Starting phenix.real_space_refine on Sat Nov 18 00:38:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvm_20493/11_2023/6pvm_20493.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvm_20493/11_2023/6pvm_20493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvm_20493/11_2023/6pvm_20493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvm_20493/11_2023/6pvm_20493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvm_20493/11_2023/6pvm_20493.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvm_20493/11_2023/6pvm_20493.pdb" } resolution = 4.5 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= 0.011 sd= 0.247 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 124 5.16 5 Na 2 4.78 5 C 13648 2.51 5 N 3480 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 696": "NH1" <-> "NH2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 696": "NH1" <-> "NH2" Residue "C ARG 712": "NH1" <-> "NH2" Residue "C PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 696": "NH1" <-> "NH2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 758": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 21006 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "B" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "C" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "D" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.41, per 1000 atoms: 0.50 Number of scatterers: 21006 At special positions: 0 Unit cell: (162.18, 162.18, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 Na 2 11.00 O 3752 8.00 N 3480 7.00 C 13648 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: 8.25 Conformation dependent library (CDL) restraints added in 3.7 seconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 58.1% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.608A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.719A pdb=" N ASP A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 172 through 178 removed outlier: 4.123A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.644A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.848A pdb=" N ALA A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 237 removed outlier: 3.669A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 removed outlier: 3.856A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.661A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.876A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.903A pdb=" N SER A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.599A pdb=" N GLU A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.649A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.999A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.683A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 374' Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.566A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 420' Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.646A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 458 removed outlier: 3.536A pdb=" N SER A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 505 removed outlier: 4.369A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 497 " --> pdb=" O TRP A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 540 removed outlier: 3.777A pdb=" N HIS A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.629A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 581 through 586 removed outlier: 4.507A pdb=" N HIS A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 4.326A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 607 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.540A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 664 removed outlier: 3.654A pdb=" N ILE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 685 removed outlier: 3.639A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.617A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.609A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.720A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 172 through 178 removed outlier: 4.123A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 196 removed outlier: 3.645A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.848A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 237 removed outlier: 3.669A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 removed outlier: 3.856A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.660A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.877A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.903A pdb=" N SER B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.598A pdb=" N GLU B 334 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.648A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.999A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.683A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 374 " --> pdb=" O ARG B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 374' Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.566A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 420' Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.647A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 458 removed outlier: 3.536A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 505 removed outlier: 4.369A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 497 " --> pdb=" O TRP B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 540 removed outlier: 3.776A pdb=" N HIS B 523 " --> pdb=" O ASP B 519 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 removed outlier: 3.629A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 554 " --> pdb=" O CYS B 550 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 581 through 586 removed outlier: 4.506A pdb=" N HIS B 585 " --> pdb=" O LYS B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 608 removed outlier: 4.326A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 607 " --> pdb=" O VAL B 603 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 removed outlier: 3.539A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 664 removed outlier: 3.654A pdb=" N ILE B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 685 removed outlier: 3.639A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 681 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.617A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 129 removed outlier: 3.609A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.720A pdb=" N ASP C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 172 through 178 removed outlier: 4.123A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 196 removed outlier: 3.645A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.847A pdb=" N ALA C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.669A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 272 removed outlier: 3.857A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.661A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 279 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.877A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.902A pdb=" N SER C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.598A pdb=" N GLU C 334 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.648A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.998A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.683A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 370 through 374' Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.567A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 420' Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.647A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 458 removed outlier: 3.535A pdb=" N SER C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 505 removed outlier: 4.369A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE C 497 " --> pdb=" O TRP C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 540 removed outlier: 3.776A pdb=" N HIS C 523 " --> pdb=" O ASP C 519 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 561 removed outlier: 3.628A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 556 " --> pdb=" O VAL C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 581 through 586 removed outlier: 4.506A pdb=" N HIS C 585 " --> pdb=" O LYS C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 608 removed outlier: 4.326A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 607 " --> pdb=" O VAL C 603 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.539A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 664 removed outlier: 3.654A pdb=" N ILE C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C 660 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 685 removed outlier: 3.638A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 681 " --> pdb=" O MET C 677 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.616A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 removed outlier: 3.608A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 147 removed outlier: 3.719A pdb=" N ASP D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 172 through 178 removed outlier: 4.123A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 196 removed outlier: 3.645A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.847A pdb=" N ALA D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 237 removed outlier: 3.669A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 272 removed outlier: 3.856A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.661A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.876A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.901A pdb=" N SER D 328 " --> pdb=" O ILE D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.598A pdb=" N GLU D 334 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.649A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.999A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.682A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 374 " --> pdb=" O ARG D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 374' Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.566A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 420' Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.647A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 458 removed outlier: 3.535A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 505 removed outlier: 4.369A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE D 497 " --> pdb=" O TRP D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 540 removed outlier: 3.777A pdb=" N HIS D 523 " --> pdb=" O ASP D 519 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 removed outlier: 3.629A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 554 " --> pdb=" O CYS D 550 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA D 556 " --> pdb=" O VAL D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 581 through 586 removed outlier: 4.507A pdb=" N HIS D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 608 removed outlier: 4.325A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 607 " --> pdb=" O VAL D 603 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 removed outlier: 3.539A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 664 removed outlier: 3.654A pdb=" N ILE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 660 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU D 664 " --> pdb=" O THR D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 685 removed outlier: 3.639A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 681 " --> pdb=" O MET D 677 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.616A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA2, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AA3, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AA4, first strand: chain 'D' and resid 387 through 388 736 hydrogen bonds defined for protein. 2160 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: 5.76 Time building geometry restraints manager: 8.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6493 1.34 - 1.46: 4374 1.46 - 1.58: 10389 1.58 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 21460 Sorted by residual: bond pdb=" C LEU A 469 " pdb=" N PRO A 470 " ideal model delta sigma weight residual 1.334 1.391 -0.058 2.34e-02 1.83e+03 6.04e+00 bond pdb=" C LEU B 469 " pdb=" N PRO B 470 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.96e+00 bond pdb=" C LEU C 469 " pdb=" N PRO C 470 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.95e+00 bond pdb=" C LEU D 469 " pdb=" N PRO D 470 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.89e+00 bond pdb=" C ARG B 509 " pdb=" N PRO B 510 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.81e+00 ... (remaining 21455 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.50: 312 105.50 - 112.63: 10743 112.63 - 119.76: 7927 119.76 - 126.89: 9763 126.89 - 134.02: 287 Bond angle restraints: 29032 Sorted by residual: angle pdb=" C TRP B 739 " pdb=" N THR B 740 " pdb=" CA THR B 740 " ideal model delta sigma weight residual 121.54 132.44 -10.90 1.91e+00 2.74e-01 3.26e+01 angle pdb=" C TRP C 739 " pdb=" N THR C 740 " pdb=" CA THR C 740 " ideal model delta sigma weight residual 121.54 132.43 -10.89 1.91e+00 2.74e-01 3.25e+01 angle pdb=" C TRP A 739 " pdb=" N THR A 740 " pdb=" CA THR A 740 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C TRP D 739 " pdb=" N THR D 740 " pdb=" CA THR D 740 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.23e+01 angle pdb=" N ILE D 503 " pdb=" CA ILE D 503 " pdb=" C ILE D 503 " ideal model delta sigma weight residual 112.96 107.49 5.47 1.00e+00 1.00e+00 2.99e+01 ... (remaining 29027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 11556 14.98 - 29.97: 935 29.97 - 44.95: 309 44.95 - 59.93: 36 59.93 - 74.91: 20 Dihedral angle restraints: 12856 sinusoidal: 5252 harmonic: 7604 Sorted by residual: dihedral pdb=" CA HIS C 256 " pdb=" C HIS C 256 " pdb=" N GLU C 257 " pdb=" CA GLU C 257 " ideal model delta harmonic sigma weight residual -180.00 -135.43 -44.57 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA HIS B 256 " pdb=" C HIS B 256 " pdb=" N GLU B 257 " pdb=" CA GLU B 257 " ideal model delta harmonic sigma weight residual -180.00 -135.43 -44.57 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA HIS D 256 " pdb=" C HIS D 256 " pdb=" N GLU D 257 " pdb=" CA GLU D 257 " ideal model delta harmonic sigma weight residual -180.00 -135.49 -44.51 0 5.00e+00 4.00e-02 7.93e+01 ... (remaining 12853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2075 0.048 - 0.095: 908 0.095 - 0.143: 227 0.143 - 0.191: 81 0.191 - 0.238: 17 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CB ILE D 199 " pdb=" CA ILE D 199 " pdb=" CG1 ILE D 199 " pdb=" CG2 ILE D 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE B 199 " pdb=" CA ILE B 199 " pdb=" CG1 ILE B 199 " pdb=" CG2 ILE B 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE A 199 " pdb=" CA ILE A 199 " pdb=" CG1 ILE A 199 " pdb=" CG2 ILE A 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3305 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 754 " 0.052 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO D 755 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 755 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 755 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 754 " 0.052 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO A 755 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 755 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 755 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 754 " 0.051 5.00e-02 4.00e+02 7.77e-02 9.66e+00 pdb=" N PRO B 755 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 755 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 755 " 0.042 5.00e-02 4.00e+02 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 636 2.70 - 3.25: 20772 3.25 - 3.80: 32076 3.80 - 4.35: 39228 4.35 - 4.90: 62291 Nonbonded interactions: 155003 Sorted by model distance: nonbonded pdb=" OE1 GLU A 751 " pdb=" OH TYR D 213 " model vdw 2.154 2.440 nonbonded pdb=" OH TYR C 213 " pdb=" OE1 GLU D 751 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR A 460 " pdb=" OG SER D 607 " model vdw 2.240 2.440 nonbonded pdb=" OH TYR A 213 " pdb=" OE1 GLU B 751 " model vdw 2.254 2.440 nonbonded pdb=" OG SER A 607 " pdb=" OH TYR B 460 " model vdw 2.282 2.440 ... (remaining 154998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 115 through 758) selection = chain 'B' selection = (chain 'C' and resid 115 through 758) 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: 0.750 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: 3.580 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 52.550 Find NCS groups from input model: 1.560 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.006 0.060 21460 Z= 0.378 Angle : 1.184 14.755 29032 Z= 0.623 Chirality : 0.059 0.238 3308 Planarity : 0.007 0.078 3624 Dihedral : 12.600 74.915 7920 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.62 % Favored : 84.07 % Rotamer: Outliers : 0.87 % Allowed : 8.30 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -6.13 (0.11), residues: 2568 helix: -4.24 (0.07), residues: 1252 sheet: -4.71 (0.36), residues: 56 loop : -3.86 (0.15), residues: 1260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1034 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 4 residues processed: 1049 average time/residue: 0.3134 time to fit residues: 506.2914 Evaluate side-chains 744 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 740 time to evaluate : 2.174 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1719 time to fit residues: 4.3093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 232 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 313 GLN A 314 ASN A 452 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 313 GLN B 314 ASN B 452 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS C 313 GLN C 314 ASN C 452 ASN C 647 ASN D 160 HIS D 313 GLN D 314 ASN D 417 HIS D 452 ASN D 647 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21460 Z= 0.274 Angle : 0.832 10.889 29032 Z= 0.427 Chirality : 0.045 0.143 3308 Planarity : 0.006 0.069 3624 Dihedral : 7.302 35.658 2808 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.29 % Favored : 85.40 % Rotamer: Outliers : 0.04 % Allowed : 5.61 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -4.32 (0.14), residues: 2568 helix: -2.19 (0.12), residues: 1272 sheet: -4.85 (0.36), residues: 56 loop : -3.57 (0.16), residues: 1240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 771 time to evaluate : 2.449 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 outliers start: 1 outliers final: 0 residues processed: 771 average time/residue: 0.2915 time to fit residues: 358.5370 Evaluate side-chains 652 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 652 time to evaluate : 2.330 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.3980 chunk 72 optimal weight: 9.9990 chunk 193 optimal weight: 0.0170 chunk 158 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 chunk 232 optimal weight: 30.0000 chunk 251 optimal weight: 0.0270 chunk 207 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 overall best weight: 1.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 417 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN B 417 HIS B 647 ASN C 279 GLN C 297 ASN C 417 HIS ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21460 Z= 0.180 Angle : 0.736 10.237 29032 Z= 0.372 Chirality : 0.042 0.153 3308 Planarity : 0.005 0.064 3624 Dihedral : 6.832 36.756 2808 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.94 % Favored : 85.75 % Rotamer: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -3.42 (0.16), residues: 2568 helix: -1.24 (0.13), residues: 1300 sheet: -4.96 (0.36), residues: 56 loop : -3.39 (0.17), residues: 1212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 753 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 753 average time/residue: 0.2815 time to fit residues: 339.2893 Evaluate side-chains 621 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 621 time to evaluate : 2.387 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 25 optimal weight: 0.0670 chunk 111 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 233 optimal weight: 8.9990 chunk 247 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 292 GLN A 417 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 GLN B 279 GLN B 292 GLN B 417 HIS ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN C 160 HIS ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS C 647 ASN C 695 GLN D 160 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS D 647 ASN D 695 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21460 Z= 0.210 Angle : 0.739 10.052 29032 Z= 0.376 Chirality : 0.043 0.148 3308 Planarity : 0.005 0.062 3624 Dihedral : 6.674 34.769 2808 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.17 % Favored : 85.51 % Rotamer: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.07 (0.16), residues: 2568 helix: -0.83 (0.14), residues: 1320 sheet: -4.31 (0.38), residues: 76 loop : -3.39 (0.18), residues: 1172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 717 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 718 average time/residue: 0.2731 time to fit residues: 318.6693 Evaluate side-chains 612 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 611 time to evaluate : 2.494 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2334 time to fit residues: 3.8589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 184 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 171 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 126 optimal weight: 0.3980 chunk 222 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS A 426 HIS A 471 HIS ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS C 647 ASN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS D 647 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21460 Z= 0.244 Angle : 0.772 9.923 29032 Z= 0.389 Chirality : 0.044 0.146 3308 Planarity : 0.005 0.065 3624 Dihedral : 6.731 35.512 2808 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.54 % Favored : 84.15 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.17), residues: 2568 helix: -0.64 (0.14), residues: 1324 sheet: -4.13 (0.42), residues: 72 loop : -3.31 (0.18), residues: 1172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 706 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 706 average time/residue: 0.2919 time to fit residues: 335.2567 Evaluate side-chains 592 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 592 time to evaluate : 2.436 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 247 optimal weight: 4.9990 chunk 205 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 417 HIS A 647 ASN B 292 GLN B 314 ASN B 417 HIS B 647 ASN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 417 HIS C 647 ASN D 292 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS D 647 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21460 Z= 0.235 Angle : 0.767 10.095 29032 Z= 0.386 Chirality : 0.044 0.180 3308 Planarity : 0.005 0.061 3624 Dihedral : 6.631 34.119 2808 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 15.38 % Favored : 84.38 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.17), residues: 2568 helix: -0.61 (0.14), residues: 1352 sheet: -4.20 (0.40), residues: 76 loop : -3.40 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 692 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 692 average time/residue: 0.2834 time to fit residues: 317.4823 Evaluate side-chains 579 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 579 time to evaluate : 2.556 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 6.9990 chunk 27 optimal weight: 0.2980 chunk 141 optimal weight: 8.9990 chunk 180 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 138 optimal weight: 0.6980 chunk 246 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 417 HIS ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 417 HIS D 647 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21460 Z= 0.194 Angle : 0.755 10.335 29032 Z= 0.377 Chirality : 0.043 0.162 3308 Planarity : 0.005 0.061 3624 Dihedral : 6.504 33.978 2808 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.80 % Favored : 84.89 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.17), residues: 2568 helix: -0.46 (0.14), residues: 1316 sheet: -3.90 (0.42), residues: 72 loop : -3.18 (0.19), residues: 1180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 698 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 698 average time/residue: 0.2853 time to fit residues: 321.4849 Evaluate side-chains 583 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 583 time to evaluate : 2.577 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 22 optimal weight: 0.3980 chunk 193 optimal weight: 8.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN A 417 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN B 314 ASN B 417 HIS B 647 ASN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 417 HIS C 647 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS D 647 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21460 Z= 0.200 Angle : 0.777 9.997 29032 Z= 0.386 Chirality : 0.044 0.234 3308 Planarity : 0.005 0.057 3624 Dihedral : 6.427 35.842 2808 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.72 % Favored : 85.05 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.17), residues: 2568 helix: -0.47 (0.14), residues: 1340 sheet: -3.59 (0.49), residues: 68 loop : -3.31 (0.18), residues: 1160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 693 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 693 average time/residue: 0.2867 time to fit residues: 322.3052 Evaluate side-chains 582 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 582 time to evaluate : 2.335 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 7.9990 chunk 236 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 chunk 138 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 180 optimal weight: 0.0020 chunk 70 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 417 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 GLN D 647 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21460 Z= 0.191 Angle : 0.773 10.052 29032 Z= 0.382 Chirality : 0.043 0.169 3308 Planarity : 0.005 0.070 3624 Dihedral : 6.275 34.869 2808 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.52 % Favored : 85.20 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.17), residues: 2568 helix: -0.45 (0.14), residues: 1344 sheet: -3.55 (0.49), residues: 68 loop : -3.26 (0.19), residues: 1156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 689 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 689 average time/residue: 0.2936 time to fit residues: 327.8409 Evaluate side-chains 585 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 585 time to evaluate : 2.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 255 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN B 580 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 647 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21460 Z= 0.227 Angle : 0.796 12.249 29032 Z= 0.394 Chirality : 0.045 0.223 3308 Planarity : 0.005 0.056 3624 Dihedral : 6.333 35.356 2808 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.26 % Favored : 84.54 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.17), residues: 2568 helix: -0.44 (0.14), residues: 1364 sheet: -3.57 (0.50), residues: 68 loop : -3.33 (0.19), residues: 1136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 679 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 679 average time/residue: 0.2777 time to fit residues: 305.8123 Evaluate side-chains 565 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 565 time to evaluate : 2.420 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.0050 chunk 62 optimal weight: 9.9990 chunk 187 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 chunk 208 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 overall best weight: 0.6774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 GLN B 301 HIS ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113558 restraints weight = 51635.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116743 restraints weight = 30428.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118955 restraints weight = 20552.693| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.6254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21460 Z= 0.189 Angle : 0.795 13.581 29032 Z= 0.385 Chirality : 0.044 0.243 3308 Planarity : 0.005 0.058 3624 Dihedral : 6.120 35.023 2808 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.55 % Favored : 86.14 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.17), residues: 2568 helix: -0.47 (0.14), residues: 1384 sheet: -3.91 (0.45), residues: 76 loop : -3.41 (0.19), residues: 1108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5624.92 seconds wall clock time: 102 minutes 5.24 seconds (6125.24 seconds total)