A 423 " ideal model delta sigma weight residual 1.331 1.245 0.086 2.07e-02 2.33e+03 1.72e+01 bond pdb=" N VAL D 301 " pdb=" CA VAL D 301 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.22e-02 6.72e+03 8.77e+00 ... (remaining 22503 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.48: 566 106.48 - 113.36: 12300 113.36 - 120.24: 8581 120.24 - 127.13: 8733 127.13 - 134.01: 280 Bond angle restraints: 30460 Sorted by residual: angle pdb=" CA GLU B 340 " pdb=" CB GLU B 340 " pdb=" CG GLU B 340 " ideal model delta sigma weight residual 114.10 125.10 -11.00 2.00e+00 2.50e-01 3.02e+01 angle pdb=" CA GLU A 340 " pdb=" CB GLU A 340 " pdb=" CG GLU A 340 " ideal model delta sigma weight residual 114.10 125.08 -10.98 2.00e+00 2.50e-01 3.01e+01 angle pdb=" CA GLU C 340 " pdb=" CB GLU C 340 " pdb=" CG GLU C 340 " ideal model delta sigma weight residual 114.10 125.08 -10.98 2.00e+00 2.50e-01 3.01e+01 angle pdb=" CA GLU D 340 " pdb=" CB GLU D 340 " pdb=" CG GLU D 340 " ideal model delta sigma weight residual 114.10 125.06 -10.96 2.00e+00 2.50e-01 3.00e+01 angle pdb=" CB MET C 245 " pdb=" CG MET C 245 " pdb=" SD MET C 245 " ideal model delta sigma weight residual 112.70 125.78 -13.08 3.00e+00 1.11e-01 1.90e+01 ... (remaining 30455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 11553 17.68 - 35.36: 1220 35.36 - 53.05: 502 53.05 - 70.73: 141 70.73 - 88.41: 60 Dihedral angle restraints: 13476 sinusoidal: 5496 harmonic: 7980 Sorted by residual: dihedral pdb=" CA LYS B 544 " pdb=" C LYS B 544 " pdb=" N PHE B 545 " pdb=" CA PHE B 545 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS D 544 " pdb=" C LYS D 544 " pdb=" N PHE D 545 " pdb=" CA PHE D 545 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS C 544 " pdb=" C LYS C 544 " pdb=" N PHE C 545 " pdb=" CA PHE C 545 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 13473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2209 0.038 - 0.076: 838 0.076 - 0.114: 226 0.114 - 0.152: 34 0.152 - 0.190: 9 Chirality restraints: 3316 Sorted by residual: chirality pdb=" CA GLU D 340 " pdb=" N GLU D 340 " pdb=" C GLU D 340 " pdb=" CB GLU D 340 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA GLU A 340 " pdb=" N GLU A 340 " pdb=" C GLU A 340 " pdb=" CB GLU A 340 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA GLU C 340 " pdb=" N GLU C 340 " pdb=" C GLU C 340 " pdb=" CB GLU C 340 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.70e-01 ... (remaining 3313 not shown) Planarity restraints: 3920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 384 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO B 385 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 385 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 385 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 384 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A 385 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 384 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO D 385 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 385 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 385 " 0.028 5.00e-02 4.00e+02 ... (remaining 3917 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 360 2.53 - 3.12: 19673 3.12 - 3.72: 37344 3.72 - 4.31: 48261 4.31 - 4.90: 77085 Nonbonded interactions: 182723 Sorted by model distance: nonbonded pdb=" O LEU D 297 " pdb=" CG1 VAL D 301 " model vdw 1.938 3.460 nonbonded pdb=" OD1 ASP A 365 " pdb=" N ILE A 366 " model vdw 2.088 2.520 nonbonded pdb=" OD1 ASP C 365 " pdb=" N ILE C 366 " model vdw 2.088 2.520 nonbonded pdb=" OD1 ASP D 365 " pdb=" N ILE D 366 " model vdw 2.088 2.520 nonbonded pdb=" OD1 ASP B 365 " pdb=" N ILE B 366 " model vdw 2.089 2.520 ... (remaining 182718 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 6.140 Check model and map are aligned: 0.310 Set scattering table: 0.210 Process input model: 55.940 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.110 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 0.005 0.087 22508 Z= 0.356 Angle : 0.760 13.075 30460 Z= 0.440 Chirality : 0.043 0.190 3316 Planarity : 0.004 0.051 3920 Dihedral : 18.817 88.412 8332 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 15.58 % Allowed : 18.09 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -3.57 (0.13), residues: 2744 helix: -2.03 (0.10), residues: 1724 sheet: None (None), residues: 0 loop : -2.78 (0.16), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 321 HIS 0.004 0.001 HIS D 334 PHE 0.009 0.001 PHE D 294 TYR 0.012 0.001 TYR A 466 ARG 0.005 0.001 ARG D 593 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 216 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 SER cc_start: 0.5129 (OUTLIER) cc_final: 0.4719 (p) REVERT: B 146 PHE cc_start: 0.6287 (t80) cc_final: 0.5938 (t80) REVERT: B 148 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6360 (mmm) REVERT: B 183 MET cc_start: 0.8390 (mmm) cc_final: 0.7894 (tpp) REVERT: B 194 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7422 (mmm) REVERT: B 450 MET cc_start: 0.6141 (mmt) cc_final: 0.5757 (mmt) REVERT: B 459 ASP cc_start: 0.5463 (OUTLIER) cc_final: 0.5227 (p0) REVERT: B 541 ASN cc_start: 0.7438 (t0) cc_final: 0.7171 (t0) REVERT: B 555 MET cc_start: 0.8121 (tpp) cc_final: 0.7858 (mmm) REVERT: B 569 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7237 (p0) REVERT: B 607 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8151 (tt) REVERT: B 610 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8122 (mt) REVERT: B 622 ARG cc_start: 0.7389 (mtm110) cc_final: 0.7068 (mtp85) REVERT: B 725 CYS cc_start: 0.6039 (OUTLIER) cc_final: 0.5326 (m) REVERT: C 100 SER cc_start: 0.5323 (OUTLIER) cc_final: 0.4790 (p) REVERT: C 148 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6437 (mmt) REVERT: C 153 MET cc_start: 0.8212 (mtp) cc_final: 0.7979 (mmm) REVERT: C 183 MET cc_start: 0.8429 (mmm) cc_final: 0.7648 (ppp) REVERT: C 191 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.5263 (tm-30) REVERT: C 240 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8195 (p0) REVERT: C 256 MET cc_start: 0.7292 (mmm) cc_final: 0.6559 (tmm) REVERT: C 257 VAL cc_start: 0.5695 (OUTLIER) cc_final: 0.5447 (t) REVERT: C 378 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8895 (tp) REVERT: C 400 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7356 (tt) REVERT: C 450 MET cc_start: 0.6383 (mmt) cc_final: 0.5842 (mmt) REVERT: C 459 ASP cc_start: 0.5766 (OUTLIER) cc_final: 0.5451 (t0) REVERT: C 480 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7607 (mt-10) REVERT: C 607 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8195 (tt) REVERT: C 725 CYS cc_start: 0.5780 (OUTLIER) cc_final: 0.4695 (m) REVERT: C 734 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: D 123 PHE cc_start: 0.7657 (m-80) cc_final: 0.7082 (m-80) REVERT: D 125 SER cc_start: 0.7884 (OUTLIER) cc_final: 0.7607 (m) REVERT: D 240 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7589 (t0) REVERT: D 245 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7136 (mmm) REVERT: D 257 VAL cc_start: 0.6272 (OUTLIER) cc_final: 0.5291 (m) REVERT: D 271 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6609 (t70) REVERT: D 293 CYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7240 (t) REVERT: D 321 TRP cc_start: 0.7886 (m100) cc_final: 0.7518 (m100) REVERT: D 353 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.6796 (t70) REVERT: D 366 ILE cc_start: 0.8616 (tt) cc_final: 0.8410 (tp) REVERT: D 412 MET cc_start: 0.8023 (mtt) cc_final: 0.7787 (mmm) REVERT: D 569 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7528 (p0) REVERT: D 684 CYS cc_start: 0.7670 (m) cc_final: 0.7131 (m) REVERT: D 734 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: A 125 SER cc_start: 0.7557 (OUTLIER) cc_final: 0.7352 (m) REVERT: A 240 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: A 266 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8403 (ptpp) REVERT: A 321 TRP cc_start: 0.7961 (m100) cc_final: 0.7454 (m100) REVERT: A 353 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7554 (t70) REVERT: A 360 ASN cc_start: 0.7045 (OUTLIER) cc_final: 0.6214 (p0) REVERT: A 569 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7614 (p0) REVERT: A 695 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6945 (mp0) outliers start: 372 outliers final: 107 residues processed: 543 average time/residue: 0.3122 time to fit residues: 269.2775 Evaluate side-chains 253 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 111 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 685 CYS Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 605 GLU Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 635 LYS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 293 CYS Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 399 CYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 605 GLU Chi-restraints excluded: chain D residue 645 ASP Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 674 SER Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 685 CYS Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 695 GLU Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 710 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 HIS B 414 ASN B 442 GLN B 531 ASN B 590 HIS B 678 GLN B 709 GLN B 764 GLN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN C 678 GLN C 696 ASN C 709 GLN C 764 GLN D 166 ASN D 334 HIS D 357 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN D 551 GLN D 696 ASN D 709 GLN D 757 HIS D 764 GLN A 291 GLN A 334 HIS A 357 HIS A 405 ASN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 551 GLN A 696 ASN A 709 GLN A 757 HIS ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22508 Z= 0.248 Angle : 0.650 10.213 30460 Z= 0.334 Chirality : 0.042 0.176 3316 Planarity : 0.005 0.049 3920 Dihedral : 9.600 163.806 3246 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 7.29 % Allowed : 20.98 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.79 (0.14), residues: 2744 helix: -0.42 (0.11), residues: 1732 sheet: None (None), residues: 0 loop : -2.49 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 129 HIS 0.009 0.002 HIS B 334 PHE 0.017 0.002 PHE B 566 TYR 0.016 0.002 TYR A 413 ARG 0.010 0.001 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 120 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 ARG cc_start: 0.7953 (tpt90) cc_final: 0.7740 (tmt-80) REVERT: B 183 MET cc_start: 0.8493 (mmm) cc_final: 0.7908 (tpp) REVERT: B 480 GLU cc_start: 0.8088 (tt0) cc_final: 0.7790 (mt-10) REVERT: B 599 ASN cc_start: 0.6257 (OUTLIER) cc_final: 0.6045 (m-40) REVERT: B 607 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8220 (tp) REVERT: C 153 MET cc_start: 0.8176 (mtp) cc_final: 0.7975 (mmm) REVERT: C 183 MET cc_start: 0.8337 (mmm) cc_final: 0.7813 (ppp) REVERT: C 240 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8266 (p0) REVERT: C 256 MET cc_start: 0.7055 (mmm) cc_final: 0.6383 (tmm) REVERT: C 398 PHE cc_start: 0.6069 (m-80) cc_final: 0.5704 (m-80) REVERT: C 400 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7446 (tt) REVERT: C 450 MET cc_start: 0.6212 (mmt) cc_final: 0.5580 (mmt) REVERT: C 476 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7934 (mt) REVERT: C 480 GLU cc_start: 0.8110 (tt0) cc_final: 0.7857 (mt-10) REVERT: D 123 PHE cc_start: 0.8076 (m-80) cc_final: 0.7400 (m-80) REVERT: D 125 SER cc_start: 0.7968 (OUTLIER) cc_final: 0.7721 (m) REVERT: D 183 MET cc_start: 0.6078 (ppp) cc_final: 0.5878 (ppp) REVERT: D 245 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7415 (mmm) REVERT: D 321 TRP cc_start: 0.7959 (m100) cc_final: 0.7489 (m100) REVERT: D 614 ASP cc_start: 0.6441 (m-30) cc_final: 0.6209 (m-30) REVERT: D 684 CYS cc_start: 0.7622 (m) cc_final: 0.7073 (m) REVERT: A 194 MET cc_start: 0.6644 (ttm) cc_final: 0.6425 (ttt) REVERT: A 240 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7549 (t0) REVERT: A 321 TRP cc_start: 0.8066 (m100) cc_final: 0.7485 (m100) REVERT: A 335 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.6779 (m-10) REVERT: A 353 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7481 (t70) REVERT: A 632 TRP cc_start: 0.7693 (OUTLIER) cc_final: 0.7254 (t60) outliers start: 174 outliers final: 94 residues processed: 282 average time/residue: 0.2750 time to fit residues: 128.4506 Evaluate side-chains 209 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 104 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 645 ASP Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 735 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 168 optimal weight: 0.0470 chunk 68 optimal weight: 20.0000 chunk 247 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 245 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 198 optimal weight: 7.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 675 GLN B 696 ASN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 HIS D 414 ASN D 523 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22508 Z= 0.226 Angle : 0.621 11.077 30460 Z= 0.318 Chirality : 0.040 0.174 3316 Planarity : 0.005 0.044 3920 Dihedral : 6.737 79.017 3093 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 6.53 % Allowed : 20.31 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.18 (0.15), residues: 2744 helix: 0.08 (0.12), residues: 1740 sheet: None (None), residues: 0 loop : -2.30 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 129 HIS 0.007 0.002 HIS C 334 PHE 0.015 0.002 PHE D 198 TYR 0.014 0.002 TYR D 413 ARG 0.006 0.001 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 112 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7902 (mmt) cc_final: 0.7702 (mmm) REVERT: B 245 MET cc_start: 0.7291 (ptm) cc_final: 0.6982 (ptp) REVERT: B 256 MET cc_start: 0.6454 (tmm) cc_final: 0.6196 (tmm) REVERT: B 480 GLU cc_start: 0.8059 (tt0) cc_final: 0.7813 (mt-10) REVERT: B 591 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7642 (m-80) REVERT: C 153 MET cc_start: 0.8167 (mtp) cc_final: 0.7940 (mmm) REVERT: C 183 MET cc_start: 0.8432 (mmm) cc_final: 0.7900 (ppp) REVERT: C 219 ASP cc_start: 0.7061 (p0) cc_final: 0.6718 (t0) REVERT: C 400 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7482 (tt) REVERT: C 476 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7671 (mt) REVERT: C 480 GLU cc_start: 0.8153 (tt0) cc_final: 0.7895 (mt-10) REVERT: C 545 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.5866 (p90) REVERT: D 114 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.5764 (ttm110) REVERT: D 123 PHE cc_start: 0.8375 (m-80) cc_final: 0.7638 (m-80) REVERT: D 245 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7443 (mmm) REVERT: D 321 TRP cc_start: 0.7906 (m100) cc_final: 0.7380 (m100) REVERT: D 480 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8109 (tm-30) REVERT: A 240 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7530 (t0) REVERT: A 321 TRP cc_start: 0.8041 (m100) cc_final: 0.7471 (m100) REVERT: A 353 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7463 (t70) REVERT: A 632 TRP cc_start: 0.7711 (OUTLIER) cc_final: 0.6783 (t60) REVERT: A 687 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8378 (pt) outliers start: 156 outliers final: 102 residues processed: 262 average time/residue: 0.2947 time to fit residues: 125.9007 Evaluate side-chains 206 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 94 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 645 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 735 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 6.9990 chunk 186 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 27 optimal weight: 0.0050 chunk 118 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 overall best weight: 2.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 HIS D 678 GLN A 180 GLN A 764 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22508 Z= 0.156 Angle : 0.546 10.557 30460 Z= 0.274 Chirality : 0.039 0.163 3316 Planarity : 0.004 0.047 3920 Dihedral : 5.977 77.716 3075 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.23 % Allowed : 22.19 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.51 (0.16), residues: 2744 helix: 0.67 (0.13), residues: 1728 sheet: None (None), residues: 0 loop : -2.15 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 129 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE D 198 TYR 0.012 0.001 TYR D 413 ARG 0.005 0.000 ARG D 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 112 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8134 (mm-30) REVERT: B 245 MET cc_start: 0.7398 (ptm) cc_final: 0.7108 (ptp) REVERT: B 266 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7391 (mmtm) REVERT: B 480 GLU cc_start: 0.8047 (tt0) cc_final: 0.7641 (mt-10) REVERT: C 153 MET cc_start: 0.8138 (mtp) cc_final: 0.7913 (mmm) REVERT: C 183 MET cc_start: 0.8458 (mmm) cc_final: 0.8016 (ppp) REVERT: C 400 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7485 (tt) REVERT: C 480 GLU cc_start: 0.8056 (tt0) cc_final: 0.7701 (mt-10) REVERT: C 545 PHE cc_start: 0.6084 (OUTLIER) cc_final: 0.5840 (p90) REVERT: C 591 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: D 123 PHE cc_start: 0.8238 (m-80) cc_final: 0.7581 (m-80) REVERT: D 148 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5599 (mmp) REVERT: D 183 MET cc_start: 0.6321 (ppp) cc_final: 0.5935 (ppp) REVERT: D 321 TRP cc_start: 0.7895 (m100) cc_final: 0.7397 (m100) REVERT: D 480 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 147 MET cc_start: 0.7490 (mmm) cc_final: 0.7172 (mmm) REVERT: A 148 MET cc_start: 0.6323 (mmp) cc_final: 0.5531 (mmp) REVERT: A 183 MET cc_start: 0.6950 (mtp) cc_final: 0.6716 (mtm) REVERT: A 321 TRP cc_start: 0.7957 (m100) cc_final: 0.7223 (m100) REVERT: A 353 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7449 (t70) REVERT: A 669 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7622 (m-30) outliers start: 125 outliers final: 80 residues processed: 226 average time/residue: 0.2930 time to fit residues: 107.7856 Evaluate side-chains 187 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 99 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 715 GLN B 738 HIS C 334 HIS ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN D 523 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22508 Z= 0.337 Angle : 0.754 11.607 30460 Z= 0.383 Chirality : 0.044 0.213 3316 Planarity : 0.006 0.048 3920 Dihedral : 6.548 76.967 3055 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 7.45 % Allowed : 20.85 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.44 (0.15), residues: 2744 helix: -0.15 (0.12), residues: 1724 sheet: None (None), residues: 0 loop : -2.34 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 129 HIS 0.008 0.002 HIS B 334 PHE 0.018 0.002 PHE D 763 TYR 0.019 0.003 TYR A 413 ARG 0.008 0.001 ARG D 652 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 102 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7715 (mmt) cc_final: 0.7311 (mmt) REVERT: B 245 MET cc_start: 0.7689 (ptm) cc_final: 0.7421 (ptp) REVERT: B 480 GLU cc_start: 0.8125 (tt0) cc_final: 0.7871 (mt-10) REVERT: B 591 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: C 153 MET cc_start: 0.8186 (mtp) cc_final: 0.7942 (mmm) REVERT: C 194 MET cc_start: 0.7711 (mmt) cc_final: 0.7379 (mmp) REVERT: C 476 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7738 (mt) REVERT: C 480 GLU cc_start: 0.8198 (tt0) cc_final: 0.7915 (mt-10) REVERT: C 591 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: D 321 TRP cc_start: 0.7976 (m100) cc_final: 0.7383 (m100) REVERT: D 480 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 147 MET cc_start: 0.7482 (mmm) cc_final: 0.7153 (tpt) REVERT: A 148 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5544 (mmp) REVERT: A 183 MET cc_start: 0.6581 (mtp) cc_final: 0.6352 (mtm) REVERT: A 256 MET cc_start: 0.7230 (mmm) cc_final: 0.7005 (tmm) REVERT: A 321 TRP cc_start: 0.7989 (m100) cc_final: 0.7439 (m100) REVERT: A 335 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.6571 (m-10) REVERT: A 353 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7300 (t70) REVERT: A 632 TRP cc_start: 0.7703 (OUTLIER) cc_final: 0.6698 (t60) REVERT: A 713 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: A 731 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7900 (mp) outliers start: 178 outliers final: 125 residues processed: 269 average time/residue: 0.2771 time to fit residues: 122.7773 Evaluate side-chains 225 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 91 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 735 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 154 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 0.0870 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 overall best weight: 2.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 590 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22508 Z= 0.180 Angle : 0.586 10.793 30460 Z= 0.295 Chirality : 0.040 0.180 3316 Planarity : 0.004 0.043 3920 Dihedral : 5.679 77.978 3047 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.11 % Allowed : 23.53 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.83 (0.15), residues: 2744 helix: 0.42 (0.12), residues: 1744 sheet: None (None), residues: 0 loop : -2.32 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 129 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE C 146 TYR 0.011 0.001 TYR D 413 ARG 0.007 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 103 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8166 (mm-30) REVERT: B 194 MET cc_start: 0.7703 (mmt) cc_final: 0.7323 (mmt) REVERT: B 480 GLU cc_start: 0.8153 (tt0) cc_final: 0.7860 (mt-10) REVERT: B 591 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: C 194 MET cc_start: 0.7687 (mmt) cc_final: 0.7370 (mmp) REVERT: C 476 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7618 (mt) REVERT: C 591 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: D 148 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.5650 (mmp) REVERT: D 183 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6794 (mtt) REVERT: D 321 TRP cc_start: 0.7870 (m100) cc_final: 0.7388 (m100) REVERT: A 147 MET cc_start: 0.7463 (mmm) cc_final: 0.7174 (tpt) REVERT: A 256 MET cc_start: 0.7232 (mmm) cc_final: 0.6964 (tmm) REVERT: A 257 VAL cc_start: 0.6704 (OUTLIER) cc_final: 0.6028 (m) REVERT: A 321 TRP cc_start: 0.7920 (m100) cc_final: 0.7378 (m100) REVERT: A 353 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7363 (t70) REVERT: A 632 TRP cc_start: 0.7795 (OUTLIER) cc_final: 0.6742 (t60) outliers start: 122 outliers final: 90 residues processed: 215 average time/residue: 0.2783 time to fit residues: 100.5894 Evaluate side-chains 193 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 94 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 221 optimal weight: 0.0970 chunk 146 optimal weight: 6.9990 chunk 262 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22508 Z= 0.181 Angle : 0.592 10.790 30460 Z= 0.294 Chirality : 0.039 0.208 3316 Planarity : 0.004 0.041 3920 Dihedral : 5.478 78.945 3044 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.90 % Allowed : 23.32 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.60 (0.16), residues: 2744 helix: 0.63 (0.13), residues: 1732 sheet: None (None), residues: 0 loop : -2.26 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 129 HIS 0.004 0.001 HIS C 334 PHE 0.012 0.001 PHE D 198 TYR 0.012 0.001 TYR A 413 ARG 0.009 0.001 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 99 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7683 (mmt) cc_final: 0.7329 (mmt) REVERT: B 480 GLU cc_start: 0.8136 (tt0) cc_final: 0.7826 (mt-10) REVERT: B 591 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: B 714 MET cc_start: 0.8571 (tpt) cc_final: 0.8304 (tpp) REVERT: C 183 MET cc_start: 0.7536 (ppp) cc_final: 0.7254 (ppp) REVERT: C 194 MET cc_start: 0.7674 (mmt) cc_final: 0.7248 (mmp) REVERT: C 591 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: D 148 MET cc_start: 0.6058 (OUTLIER) cc_final: 0.5477 (mmp) REVERT: D 245 MET cc_start: 0.7588 (mpp) cc_final: 0.7221 (mpp) REVERT: D 321 TRP cc_start: 0.7809 (m100) cc_final: 0.7334 (m100) REVERT: D 468 MET cc_start: 0.7385 (tmm) cc_final: 0.7081 (tmm) REVERT: D 632 TRP cc_start: 0.7787 (OUTLIER) cc_final: 0.6740 (t60) REVERT: A 147 MET cc_start: 0.7386 (mmm) cc_final: 0.7105 (tpt) REVERT: A 321 TRP cc_start: 0.7868 (m100) cc_final: 0.7355 (m100) REVERT: A 353 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7216 (t70) REVERT: A 632 TRP cc_start: 0.7791 (OUTLIER) cc_final: 0.6721 (t60) outliers start: 117 outliers final: 95 residues processed: 207 average time/residue: 0.2877 time to fit residues: 99.5679 Evaluate side-chains 194 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 93 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 206 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22508 Z= 0.166 Angle : 0.571 11.211 30460 Z= 0.282 Chirality : 0.039 0.144 3316 Planarity : 0.004 0.038 3920 Dihedral : 5.248 78.836 3042 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.40 % Allowed : 23.28 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2744 helix: 0.80 (0.13), residues: 1752 sheet: None (None), residues: 0 loop : -2.19 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 129 HIS 0.003 0.001 HIS B 168 PHE 0.011 0.001 PHE D 198 TYR 0.011 0.001 TYR D 413 ARG 0.008 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 102 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7773 (mmt) cc_final: 0.7316 (mmt) REVERT: B 266 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7379 (mmtm) REVERT: B 468 MET cc_start: 0.7372 (tpp) cc_final: 0.7056 (ttt) REVERT: B 480 GLU cc_start: 0.8113 (tt0) cc_final: 0.7659 (mt-10) REVERT: B 714 MET cc_start: 0.8587 (tpt) cc_final: 0.8230 (tpp) REVERT: C 194 MET cc_start: 0.7756 (mmt) cc_final: 0.7388 (mmp) REVERT: C 256 MET cc_start: 0.6803 (mmm) cc_final: 0.6548 (mtt) REVERT: C 591 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: C 621 LEU cc_start: 0.8424 (mt) cc_final: 0.8171 (mt) REVERT: D 148 MET cc_start: 0.5945 (OUTLIER) cc_final: 0.5412 (mmp) REVERT: D 245 MET cc_start: 0.7643 (mpp) cc_final: 0.7311 (mpp) REVERT: D 321 TRP cc_start: 0.7797 (m100) cc_final: 0.7344 (m100) REVERT: D 468 MET cc_start: 0.7359 (tmm) cc_final: 0.7082 (tmm) REVERT: D 632 TRP cc_start: 0.7809 (OUTLIER) cc_final: 0.6779 (t60) REVERT: A 83 MET cc_start: 0.7001 (mtm) cc_final: 0.6748 (pmm) REVERT: A 147 MET cc_start: 0.7381 (mmm) cc_final: 0.7082 (tpt) REVERT: A 148 MET cc_start: 0.6210 (mmp) cc_final: 0.5420 (mmp) REVERT: A 321 TRP cc_start: 0.7850 (m100) cc_final: 0.7333 (m100) REVERT: A 353 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7117 (t70) REVERT: A 632 TRP cc_start: 0.7789 (OUTLIER) cc_final: 0.6589 (t60) REVERT: A 713 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7802 (pm20) outliers start: 105 outliers final: 86 residues processed: 198 average time/residue: 0.2798 time to fit residues: 94.2594 Evaluate side-chains 189 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 96 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 0.2980 chunk 251 optimal weight: 7.9990 chunk 229 optimal weight: 0.7980 chunk 244 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 220 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22508 Z= 0.193 Angle : 0.608 10.745 30460 Z= 0.300 Chirality : 0.040 0.149 3316 Planarity : 0.004 0.041 3920 Dihedral : 5.304 78.887 3040 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.36 % Allowed : 23.53 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2744 helix: 0.73 (0.13), residues: 1748 sheet: None (None), residues: 0 loop : -2.14 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 129 HIS 0.005 0.001 HIS C 334 PHE 0.012 0.001 PHE D 198 TYR 0.012 0.001 TYR D 413 ARG 0.008 0.001 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 97 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7823 (mmt) cc_final: 0.7346 (mmt) REVERT: B 468 MET cc_start: 0.7399 (tpp) cc_final: 0.7115 (ttt) REVERT: B 480 GLU cc_start: 0.8133 (tt0) cc_final: 0.7693 (mt-10) REVERT: B 714 MET cc_start: 0.8561 (tpt) cc_final: 0.8103 (tpp) REVERT: C 194 MET cc_start: 0.7626 (mmt) cc_final: 0.7269 (mmp) REVERT: C 256 MET cc_start: 0.6789 (mmm) cc_final: 0.6553 (mtt) REVERT: C 591 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: D 148 MET cc_start: 0.5947 (OUTLIER) cc_final: 0.5431 (mmp) REVERT: D 245 MET cc_start: 0.7693 (mpp) cc_final: 0.7345 (mpp) REVERT: D 321 TRP cc_start: 0.7821 (m100) cc_final: 0.7360 (m100) REVERT: D 632 TRP cc_start: 0.7792 (OUTLIER) cc_final: 0.6688 (t60) REVERT: A 83 MET cc_start: 0.7020 (mtm) cc_final: 0.6791 (pmm) REVERT: A 321 TRP cc_start: 0.7878 (m100) cc_final: 0.7358 (m100) REVERT: A 353 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7124 (t70) REVERT: A 632 TRP cc_start: 0.7797 (OUTLIER) cc_final: 0.6629 (t60) outliers start: 104 outliers final: 91 residues processed: 193 average time/residue: 0.2688 time to fit residues: 88.7876 Evaluate side-chains 189 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 93 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22508 Z= 0.243 Angle : 0.669 11.102 30460 Z= 0.332 Chirality : 0.041 0.156 3316 Planarity : 0.005 0.045 3920 Dihedral : 5.593 79.065 3040 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.52 % Allowed : 23.37 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.80 (0.16), residues: 2744 helix: 0.41 (0.12), residues: 1736 sheet: None (None), residues: 0 loop : -2.21 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 632 HIS 0.005 0.001 HIS C 334 PHE 0.016 0.002 PHE B 591 TYR 0.015 0.002 TYR D 413 ARG 0.008 0.001 ARG A 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 92 time to evaluate : 2.582 Fit side-chains revert: symmetry clash REVERT: B 183 MET cc_start: 0.8820 (mmm) cc_final: 0.8532 (mmm) REVERT: B 194 MET cc_start: 0.7710 (mmt) cc_final: 0.7335 (mmt) REVERT: B 480 GLU cc_start: 0.8218 (tt0) cc_final: 0.7919 (mt-10) REVERT: B 714 MET cc_start: 0.8528 (tpt) cc_final: 0.8182 (tpp) REVERT: C 194 MET cc_start: 0.7634 (mmt) cc_final: 0.7285 (mmp) REVERT: C 256 MET cc_start: 0.6892 (mmm) cc_final: 0.6573 (mtt) REVERT: C 591 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: D 148 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.5431 (mmp) REVERT: D 321 TRP cc_start: 0.7862 (m100) cc_final: 0.7393 (m100) REVERT: D 632 TRP cc_start: 0.7770 (OUTLIER) cc_final: 0.6666 (t60) REVERT: A 83 MET cc_start: 0.7172 (mtm) cc_final: 0.6900 (pmm) REVERT: A 321 TRP cc_start: 0.7995 (m100) cc_final: 0.7490 (m100) REVERT: A 353 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7055 (t70) REVERT: A 632 TRP cc_start: 0.7723 (OUTLIER) cc_final: 0.6477 (t60) outliers start: 108 outliers final: 97 residues processed: 194 average time/residue: 0.2765 time to fit residues: 92.3686 Evaluate side-chains 195 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 93 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.041784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.035160 restraints weight = 234525.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.036085 restraints weight = 120518.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.036711 restraints weight = 76486.056| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22508 Z= 0.164 Angle : 0.591 12.546 30460 Z= 0.288 Chirality : 0.039 0.146 3316 Planarity : 0.004 0.039 3920 Dihedral : 5.171 79.955 3040 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.27 % Allowed : 23.49 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.28 (0.16), residues: 2744 helix: 0.82 (0.13), residues: 1744 sheet: None (None), residues: 0 loop : -2.03 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 632 HIS 0.004 0.001 HIS D 401 PHE 0.012 0.001 PHE D 198 TYR 0.011 0.001 TYR D 413 ARG 0.008 0.000 ARG A 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3497.06 seconds wall clock time: 65 minutes 17.73 seconds (3917.73 seconds total)