Starting phenix.real_space_refine on Tue Dec 12 16:48:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6p_35202/12_2023/8i6p_35202.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6p_35202/12_2023/8i6p_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_35202/12_2023/8i6p_35202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6p_35202/12_2023/8i6p_35202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6p_35202/12_2023/8i6p_35202.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6p_35202/12_2023/8i6p_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 12.09, per 1000 atoms: 0.55 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: 9.60 Conformation dependent library (CDL) restraints added in 4.3 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: 2.49 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: 7.06 Time building geometry restraints manager: 10.27 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.380 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 60.610 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.430 ------------------------------------------------------------------------------- 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 : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 372 outliers final: 107 residues processed: 543 average time/residue: 0.3196 time to fit residues: 274.5524 Evaluate side-chains 208 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 101 time to evaluate : 2.885 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 0 residues processed: 107 average time/residue: 0.2007 time to fit residues: 43.9431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 70 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS A 357 HIS ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 414 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: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22508 Z= 0.258 Angle : 0.675 10.206 30460 Z= 0.345 Chirality : 0.043 0.177 3316 Planarity : 0.005 0.050 3920 Dihedral : 4.589 24.185 3016 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.44 % Allowed : 22.70 % Favored : 72.86 % 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: -1.82 (0.14), residues: 2744 helix: -0.45 (0.11), residues: 1732 sheet: None (None), residues: 0 loop : -2.50 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 129 HIS 0.012 0.002 HIS C 334 PHE 0.018 0.002 PHE B 566 TYR 0.016 0.002 TYR A 413 ARG 0.018 0.001 ARG C 348 *********************** 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 229 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 123 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 48 residues processed: 221 average time/residue: 0.2992 time to fit residues: 109.7435 Evaluate side-chains 144 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 96 time to evaluate : 2.517 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.2010 time to fit residues: 21.1324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 247 optimal weight: 9.9990 chunk 267 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 198 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 675 GLN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN D 401 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 678 GLN ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3777 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= 0.269 Angle : 0.676 11.228 30460 Z= 0.346 Chirality : 0.042 0.169 3316 Planarity : 0.005 0.048 3920 Dihedral : 4.727 29.462 3016 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.15 % Allowed : 22.19 % Favored : 73.66 % 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: -1.54 (0.15), residues: 2744 helix: -0.22 (0.12), residues: 1740 sheet: None (None), residues: 0 loop : -2.40 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 129 HIS 0.009 0.002 HIS C 334 PHE 0.017 0.002 PHE A 335 TYR 0.018 0.002 TYR D 413 ARG 0.007 0.001 ARG C 574 *********************** 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 205 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 106 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 51 residues processed: 201 average time/residue: 0.3207 time to fit residues: 104.6097 Evaluate side-chains 139 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 88 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2158 time to fit residues: 24.1262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 118 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 235 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- 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 590 HIS D 414 ASN D 764 GLN A 360 ASN A 764 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22508 Z= 0.140 Angle : 0.535 10.311 30460 Z= 0.270 Chirality : 0.039 0.155 3316 Planarity : 0.003 0.048 3920 Dihedral : 4.008 19.035 3016 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.55 % Allowed : 23.24 % Favored : 75.21 % 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: -0.43 (0.16), residues: 2744 helix: 0.79 (0.13), residues: 1724 sheet: None (None), residues: 0 loop : -2.22 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 129 HIS 0.002 0.001 HIS C 357 PHE 0.011 0.001 PHE C 146 TYR 0.011 0.001 TYR D 413 ARG 0.009 0.000 ARG B 348 *********************** 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 163 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 7 residues processed: 158 average time/residue: 0.3473 time to fit residues: 87.8386 Evaluate side-chains 106 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 2.913 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2284 time to fit residues: 6.6786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 7.9990 chunk 149 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 224 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 696 ASN B 715 GLN C 334 HIS ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22508 Z= 0.277 Angle : 0.686 11.380 30460 Z= 0.348 Chirality : 0.042 0.176 3316 Planarity : 0.005 0.046 3920 Dihedral : 4.580 25.937 3016 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.93 % Allowed : 23.41 % Favored : 73.66 % 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: -0.95 (0.15), residues: 2744 helix: 0.28 (0.12), residues: 1728 sheet: None (None), residues: 0 loop : -2.23 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 632 HIS 0.007 0.002 HIS A 357 PHE 0.016 0.002 PHE C 304 TYR 0.016 0.002 TYR A 413 ARG 0.010 0.001 ARG B 622 *********************** 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 168 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 98 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 35 residues processed: 162 average time/residue: 0.3260 time to fit residues: 85.8449 Evaluate side-chains 127 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 92 time to evaluate : 2.658 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2598 time to fit residues: 20.2363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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** B 738 HIS ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 22508 Z= 0.369 Angle : 0.804 12.175 30460 Z= 0.413 Chirality : 0.045 0.223 3316 Planarity : 0.006 0.053 3920 Dihedral : 5.207 31.186 3016 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.43 % Allowed : 24.71 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.84 (0.15), residues: 2744 helix: -0.47 (0.12), residues: 1720 sheet: None (None), residues: 0 loop : -2.48 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 632 HIS 0.008 0.002 HIS A 357 PHE 0.021 0.002 PHE C 146 TYR 0.020 0.003 TYR D 413 ARG 0.010 0.001 ARG A 652 *********************** 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 164 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 106 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 28 residues processed: 156 average time/residue: 0.3098 time to fit residues: 80.8904 Evaluate side-chains 122 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 2.837 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2030 time to fit residues: 14.4296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 221 optimal weight: 0.5980 chunk 146 optimal weight: 9.9990 chunk 262 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 overall best weight: 3.8386 ------------------------------------------------------------------------------- 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 357 HIS ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN D 188 HIS ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22508 Z= 0.220 Angle : 0.640 11.541 30460 Z= 0.323 Chirality : 0.041 0.176 3316 Planarity : 0.004 0.045 3920 Dihedral : 4.615 23.692 3016 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.96 % Allowed : 26.26 % Favored : 72.78 % 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: -1.31 (0.15), residues: 2744 helix: 0.05 (0.12), residues: 1728 sheet: None (None), residues: 0 loop : -2.49 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 129 HIS 0.005 0.001 HIS C 334 PHE 0.014 0.001 PHE C 146 TYR 0.018 0.002 TYR B 466 ARG 0.011 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 125 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 122 average time/residue: 0.3161 time to fit residues: 64.7698 Evaluate side-chains 105 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 3.202 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2264 time to fit residues: 8.0131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 166 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 206 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22508 Z= 0.166 Angle : 0.579 10.790 30460 Z= 0.289 Chirality : 0.039 0.144 3316 Planarity : 0.004 0.038 3920 Dihedral : 4.231 21.587 3016 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.92 % Allowed : 26.01 % Favored : 73.07 % 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: -0.75 (0.16), residues: 2744 helix: 0.52 (0.12), residues: 1732 sheet: None (None), residues: 0 loop : -2.34 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 129 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE C 146 TYR 0.011 0.001 TYR B 466 ARG 0.009 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 130 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 125 average time/residue: 0.3176 time to fit residues: 66.3622 Evaluate side-chains 102 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 3.036 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2227 time to fit residues: 6.8722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 0.0970 chunk 251 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 147 optimal weight: 0.0070 chunk 106 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 220 optimal weight: 6.9990 chunk 231 optimal weight: 0.6980 chunk 243 optimal weight: 5.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- 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 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22508 Z= 0.152 Angle : 0.579 14.083 30460 Z= 0.283 Chirality : 0.039 0.168 3316 Planarity : 0.004 0.036 3920 Dihedral : 3.997 19.923 3016 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.50 % Allowed : 26.05 % Favored : 73.45 % 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: -0.31 (0.16), residues: 2744 helix: 0.83 (0.13), residues: 1748 sheet: None (None), residues: 0 loop : -2.13 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 632 HIS 0.003 0.001 HIS C 168 PHE 0.015 0.001 PHE C 146 TYR 0.010 0.001 TYR B 466 ARG 0.009 0.000 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 116 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 115 average time/residue: 0.3429 time to fit residues: 66.2186 Evaluate side-chains 99 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 2.891 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2103 time to fit residues: 5.0324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 166 optimal weight: 0.0020 chunk 132 optimal weight: 5.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22508 Z= 0.157 Angle : 0.589 12.312 30460 Z= 0.288 Chirality : 0.039 0.185 3316 Planarity : 0.004 0.036 3920 Dihedral : 3.937 19.741 3016 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.13 % Allowed : 26.59 % Favored : 73.28 % 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: 0.87 (0.13), residues: 1752 sheet: None (None), residues: 0 loop : -2.16 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 129 HIS 0.002 0.001 HIS C 334 PHE 0.011 0.001 PHE D 198 TYR 0.014 0.001 TYR B 466 ARG 0.008 0.000 ARG A 185 ********************** 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 102 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 101 average time/residue: 0.3170 time to fit residues: 54.5790 Evaluate side-chains 98 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 2.603 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2130 time to fit residues: 4.3457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 8.9990 chunk 229 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 90 optimal weight: 0.0770 chunk 221 optimal weight: 0.3980 chunk 27 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 523 GLN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.042043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.035452 restraints weight = 233383.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.036385 restraints weight = 119844.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.037002 restraints weight = 75894.510| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22508 Z= 0.153 Angle : 0.580 11.877 30460 Z= 0.284 Chirality : 0.039 0.202 3316 Planarity : 0.004 0.036 3920 Dihedral : 3.876 19.691 3016 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.38 % Allowed : 26.09 % Favored : 73.53 % 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: -0.10 (0.16), residues: 2744 helix: 0.99 (0.13), residues: 1744 sheet: None (None), residues: 0 loop : -2.01 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 129 HIS 0.002 0.001 HIS A 357 PHE 0.013 0.001 PHE C 146 TYR 0.010 0.001 TYR B 466 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: 3494.11 seconds wall clock time: 65 minutes 58.64 seconds (3958.64 seconds total)