Starting phenix.real_space_refine on Sun Mar 17 05:33:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/03_2024/7oqh_12701_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/03_2024/7oqh_12701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/03_2024/7oqh_12701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/03_2024/7oqh_12701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/03_2024/7oqh_12701_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/03_2024/7oqh_12701_updated.pdb" } resolution = 3.32 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= 0.005 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 5 5.21 5 S 54 5.16 5 C 10470 2.51 5 N 3042 2.21 5 O 3235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "B ASP 440": "OD1" <-> "OD2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "D PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 267": "OD1" <-> "OD2" Residue "E GLU 389": "OE1" <-> "OE2" Residue "E GLU 390": "OE1" <-> "OE2" Residue "E PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 423": "OE1" <-> "OE2" Residue "E GLU 430": "OE1" <-> "OE2" Residue "E GLU 508": "OE1" <-> "OE2" Residue "F ASP 385": "OD1" <-> "OD2" Residue "F PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 440": "OD1" <-> "OD2" Residue "F TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16824 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2770 Classifications: {'peptide': 363} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2787 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2775 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2797 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2772 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2732 Classifications: {'peptide': 356} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.05, per 1000 atoms: 0.54 Number of scatterers: 16824 At special positions: 0 Unit cell: (147.882, 131.451, 103.069, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 18 15.00 Mg 5 11.99 O 3235 8.00 N 3042 7.00 C 10470 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: 6.91 Conformation dependent library (CDL) restraints added in 2.8 seconds 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4010 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 12 sheets defined 37.5% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 332 through 340 Processing helix chain 'A' and resid 359 through 373 Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 411 through 431 removed outlier: 3.510A pdb=" N THR A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 452 Processing helix chain 'A' and resid 467 through 478 Proline residue: A 471 - end of helix Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 523 through 526 No H-bonds generated for 'chain 'A' and resid 523 through 526' Processing helix chain 'A' and resid 549 through 564 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 583 through 591 Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.862A pdb=" N LEU B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 373 Processing helix chain 'B' and resid 388 through 397 removed outlier: 3.875A pdb=" N THR B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 431 Processing helix chain 'B' and resid 442 through 452 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 471 through 478 Processing helix chain 'B' and resid 501 through 510 Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 549 through 563 Processing helix chain 'B' and resid 567 through 580 Processing helix chain 'B' and resid 583 through 591 Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 359 through 373 Processing helix chain 'C' and resid 388 through 397 removed outlier: 3.948A pdb=" N THR C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 431 removed outlier: 3.606A pdb=" N GLN C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 452 Processing helix chain 'C' and resid 469 through 478 removed outlier: 3.652A pdb=" N LYS C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 509 Processing helix chain 'C' and resid 522 through 526 Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 549 through 564 removed outlier: 4.066A pdb=" N GLY C 564 " --> pdb=" O ARG C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 580 removed outlier: 4.402A pdb=" N LYS C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'D' and resid 255 through 260 Processing helix chain 'D' and resid 333 through 340 Processing helix chain 'D' and resid 359 through 373 Processing helix chain 'D' and resid 388 through 397 removed outlier: 3.777A pdb=" N THR D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 430 Processing helix chain 'D' and resid 442 through 452 Processing helix chain 'D' and resid 467 through 478 Proline residue: D 471 - end of helix Processing helix chain 'D' and resid 501 through 509 Processing helix chain 'D' and resid 522 through 526 Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 549 through 564 Processing helix chain 'D' and resid 567 through 577 Processing helix chain 'D' and resid 584 through 591 Processing helix chain 'E' and resid 255 through 261 Processing helix chain 'E' and resid 336 through 339 No H-bonds generated for 'chain 'E' and resid 336 through 339' Processing helix chain 'E' and resid 359 through 373 Processing helix chain 'E' and resid 388 through 397 removed outlier: 3.784A pdb=" N THR E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 431 Processing helix chain 'E' and resid 442 through 452 Processing helix chain 'E' and resid 466 through 468 No H-bonds generated for 'chain 'E' and resid 466 through 468' Processing helix chain 'E' and resid 470 through 478 Processing helix chain 'E' and resid 501 through 510 Processing helix chain 'E' and resid 522 through 527 removed outlier: 4.086A pdb=" N ARG E 527 " --> pdb=" O LYS E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 545 No H-bonds generated for 'chain 'E' and resid 543 through 545' Processing helix chain 'E' and resid 549 through 564 Processing helix chain 'E' and resid 567 through 580 removed outlier: 4.032A pdb=" N ASP E 572 " --> pdb=" O HIS E 568 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS E 580 " --> pdb=" O SER E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 591 Processing helix chain 'F' and resid 255 through 261 Processing helix chain 'F' and resid 310 through 312 No H-bonds generated for 'chain 'F' and resid 310 through 312' Processing helix chain 'F' and resid 332 through 340 Processing helix chain 'F' and resid 359 through 373 Processing helix chain 'F' and resid 388 through 397 removed outlier: 3.530A pdb=" N THR F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 430 Processing helix chain 'F' and resid 442 through 450 Processing helix chain 'F' and resid 461 through 463 No H-bonds generated for 'chain 'F' and resid 461 through 463' Processing helix chain 'F' and resid 467 through 477 Proline residue: F 471 - end of helix Processing helix chain 'F' and resid 501 through 509 Processing helix chain 'F' and resid 522 through 526 Processing helix chain 'F' and resid 549 through 563 Processing helix chain 'F' and resid 567 through 580 Processing helix chain 'F' and resid 583 through 588 Processing sheet with id= A, first strand: chain 'A' and resid 229 through 231 Processing sheet with id= B, first strand: chain 'A' and resid 516 through 519 removed outlier: 8.177A pdb=" N ALA A 349 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 490 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE A 351 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA A 492 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N SER A 353 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ALA A 494 " --> pdb=" O SER A 353 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 435 " --> pdb=" O THR A 489 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE A 491 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 437 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR A 493 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU A 439 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N MET A 495 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N HIS A 378 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU A 438 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET A 380 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU A 401 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU A 383 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 403 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 250 through 253 removed outlier: 3.561A pdb=" N ALA B 237 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY B 228 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA B 272 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU B 294 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 516 through 519 removed outlier: 3.642A pdb=" N ALA B 516 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ALA B 349 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 490 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE B 351 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA B 492 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER B 353 " --> pdb=" O ALA B 492 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA B 494 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 435 " --> pdb=" O THR B 489 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE B 491 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 437 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N THR B 493 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU B 439 " --> pdb=" O THR B 493 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N MET B 495 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N HIS B 378 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 438 " --> pdb=" O HIS B 378 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET B 380 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP B 440 " --> pdb=" O MET B 380 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL B 382 " --> pdb=" O ASP B 440 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU B 401 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU B 383 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 403 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 228 through 231 removed outlier: 4.222A pdb=" N GLY C 228 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 516 through 520 removed outlier: 3.991A pdb=" N ALA C 516 " --> pdb=" O ARG C 348 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA C 349 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE C 490 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE C 351 " --> pdb=" O ILE C 490 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA C 492 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N SER C 353 " --> pdb=" O ALA C 492 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA C 494 " --> pdb=" O SER C 353 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 435 " --> pdb=" O THR C 489 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE C 491 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 437 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR C 493 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU C 439 " --> pdb=" O THR C 493 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N MET C 495 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N HIS C 378 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU C 438 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N MET C 380 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASP C 440 " --> pdb=" O MET C 380 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL C 382 " --> pdb=" O ASP C 440 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU C 401 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU C 383 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 403 " --> pdb=" O LEU C 383 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 237 through 240 removed outlier: 3.901A pdb=" N GLY D 228 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA D 272 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU D 294 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 516 through 520 removed outlier: 3.761A pdb=" N ALA D 516 " --> pdb=" O ARG D 348 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA D 349 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE D 490 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE D 351 " --> pdb=" O ILE D 490 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA D 492 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N SER D 353 " --> pdb=" O ALA D 492 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA D 494 " --> pdb=" O SER D 353 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 493 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N HIS D 378 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU D 438 " --> pdb=" O HIS D 378 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N MET D 380 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASP D 440 " --> pdb=" O MET D 380 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL D 382 " --> pdb=" O ASP D 440 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU D 401 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU D 383 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE D 403 " --> pdb=" O LEU D 383 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 227 through 231 removed outlier: 4.089A pdb=" N GLY E 228 " --> pdb=" O ARG E 240 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 516 through 520 removed outlier: 3.897A pdb=" N ALA E 516 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ALA E 349 " --> pdb=" O LEU E 488 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE E 490 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE E 351 " --> pdb=" O ILE E 490 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA E 492 " --> pdb=" O ILE E 351 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N SER E 353 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA E 494 " --> pdb=" O SER E 353 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR E 493 " --> pdb=" O LEU E 439 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS E 378 " --> pdb=" O VAL E 436 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU E 438 " --> pdb=" O HIS E 378 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N MET E 380 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP E 440 " --> pdb=" O MET E 380 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL E 382 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU E 401 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU E 383 " --> pdb=" O GLU E 401 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE E 403 " --> pdb=" O LEU E 383 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 268 through 270 removed outlier: 4.112A pdb=" N GLY F 228 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL F 251 " --> pdb=" O VAL F 239 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 516 through 519 removed outlier: 3.728A pdb=" N ALA F 516 " --> pdb=" O ARG F 348 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA F 349 " --> pdb=" O LEU F 488 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE F 490 " --> pdb=" O ALA F 349 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE F 351 " --> pdb=" O ILE F 490 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA F 492 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER F 353 " --> pdb=" O ALA F 492 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA F 494 " --> pdb=" O SER F 353 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 439 " --> pdb=" O ILE F 491 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS F 378 " --> pdb=" O VAL F 436 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU F 438 " --> pdb=" O HIS F 378 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N MET F 380 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ASP F 440 " --> pdb=" O MET F 380 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL F 382 " --> pdb=" O ASP F 440 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU F 401 " --> pdb=" O VAL F 381 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LEU F 383 " --> pdb=" O GLU F 401 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE F 403 " --> pdb=" O LEU F 383 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1599 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 7.43 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: 5732 1.34 - 1.46: 2062 1.46 - 1.57: 9154 1.57 - 1.69: 27 1.69 - 1.81: 101 Bond restraints: 17076 Sorted by residual: bond pdb=" CB PRO E 248 " pdb=" CG PRO E 248 " ideal model delta sigma weight residual 1.492 1.631 -0.139 5.00e-02 4.00e+02 7.69e+00 bond pdb=" C GLN E 224 " pdb=" N PRO E 225 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.19e+00 bond pdb=" N PRO E 248 " pdb=" CA PRO E 248 " ideal model delta sigma weight residual 1.473 1.461 0.011 8.50e-03 1.38e+04 1.83e+00 bond pdb=" CA ASP C 543 " pdb=" CB ASP C 543 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.68e-02 3.54e+03 1.20e+00 bond pdb=" C TYR F 318 " pdb=" N PRO F 319 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.92e-01 ... (remaining 17071 not shown) Histogram of bond angle deviations from ideal: 99.08 - 107.23: 722 107.23 - 115.37: 10614 115.37 - 123.52: 11332 123.52 - 131.66: 469 131.66 - 139.81: 22 Bond angle restraints: 23159 Sorted by residual: angle pdb=" CA PRO E 248 " pdb=" N PRO E 248 " pdb=" CD PRO E 248 " ideal model delta sigma weight residual 112.00 104.79 7.21 1.40e+00 5.10e-01 2.65e+01 angle pdb=" N TYR E 318 " pdb=" CA TYR E 318 " pdb=" C TYR E 318 " ideal model delta sigma weight residual 109.81 118.41 -8.60 2.21e+00 2.05e-01 1.51e+01 angle pdb=" C SER B 242 " pdb=" N GLY B 243 " pdb=" CA GLY B 243 " ideal model delta sigma weight residual 121.70 128.67 -6.97 1.80e+00 3.09e-01 1.50e+01 angle pdb=" C LEU E 317 " pdb=" N TYR E 318 " pdb=" CA TYR E 318 " ideal model delta sigma weight residual 121.80 131.16 -9.36 2.44e+00 1.68e-01 1.47e+01 angle pdb=" C LYS D 580 " pdb=" N THR D 581 " pdb=" CA THR D 581 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.21e+01 ... (remaining 23154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9529 17.98 - 35.97: 904 35.97 - 53.95: 205 53.95 - 71.93: 32 71.93 - 89.91: 17 Dihedral angle restraints: 10687 sinusoidal: 4479 harmonic: 6208 Sorted by residual: dihedral pdb=" CA TYR D 318 " pdb=" C TYR D 318 " pdb=" N PRO D 319 " pdb=" CA PRO D 319 " ideal model delta harmonic sigma weight residual 180.00 151.32 28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA TYR E 318 " pdb=" C TYR E 318 " pdb=" N PRO E 319 " pdb=" CA PRO E 319 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLN E 224 " pdb=" C GLN E 224 " pdb=" N PRO E 225 " pdb=" CA PRO E 225 " ideal model delta harmonic sigma weight residual 180.00 -159.48 -20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 10684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2055 0.047 - 0.093: 492 0.093 - 0.140: 155 0.140 - 0.186: 5 0.186 - 0.232: 2 Chirality restraints: 2709 Sorted by residual: chirality pdb=" CA TYR D 318 " pdb=" N TYR D 318 " pdb=" C TYR D 318 " pdb=" CB TYR D 318 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TYR E 318 " pdb=" N TYR E 318 " pdb=" C TYR E 318 " pdb=" CB TYR E 318 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA PRO E 225 " pdb=" N PRO E 225 " pdb=" C PRO E 225 " pdb=" CB PRO E 225 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 2706 not shown) Planarity restraints: 3003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 536 " -0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO B 537 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 537 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 537 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 308 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO B 309 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 309 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 309 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 548 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO C 549 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 549 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 549 " -0.030 5.00e-02 4.00e+02 ... (remaining 3000 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 161 2.55 - 3.14: 13442 3.14 - 3.73: 25791 3.73 - 4.31: 35223 4.31 - 4.90: 59646 Nonbonded interactions: 134263 Sorted by model distance: nonbonded pdb=" O2B ATP F 701 " pdb="MG MG F 702 " model vdw 1.967 2.170 nonbonded pdb=" O2B ATP D 701 " pdb="MG MG D 702 " model vdw 1.977 2.170 nonbonded pdb=" O2B ATP E 701 " pdb="MG MG E 702 " model vdw 1.978 2.170 nonbonded pdb=" O2G ATP B 701 " pdb="MG MG B 702 " model vdw 1.983 2.170 nonbonded pdb=" O2G ATP F 701 " pdb="MG MG F 702 " model vdw 2.007 2.170 ... (remaining 134258 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 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 330 or (resid 331 and (name N or name CA or name C or name O or \ name CB )) or resid 332 through 423 or (resid 424 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ )) or resid \ 425 through 455 or (resid 460 and (name N or name CA or name C or name O or nam \ e CB )) or resid 461 through 466 or (resid 467 and (name N or name CA or name C \ or name O or name CB or name OG1)) or resid 468 through 481 or (resid 482 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2)) or res \ id 483 through 589)) selection = (chain 'B' and (resid 223 through 276 or resid 288 through 306 or (resid 307 thr \ ough 308 and (name N or name CA or name C or name O or name CB )) or resid 309 t \ hrough 330 or (resid 331 and (name N or name CA or name C or name O or name CB ) \ ) or resid 332 through 348 or (resid 349 and (name N or name CA or name C or nam \ e O )) or resid 350 through 360 or (resid 361 and (name N or name CA or name C o \ r name O or name CB or name OG1)) or resid 362 through 455 or (resid 460 and (na \ me N or name CA or name C or name O or name CB )) or resid 461 through 466 or (r \ esid 467 and (name N or name CA or name C or name O or name CB or name OG1)) or \ resid 468 through 481 or (resid 482 and (name N or name CA or name C or name O o \ r name CB or name CG1 or name CG2)) or resid 483 through 526 or (resid 527 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name N \ E or name CZ )) or resid 528 through 556 or (resid 557 and (name N or name CA or \ name C or name O or name CB )) or resid 558 through 589)) selection = (chain 'C' and (resid 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 306 or (resid 307 through 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 330 or (resid 331 and (name N or na \ me CA or name C or name O or name CB )) or resid 332 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O )) or resid 350 through 360 or (resid \ 361 and (name N or name CA or name C or name O or name CB or name OG1)) or resid \ 362 through 423 or (resid 424 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name NE or name CZ )) or resid 425 through 455 or \ (resid 460 and (name N or name CA or name C or name O or name CB )) or resid 461 \ through 481 or (resid 482 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or resid 483 through 526 or (resid 527 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ )) or resid 528 through 556 or (resid 557 and (name N or name CA or name C o \ r name O or name CB )) or resid 558 through 589)) selection = (chain 'D' and (resid 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 306 or (resid 307 through 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 330 or (resid 331 and (name N or na \ me CA or name C or name O or name CB )) or resid 332 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O )) or resid 350 through 360 or (resid \ 361 and (name N or name CA or name C or name O or name CB or name OG1)) or resid \ 362 through 423 or (resid 424 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name NE or name CZ )) or resid 425 through 455 or \ (resid 460 and (name N or name CA or name C or name O or name CB )) or resid 461 \ through 466 or (resid 467 and (name N or name CA or name C or name O or name CB \ or name OG1)) or resid 468 through 481 or (resid 482 and (name N or name CA or \ name C or name O or name CB or name CG1 or name CG2)) or resid 483 through 526 o \ r (resid 527 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ )) or resid 528 through 556 or (resid 557 and (na \ me N or name CA or name C or name O or name CB )) or resid 558 through 589)) selection = (chain 'E' and (resid 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 306 or (resid 307 through 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 348 or (resid 349 and (name N or na \ me CA or name C or name O )) or resid 350 through 360 or (resid 361 and (name N \ or name CA or name C or name O or name CB or name OG1)) or resid 362 through 455 \ or (resid 460 and (name N or name CA or name C or name O or name CB )) or resid \ 461 through 466 or (resid 467 and (name N or name CA or name C or name O or nam \ e CB or name OG1)) or resid 468 through 526 or (resid 527 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name NE or name CZ )) o \ r resid 528 through 556 or (resid 557 and (name N or name CA or name C or name O \ or name CB )) or resid 558 through 589)) selection = (chain 'F' and (resid 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 306 or (resid 307 through 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 330 or (resid 331 and (name N or na \ me CA or name C or name O or name CB )) or resid 332 through 360 or (resid 361 a \ nd (name N or name CA or name C or name O or name CB or name OG1)) or resid 362 \ through 423 or (resid 424 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ )) or resid 425 through 466 or (resi \ d 467 and (name N or name CA or name C or name O or name CB or name OG1)) or res \ id 468 through 481 or (resid 482 and (name N or name CA or name C or name O or n \ ame CB or name CG1 or name CG2)) or resid 483 through 556 or (resid 557 and (nam \ e N or name CA or name C or name O or name CB )) or resid 558 through 589)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 3.310 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 45.410 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.090 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 17076 Z= 0.269 Angle : 0.621 9.361 23159 Z= 0.322 Chirality : 0.044 0.232 2709 Planarity : 0.005 0.084 3003 Dihedral : 14.789 89.914 6677 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.49 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % 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: -0.13 (0.19), residues: 2143 helix: 1.44 (0.18), residues: 844 sheet: -1.01 (0.28), residues: 350 loop : -1.10 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 556 PHE 0.012 0.001 PHE F 475 TYR 0.018 0.001 TYR E 318 ARG 0.007 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.4436 (t80) cc_final: 0.4170 (t80) REVERT: A 260 LYS cc_start: 0.7544 (mptt) cc_final: 0.7016 (mmtt) REVERT: A 330 GLU cc_start: 0.6032 (mm-30) cc_final: 0.5828 (mm-30) REVERT: A 341 MET cc_start: 0.8107 (ttt) cc_final: 0.7819 (ttt) REVERT: A 577 GLN cc_start: 0.6792 (tm-30) cc_final: 0.6577 (tm-30) REVERT: B 257 MET cc_start: 0.6348 (ttt) cc_final: 0.5800 (ttt) REVERT: B 394 MET cc_start: 0.8981 (tpt) cc_final: 0.8671 (tpp) REVERT: B 575 MET cc_start: 0.7565 (mmm) cc_final: 0.7088 (tpp) REVERT: D 263 MET cc_start: 0.7456 (mmm) cc_final: 0.6765 (mtt) REVERT: D 444 ARG cc_start: 0.7935 (mmt-90) cc_final: 0.7642 (mmm-85) REVERT: D 556 HIS cc_start: 0.7670 (t70) cc_final: 0.7391 (t70) REVERT: D 580 LYS cc_start: 0.6598 (mmtt) cc_final: 0.5385 (tptt) REVERT: E 263 MET cc_start: 0.7631 (tpp) cc_final: 0.7400 (tpp) REVERT: E 264 ARG cc_start: 0.6597 (mmt-90) cc_final: 0.5984 (mmt-90) REVERT: E 394 MET cc_start: 0.8761 (tpt) cc_final: 0.8377 (tpt) REVERT: E 556 HIS cc_start: 0.8065 (t70) cc_final: 0.7838 (t70) REVERT: F 321 GLN cc_start: 0.7473 (mt0) cc_final: 0.7258 (mt0) REVERT: F 364 GLN cc_start: 0.7866 (mt0) cc_final: 0.7634 (mt0) REVERT: F 449 TYR cc_start: 0.8378 (m-80) cc_final: 0.8071 (m-10) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2975 time to fit residues: 134.0576 Evaluate side-chains 225 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN E 249 HIS ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17076 Z= 0.400 Angle : 0.673 9.136 23159 Z= 0.340 Chirality : 0.047 0.249 2709 Planarity : 0.006 0.062 3003 Dihedral : 9.968 83.868 2574 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.86 % Favored : 93.09 % Rotamer: Outliers : 1.37 % Allowed : 8.92 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2143 helix: 1.08 (0.18), residues: 844 sheet: -1.02 (0.30), residues: 313 loop : -1.31 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 414 PHE 0.019 0.002 PHE B 475 TYR 0.020 0.002 TYR E 318 ARG 0.007 0.001 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 248 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7649 (mptt) cc_final: 0.7142 (mmtp) REVERT: A 341 MET cc_start: 0.8256 (ttt) cc_final: 0.8035 (ttt) REVERT: B 257 MET cc_start: 0.6480 (ttt) cc_final: 0.6173 (ttt) REVERT: B 394 MET cc_start: 0.9022 (tpt) cc_final: 0.8743 (tpp) REVERT: B 575 MET cc_start: 0.7946 (mmm) cc_final: 0.7610 (mpp) REVERT: C 429 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8258 (t) REVERT: D 263 MET cc_start: 0.7888 (mmm) cc_final: 0.7157 (mtt) REVERT: D 580 LYS cc_start: 0.6553 (mmtt) cc_final: 0.5222 (tptt) REVERT: E 394 MET cc_start: 0.8829 (tpt) cc_final: 0.8474 (tpt) REVERT: F 263 MET cc_start: 0.7067 (mtt) cc_final: 0.6581 (mtt) REVERT: F 347 GLN cc_start: 0.7354 (tt0) cc_final: 0.6875 (tp40) REVERT: F 449 TYR cc_start: 0.8494 (m-80) cc_final: 0.8014 (m-10) outliers start: 25 outliers final: 19 residues processed: 261 average time/residue: 0.2994 time to fit residues: 118.5650 Evaluate side-chains 250 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 230 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 575 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 195 optimal weight: 0.0470 chunk 211 optimal weight: 3.9990 chunk 174 optimal weight: 0.0770 chunk 193 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN C 536 ASN ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17076 Z= 0.168 Angle : 0.547 8.877 23159 Z= 0.276 Chirality : 0.042 0.254 2709 Planarity : 0.004 0.049 3003 Dihedral : 9.301 86.728 2574 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.42 % Allowed : 11.32 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.19), residues: 2143 helix: 1.42 (0.18), residues: 846 sheet: -0.80 (0.30), residues: 319 loop : -1.20 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 414 PHE 0.008 0.001 PHE B 311 TYR 0.014 0.001 TYR B 244 ARG 0.006 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 250 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7606 (mptt) cc_final: 0.7082 (mmtp) REVERT: A 331 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6610 (mmp80) REVERT: A 341 MET cc_start: 0.8031 (ttt) cc_final: 0.7742 (ttt) REVERT: A 577 GLN cc_start: 0.6891 (tm-30) cc_final: 0.6613 (tm-30) REVERT: B 257 MET cc_start: 0.6225 (ttt) cc_final: 0.5970 (ttt) REVERT: B 394 MET cc_start: 0.8930 (tpt) cc_final: 0.8654 (tpp) REVERT: B 575 MET cc_start: 0.7872 (mmm) cc_final: 0.7541 (mpp) REVERT: C 429 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8079 (t) REVERT: C 444 ARG cc_start: 0.7401 (mpt-90) cc_final: 0.7118 (mmt-90) REVERT: D 255 MET cc_start: 0.7382 (mmm) cc_final: 0.7155 (mmm) REVERT: D 263 MET cc_start: 0.7731 (mmm) cc_final: 0.7040 (mtt) REVERT: D 580 LYS cc_start: 0.6500 (mmtt) cc_final: 0.5184 (tptt) REVERT: E 394 MET cc_start: 0.8656 (tpt) cc_final: 0.8307 (tpt) REVERT: F 347 GLN cc_start: 0.7454 (tt0) cc_final: 0.6802 (tp40) outliers start: 26 outliers final: 20 residues processed: 268 average time/residue: 0.2873 time to fit residues: 117.8930 Evaluate side-chains 257 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 235 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 374 ASN Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 575 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 207 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17076 Z= 0.326 Angle : 0.609 8.284 23159 Z= 0.307 Chirality : 0.045 0.245 2709 Planarity : 0.005 0.053 3003 Dihedral : 9.248 86.136 2574 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.49 % Favored : 93.47 % Rotamer: Outliers : 2.13 % Allowed : 13.79 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 2143 helix: 1.21 (0.18), residues: 846 sheet: -0.96 (0.29), residues: 326 loop : -1.27 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 414 PHE 0.015 0.002 PHE B 475 TYR 0.018 0.002 TYR B 244 ARG 0.004 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 1.960 Fit side-chains revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7630 (mptt) cc_final: 0.7111 (mmtp) REVERT: A 341 MET cc_start: 0.8063 (ttt) cc_final: 0.7857 (ttt) REVERT: A 509 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6358 (mt-10) REVERT: B 257 MET cc_start: 0.6359 (ttt) cc_final: 0.6052 (ttt) REVERT: B 321 GLN cc_start: 0.6740 (mp10) cc_final: 0.6515 (mp10) REVERT: B 394 MET cc_start: 0.9043 (tpt) cc_final: 0.8777 (tpp) REVERT: B 560 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7380 (mmm-85) REVERT: B 575 MET cc_start: 0.7894 (mmm) cc_final: 0.7588 (mpp) REVERT: C 429 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8060 (t) REVERT: D 263 MET cc_start: 0.7860 (mmm) cc_final: 0.7306 (mtt) REVERT: D 580 LYS cc_start: 0.6636 (mmtt) cc_final: 0.5160 (tptt) REVERT: E 374 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8531 (p0) REVERT: F 347 GLN cc_start: 0.7582 (tt0) cc_final: 0.7029 (tp40) REVERT: F 364 GLN cc_start: 0.7943 (mt0) cc_final: 0.7728 (mt0) outliers start: 39 outliers final: 28 residues processed: 270 average time/residue: 0.2728 time to fit residues: 111.4880 Evaluate side-chains 262 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 374 ASN Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 374 ASN Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 575 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 0.6980 chunk 117 optimal weight: 0.0060 chunk 3 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.0050 chunk 186 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.9414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17076 Z= 0.208 Angle : 0.563 8.637 23159 Z= 0.284 Chirality : 0.043 0.241 2709 Planarity : 0.005 0.050 3003 Dihedral : 8.898 85.850 2574 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.46 % Allowed : 14.33 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % 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: -0.25 (0.19), residues: 2143 helix: 1.34 (0.18), residues: 846 sheet: -0.94 (0.29), residues: 324 loop : -1.25 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 414 PHE 0.012 0.001 PHE B 510 TYR 0.015 0.001 TYR E 318 ARG 0.004 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 247 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7638 (mptt) cc_final: 0.7115 (mmtp) REVERT: A 341 MET cc_start: 0.7990 (ttt) cc_final: 0.7528 (ttp) REVERT: B 257 MET cc_start: 0.6289 (ttt) cc_final: 0.6061 (ttt) REVERT: B 321 GLN cc_start: 0.6842 (mp10) cc_final: 0.6634 (mp10) REVERT: B 394 MET cc_start: 0.8961 (tpt) cc_final: 0.8697 (tpp) REVERT: B 560 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7363 (mmm-85) REVERT: B 575 MET cc_start: 0.7834 (mmm) cc_final: 0.7546 (mpp) REVERT: C 429 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8007 (t) REVERT: D 255 MET cc_start: 0.7414 (mmm) cc_final: 0.7176 (mmm) REVERT: D 263 MET cc_start: 0.7828 (mmm) cc_final: 0.7278 (mtt) REVERT: D 294 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6937 (tt) REVERT: D 329 THR cc_start: 0.9035 (m) cc_final: 0.8582 (p) REVERT: D 580 LYS cc_start: 0.6422 (mmtt) cc_final: 0.5100 (tptt) REVERT: E 374 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8345 (p0) REVERT: F 347 GLN cc_start: 0.7547 (tt0) cc_final: 0.7038 (tp40) REVERT: F 364 GLN cc_start: 0.7938 (mt0) cc_final: 0.7705 (mt0) outliers start: 45 outliers final: 34 residues processed: 281 average time/residue: 0.2629 time to fit residues: 111.4238 Evaluate side-chains 276 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 239 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 374 ASN Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 374 ASN Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 575 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 ASN ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 17076 Z= 0.494 Angle : 0.713 8.987 23159 Z= 0.361 Chirality : 0.049 0.241 2709 Planarity : 0.006 0.061 3003 Dihedral : 9.267 86.790 2574 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.33 % Favored : 92.63 % Rotamer: Outliers : 3.23 % Allowed : 15.81 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2143 helix: 0.72 (0.17), residues: 844 sheet: -1.16 (0.30), residues: 323 loop : -1.46 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 414 PHE 0.019 0.002 PHE B 475 TYR 0.022 0.002 TYR E 318 ARG 0.008 0.001 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 249 time to evaluate : 2.136 Fit side-chains REVERT: A 260 LYS cc_start: 0.7647 (mptt) cc_final: 0.7137 (mmtp) REVERT: A 341 MET cc_start: 0.8116 (ttt) cc_final: 0.7635 (ttp) REVERT: B 257 MET cc_start: 0.6744 (ttt) cc_final: 0.6504 (ttt) REVERT: B 321 GLN cc_start: 0.7013 (mp10) cc_final: 0.6785 (mp10) REVERT: B 394 MET cc_start: 0.9004 (tpt) cc_final: 0.8726 (tpp) REVERT: B 575 MET cc_start: 0.7947 (mmm) cc_final: 0.7528 (mpp) REVERT: C 429 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8010 (t) REVERT: C 447 ARG cc_start: 0.8196 (mtm110) cc_final: 0.7870 (mtp180) REVERT: D 294 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7216 (tt) REVERT: D 329 THR cc_start: 0.8993 (m) cc_final: 0.8555 (p) REVERT: E 374 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8414 (p0) REVERT: F 347 GLN cc_start: 0.7624 (tt0) cc_final: 0.7050 (tp40) REVERT: F 489 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8157 (t) outliers start: 59 outliers final: 46 residues processed: 291 average time/residue: 0.2902 time to fit residues: 125.9332 Evaluate side-chains 283 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 233 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 441 SER Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 374 ASN Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 554 ILE Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 236 TYR Chi-restraints excluded: chain F residue 374 ASN Chi-restraints excluded: chain F residue 377 CYS Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 151 optimal weight: 0.0870 chunk 117 optimal weight: 0.5980 chunk 175 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17076 Z= 0.185 Angle : 0.575 9.136 23159 Z= 0.289 Chirality : 0.043 0.252 2709 Planarity : 0.005 0.050 3003 Dihedral : 8.687 89.811 2574 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.02 % Allowed : 17.51 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % 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: -0.33 (0.19), residues: 2143 helix: 1.26 (0.18), residues: 845 sheet: -0.99 (0.30), residues: 322 loop : -1.27 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 414 PHE 0.010 0.001 PHE F 407 TYR 0.019 0.001 TYR E 318 ARG 0.004 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 248 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7611 (mptt) cc_final: 0.7073 (mmtp) REVERT: A 341 MET cc_start: 0.7727 (ttt) cc_final: 0.7311 (ttp) REVERT: A 509 GLU cc_start: 0.6547 (mt-10) cc_final: 0.6185 (mt-10) REVERT: B 257 MET cc_start: 0.6431 (ttt) cc_final: 0.6215 (ttt) REVERT: B 394 MET cc_start: 0.8946 (tpt) cc_final: 0.8648 (tpp) REVERT: B 575 MET cc_start: 0.7900 (mmm) cc_final: 0.7556 (mpp) REVERT: C 429 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.7957 (t) REVERT: C 447 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7647 (mtp180) REVERT: D 294 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6445 (tt) REVERT: D 329 THR cc_start: 0.8945 (m) cc_final: 0.8602 (p) REVERT: D 580 LYS cc_start: 0.6391 (mmtt) cc_final: 0.5041 (tptt) REVERT: E 230 LEU cc_start: 0.7401 (tt) cc_final: 0.7156 (tt) REVERT: E 374 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8318 (p0) REVERT: E 521 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: F 347 GLN cc_start: 0.7452 (tt0) cc_final: 0.7012 (tp40) REVERT: F 364 GLN cc_start: 0.7935 (mt0) cc_final: 0.7692 (mt0) outliers start: 37 outliers final: 28 residues processed: 276 average time/residue: 0.2940 time to fit residues: 120.7165 Evaluate side-chains 271 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 239 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 374 ASN Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 566 ASP Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 544 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 162 optimal weight: 0.0370 chunk 188 optimal weight: 0.5980 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN A 556 HIS ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 ASN ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17076 Z= 0.208 Angle : 0.573 8.973 23159 Z= 0.287 Chirality : 0.043 0.243 2709 Planarity : 0.005 0.051 3003 Dihedral : 8.543 89.220 2574 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.30 % Allowed : 17.83 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % 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: -0.23 (0.19), residues: 2143 helix: 1.35 (0.18), residues: 844 sheet: -0.93 (0.30), residues: 324 loop : -1.23 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 414 PHE 0.009 0.001 PHE B 475 TYR 0.019 0.001 TYR C 236 ARG 0.004 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 248 time to evaluate : 1.977 Fit side-chains revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7613 (mptt) cc_final: 0.7079 (mmtp) REVERT: A 341 MET cc_start: 0.7743 (ttt) cc_final: 0.7335 (ttp) REVERT: B 257 MET cc_start: 0.6186 (ttt) cc_final: 0.5949 (ttt) REVERT: B 394 MET cc_start: 0.8950 (tpt) cc_final: 0.8684 (tpp) REVERT: B 575 MET cc_start: 0.7898 (mmm) cc_final: 0.7554 (mpp) REVERT: C 429 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.7944 (t) REVERT: C 447 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7718 (mtp180) REVERT: D 329 THR cc_start: 0.8836 (m) cc_final: 0.8532 (p) REVERT: D 580 LYS cc_start: 0.6429 (mmtt) cc_final: 0.5059 (tptt) REVERT: E 230 LEU cc_start: 0.7428 (tt) cc_final: 0.7180 (tt) REVERT: E 374 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8337 (p0) REVERT: E 386 GLU cc_start: 0.6971 (tp30) cc_final: 0.6770 (tp30) REVERT: E 521 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: F 347 GLN cc_start: 0.7505 (tt0) cc_final: 0.6996 (tp40) REVERT: F 364 GLN cc_start: 0.7957 (mt0) cc_final: 0.7727 (mt0) REVERT: F 489 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7941 (t) outliers start: 42 outliers final: 34 residues processed: 281 average time/residue: 0.2895 time to fit residues: 121.3124 Evaluate side-chains 281 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 243 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 374 ASN Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 566 ASP Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 374 ASN Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 174 optimal weight: 0.1980 chunk 182 optimal weight: 0.7980 chunk 192 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 515 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17076 Z= 0.170 Angle : 0.553 9.109 23159 Z= 0.277 Chirality : 0.042 0.244 2709 Planarity : 0.004 0.049 3003 Dihedral : 8.229 88.327 2574 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.02 % Allowed : 18.27 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % 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: -0.09 (0.19), residues: 2143 helix: 1.50 (0.18), residues: 845 sheet: -1.01 (0.29), residues: 343 loop : -1.10 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HIS E 414 PHE 0.008 0.001 PHE F 407 TYR 0.016 0.001 TYR C 252 ARG 0.004 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7617 (mptt) cc_final: 0.7084 (mmtp) REVERT: A 341 MET cc_start: 0.7539 (ttt) cc_final: 0.7130 (ttp) REVERT: A 431 GLN cc_start: 0.7788 (tp40) cc_final: 0.7579 (tp-100) REVERT: B 257 MET cc_start: 0.6234 (ttt) cc_final: 0.6018 (ttt) REVERT: B 394 MET cc_start: 0.8948 (tpt) cc_final: 0.8670 (tpp) REVERT: B 575 MET cc_start: 0.7893 (mmm) cc_final: 0.7586 (mpp) REVERT: C 429 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.7878 (t) REVERT: D 329 THR cc_start: 0.8815 (m) cc_final: 0.8534 (p) REVERT: D 580 LYS cc_start: 0.6340 (mmtt) cc_final: 0.5026 (tptt) REVERT: E 232 VAL cc_start: 0.6336 (OUTLIER) cc_final: 0.6088 (t) REVERT: E 260 LYS cc_start: 0.7554 (mtmt) cc_final: 0.7328 (mtmt) REVERT: E 374 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8330 (p0) REVERT: E 386 GLU cc_start: 0.6909 (tp30) cc_final: 0.6692 (tp30) REVERT: E 394 MET cc_start: 0.8427 (tpt) cc_final: 0.8106 (tpt) REVERT: E 521 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: F 347 GLN cc_start: 0.7447 (tt0) cc_final: 0.6953 (tp40) REVERT: F 364 GLN cc_start: 0.8091 (mt0) cc_final: 0.7852 (mt0) REVERT: F 489 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7868 (t) REVERT: F 508 GLU cc_start: 0.6194 (mt-10) cc_final: 0.5990 (mt-10) outliers start: 37 outliers final: 30 residues processed: 275 average time/residue: 0.2910 time to fit residues: 119.8590 Evaluate side-chains 276 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 241 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 374 ASN Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 566 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 374 ASN Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 214 optimal weight: 8.9990 chunk 197 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.210 17076 Z= 0.219 Angle : 0.744 59.194 23159 Z= 0.411 Chirality : 0.043 0.242 2709 Planarity : 0.005 0.049 3003 Dihedral : 8.242 88.325 2574 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.31 % Rotamer: Outliers : 1.97 % Allowed : 18.44 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % 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: -0.09 (0.19), residues: 2143 helix: 1.50 (0.18), residues: 845 sheet: -1.00 (0.29), residues: 343 loop : -1.10 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 414 PHE 0.008 0.001 PHE F 407 TYR 0.015 0.001 TYR E 318 ARG 0.007 0.000 ARG E 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 239 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7616 (mptt) cc_final: 0.7084 (mmtp) REVERT: A 341 MET cc_start: 0.7545 (ttt) cc_final: 0.7138 (ttp) REVERT: A 431 GLN cc_start: 0.7788 (tp40) cc_final: 0.7577 (tp-100) REVERT: B 257 MET cc_start: 0.6236 (ttt) cc_final: 0.6023 (ttt) REVERT: B 394 MET cc_start: 0.8951 (tpt) cc_final: 0.8674 (tpp) REVERT: B 575 MET cc_start: 0.7899 (mmm) cc_final: 0.7589 (mpp) REVERT: C 429 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.7884 (t) REVERT: D 329 THR cc_start: 0.8818 (m) cc_final: 0.8529 (p) REVERT: D 580 LYS cc_start: 0.6347 (mmtt) cc_final: 0.5029 (tptt) REVERT: E 232 VAL cc_start: 0.6300 (OUTLIER) cc_final: 0.6099 (t) REVERT: E 260 LYS cc_start: 0.7451 (mtmt) cc_final: 0.7199 (mtmt) REVERT: E 374 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8359 (p0) REVERT: E 521 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: F 347 GLN cc_start: 0.7448 (tt0) cc_final: 0.6933 (tp40) REVERT: F 364 GLN cc_start: 0.8090 (mt0) cc_final: 0.7852 (mt0) REVERT: F 489 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7870 (t) outliers start: 36 outliers final: 30 residues processed: 268 average time/residue: 0.2959 time to fit residues: 118.8926 Evaluate side-chains 274 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 239 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 374 ASN Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 566 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 374 ASN Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 149 optimal weight: 0.4980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.163932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132335 restraints weight = 21393.037| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.17 r_work: 0.3406 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.210 17076 Z= 0.219 Angle : 0.744 59.194 23159 Z= 0.411 Chirality : 0.043 0.242 2709 Planarity : 0.005 0.049 3003 Dihedral : 8.242 88.325 2574 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.31 % Rotamer: Outliers : 1.91 % Allowed : 18.44 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % 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: -0.09 (0.19), residues: 2143 helix: 1.50 (0.18), residues: 845 sheet: -1.00 (0.29), residues: 343 loop : -1.10 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 414 PHE 0.008 0.001 PHE F 407 TYR 0.015 0.001 TYR E 318 ARG 0.007 0.000 ARG E 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3608.19 seconds wall clock time: 65 minutes 34.24 seconds (3934.24 seconds total)