Starting phenix.real_space_refine on Sat Feb 17 03:01:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqr_25391/02_2024/7sqr_25391.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqr_25391/02_2024/7sqr_25391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqr_25391/02_2024/7sqr_25391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqr_25391/02_2024/7sqr_25391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqr_25391/02_2024/7sqr_25391.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqr_25391/02_2024/7sqr_25391.pdb" } resolution = 3.4 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 10772 2.51 5 N 3128 2.21 5 O 3316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "C TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 432": "OD1" <-> "OD2" Residue "D ASP 540": "OD1" <-> "OD2" Residue "F TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 432": "OD1" <-> "OD2" Residue "G ASP 540": "OD1" <-> "OD2" Residue "I TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 79": "OE1" <-> "OE2" Residue "J TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 432": "OD1" <-> "OD2" Residue "J ASP 540": "OD1" <-> "OD2" Residue "L TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17272 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4072 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 23, 'TRANS': 498} Chain breaks: 1 Chain: "B" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 163 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 83 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "D" Number of atoms: 4072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4072 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 23, 'TRANS': 498} Chain breaks: 1 Chain: "E" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 163 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 83 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "G" Number of atoms: 4072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4072 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 23, 'TRANS': 498} Chain breaks: 1 Chain: "H" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 163 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 83 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "J" Number of atoms: 4072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4072 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 23, 'TRANS': 498} Chain breaks: 1 Chain: "K" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 163 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "L" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 83 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Time building chain proxies: 9.35, per 1000 atoms: 0.54 Number of scatterers: 17272 At special positions: 0 Unit cell: (123.091, 123.091, 86.5695, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 3316 8.00 N 3128 7.00 C 10772 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: 7.25 Conformation dependent library (CDL) restraints added in 3.2 seconds 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4080 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 20 sheets defined 41.6% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.879A pdb=" N SER A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.814A pdb=" N VAL A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 162' Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP A 201 " --> pdb=" O VAL A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 202 through 226 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 360 through 367 Proline residue: A 365 - end of helix Processing helix chain 'A' and resid 379 through 386 removed outlier: 4.033A pdb=" N MET A 385 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.811A pdb=" N LEU A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG A 465 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.847A pdb=" N GLN A 472 " --> pdb=" O HIS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 544 Processing helix chain 'A' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 601 removed outlier: 3.502A pdb=" N ASN B 600 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 601 " --> pdb=" O ILE B 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 597 through 601' Processing helix chain 'D' and resid 49 through 55 Processing helix chain 'D' and resid 67 through 84 Processing helix chain 'D' and resid 157 through 162 removed outlier: 3.814A pdb=" N VAL D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 157 through 162' Processing helix chain 'D' and resid 163 through 179 Processing helix chain 'D' and resid 198 through 201 removed outlier: 3.716A pdb=" N ASP D 201 " --> pdb=" O VAL D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 202 through 226 Processing helix chain 'D' and resid 231 through 236 removed outlier: 3.991A pdb=" N LYS D 236 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 358 Processing helix chain 'D' and resid 360 through 367 Proline residue: D 365 - end of helix Processing helix chain 'D' and resid 379 through 386 removed outlier: 4.033A pdb=" N MET D 385 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU D 434 " --> pdb=" O GLN D 430 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 458 Processing helix chain 'D' and resid 462 through 466 removed outlier: 3.667A pdb=" N ARG D 465 " --> pdb=" O GLY D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 472 removed outlier: 3.847A pdb=" N GLN D 472 " --> pdb=" O HIS D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 499 No H-bonds generated for 'chain 'D' and resid 497 through 499' Processing helix chain 'D' and resid 500 through 508 Processing helix chain 'D' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN D 522 " --> pdb=" O PHE D 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 523 " --> pdb=" O TYR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 544 Processing helix chain 'D' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE D 564 " --> pdb=" O ASN D 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 601 removed outlier: 3.502A pdb=" N ASN E 600 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN E 601 " --> pdb=" O ILE E 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 597 through 601' Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 67 through 84 Processing helix chain 'G' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL G 161 " --> pdb=" O ASP G 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE G 162 " --> pdb=" O VAL G 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 157 through 162' Processing helix chain 'G' and resid 163 through 179 Processing helix chain 'G' and resid 198 through 201 removed outlier: 3.716A pdb=" N ASP G 201 " --> pdb=" O VAL G 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 201' Processing helix chain 'G' and resid 202 through 226 Processing helix chain 'G' and resid 231 through 236 removed outlier: 3.991A pdb=" N LYS G 236 " --> pdb=" O ALA G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR G 346 " --> pdb=" O THR G 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP G 347 " --> pdb=" O PRO G 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE G 348 " --> pdb=" O GLU G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 358 Processing helix chain 'G' and resid 360 through 367 Proline residue: G 365 - end of helix Processing helix chain 'G' and resid 379 through 386 removed outlier: 4.033A pdb=" N MET G 385 " --> pdb=" O LEU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY G 405 " --> pdb=" O ASP G 401 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN G 406 " --> pdb=" O ALA G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU G 434 " --> pdb=" O GLN G 430 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY G 440 " --> pdb=" O LEU G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 458 Processing helix chain 'G' and resid 462 through 466 removed outlier: 3.667A pdb=" N ARG G 465 " --> pdb=" O GLY G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 468 through 472 removed outlier: 3.847A pdb=" N GLN G 472 " --> pdb=" O HIS G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 499 No H-bonds generated for 'chain 'G' and resid 497 through 499' Processing helix chain 'G' and resid 500 through 508 Processing helix chain 'G' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE G 515 " --> pdb=" O ASN G 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN G 522 " --> pdb=" O PHE G 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU G 523 " --> pdb=" O TYR G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 528 through 544 Processing helix chain 'G' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE G 564 " --> pdb=" O ASN G 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU G 565 " --> pdb=" O ALA G 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 597 through 601 removed outlier: 3.502A pdb=" N ASN H 600 " --> pdb=" O VAL H 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN H 601 " --> pdb=" O ILE H 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 597 through 601' Processing helix chain 'J' and resid 49 through 55 Processing helix chain 'J' and resid 67 through 84 Processing helix chain 'J' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL J 161 " --> pdb=" O ASP J 157 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE J 162 " --> pdb=" O VAL J 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 157 through 162' Processing helix chain 'J' and resid 163 through 179 Processing helix chain 'J' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP J 201 " --> pdb=" O VAL J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 198 through 201' Processing helix chain 'J' and resid 202 through 226 Processing helix chain 'J' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS J 236 " --> pdb=" O ALA J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR J 346 " --> pdb=" O THR J 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP J 347 " --> pdb=" O PRO J 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE J 348 " --> pdb=" O GLU J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 358 Processing helix chain 'J' and resid 360 through 367 Proline residue: J 365 - end of helix Processing helix chain 'J' and resid 379 through 386 removed outlier: 4.034A pdb=" N MET J 385 " --> pdb=" O LEU J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY J 405 " --> pdb=" O ASP J 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN J 406 " --> pdb=" O ALA J 402 " (cutoff:3.500A) Processing helix chain 'J' and resid 428 through 440 removed outlier: 3.811A pdb=" N LEU J 434 " --> pdb=" O GLN J 430 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY J 440 " --> pdb=" O LEU J 436 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 458 Processing helix chain 'J' and resid 462 through 466 removed outlier: 3.667A pdb=" N ARG J 465 " --> pdb=" O GLY J 462 " (cutoff:3.500A) Processing helix chain 'J' and resid 468 through 472 removed outlier: 3.847A pdb=" N GLN J 472 " --> pdb=" O HIS J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 499 No H-bonds generated for 'chain 'J' and resid 497 through 499' Processing helix chain 'J' and resid 500 through 508 Processing helix chain 'J' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE J 515 " --> pdb=" O ASN J 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN J 522 " --> pdb=" O PHE J 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU J 523 " --> pdb=" O TYR J 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 528 through 544 Processing helix chain 'J' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE J 564 " --> pdb=" O ASN J 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU J 565 " --> pdb=" O ALA J 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 597 through 601 removed outlier: 3.502A pdb=" N ASN K 600 " --> pdb=" O VAL K 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN K 601 " --> pdb=" O ILE K 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 597 through 601' Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 145 removed outlier: 3.511A pdb=" N ILE A 143 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU A 476 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR A 559 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR A 478 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS A 557 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN A 480 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU A 555 " --> pdb=" O GLN A 480 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A 482 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS A 553 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 484 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 559 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE A 418 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP A 331 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA A 294 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL A 332 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN A 292 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 291 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 270 " --> pdb=" O ASN A 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 243 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 96 Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 96 Processing sheet with id=AA8, first strand: chain 'D' and resid 140 through 145 removed outlier: 3.511A pdb=" N ILE D 143 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 493 through 495 removed outlier: 6.000A pdb=" N GLU D 476 " --> pdb=" O TYR D 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR D 559 " --> pdb=" O GLU D 476 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR D 478 " --> pdb=" O CYS D 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS D 557 " --> pdb=" O THR D 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN D 480 " --> pdb=" O GLU D 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU D 555 " --> pdb=" O GLN D 480 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 482 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS D 553 " --> pdb=" O ILE D 482 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU D 484 " --> pdb=" O THR D 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D 559 " --> pdb=" O PHE D 418 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE D 418 " --> pdb=" O TYR D 559 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP D 331 " --> pdb=" O ASP D 421 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA D 294 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL D 332 " --> pdb=" O GLN D 292 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN D 292 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN D 291 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR D 270 " --> pdb=" O ASN D 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU D 243 " --> pdb=" O THR D 579 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 254 through 255 Processing sheet with id=AB2, first strand: chain 'G' and resid 92 through 96 Processing sheet with id=AB3, first strand: chain 'G' and resid 92 through 96 Processing sheet with id=AB4, first strand: chain 'G' and resid 140 through 145 removed outlier: 3.510A pdb=" N ILE G 143 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 493 through 495 removed outlier: 6.000A pdb=" N GLU G 476 " --> pdb=" O TYR G 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR G 559 " --> pdb=" O GLU G 476 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR G 478 " --> pdb=" O CYS G 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS G 557 " --> pdb=" O THR G 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN G 480 " --> pdb=" O GLU G 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU G 555 " --> pdb=" O GLN G 480 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE G 482 " --> pdb=" O LYS G 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS G 553 " --> pdb=" O ILE G 482 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU G 484 " --> pdb=" O THR G 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR G 559 " --> pdb=" O PHE G 418 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE G 418 " --> pdb=" O TYR G 559 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP G 331 " --> pdb=" O ASP G 421 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA G 294 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL G 332 " --> pdb=" O GLN G 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN G 292 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN G 291 " --> pdb=" O THR G 270 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR G 270 " --> pdb=" O ASN G 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU G 243 " --> pdb=" O THR G 579 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 254 through 255 Processing sheet with id=AB7, first strand: chain 'J' and resid 92 through 96 Processing sheet with id=AB8, first strand: chain 'J' and resid 92 through 96 Processing sheet with id=AB9, first strand: chain 'J' and resid 140 through 145 removed outlier: 3.510A pdb=" N ILE J 143 " --> pdb=" O ASP J 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU J 476 " --> pdb=" O TYR J 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR J 559 " --> pdb=" O GLU J 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR J 478 " --> pdb=" O CYS J 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS J 557 " --> pdb=" O THR J 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN J 480 " --> pdb=" O GLU J 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU J 555 " --> pdb=" O GLN J 480 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE J 482 " --> pdb=" O LYS J 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS J 553 " --> pdb=" O ILE J 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU J 484 " --> pdb=" O THR J 551 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR J 559 " --> pdb=" O PHE J 418 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE J 418 " --> pdb=" O TYR J 559 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP J 331 " --> pdb=" O ASP J 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA J 294 " --> pdb=" O THR J 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL J 332 " --> pdb=" O GLN J 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN J 292 " --> pdb=" O VAL J 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN J 291 " --> pdb=" O THR J 270 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR J 270 " --> pdb=" O ASN J 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU J 243 " --> pdb=" O THR J 579 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 254 through 255 764 hydrogen bonds defined for protein. 1968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.37 Time building geometry restraints manager: 7.74 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: 5998 1.34 - 1.46: 2144 1.46 - 1.57: 9342 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 17588 Sorted by residual: bond pdb=" CG LEU G 527 " pdb=" CD2 LEU G 527 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.95e+00 bond pdb=" CG LEU D 527 " pdb=" CD2 LEU D 527 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.95e+00 bond pdb=" CG LEU J 527 " pdb=" CD2 LEU J 527 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.89e+00 bond pdb=" CG LEU A 527 " pdb=" CD2 LEU A 527 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.89e+00 bond pdb=" CA ASN A 511 " pdb=" CB ASN A 511 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.27e-02 6.20e+03 1.94e+00 ... (remaining 17583 not shown) Histogram of bond angle deviations from ideal: 96.18 - 103.75: 235 103.75 - 111.33: 7082 111.33 - 118.90: 6862 118.90 - 126.48: 9437 126.48 - 134.05: 228 Bond angle restraints: 23844 Sorted by residual: angle pdb=" CA GLN A 278 " pdb=" C GLN A 278 " pdb=" N GLN A 279 " ideal model delta sigma weight residual 114.90 119.72 -4.82 1.37e+00 5.33e-01 1.24e+01 angle pdb=" CA GLN D 278 " pdb=" C GLN D 278 " pdb=" N GLN D 279 " ideal model delta sigma weight residual 114.90 119.71 -4.81 1.37e+00 5.33e-01 1.24e+01 angle pdb=" CA GLN J 278 " pdb=" C GLN J 278 " pdb=" N GLN J 279 " ideal model delta sigma weight residual 114.90 119.70 -4.80 1.37e+00 5.33e-01 1.23e+01 angle pdb=" CA GLN G 278 " pdb=" C GLN G 278 " pdb=" N GLN G 279 " ideal model delta sigma weight residual 114.90 119.69 -4.79 1.37e+00 5.33e-01 1.22e+01 angle pdb=" CA GLN A 411 " pdb=" CB GLN A 411 " pdb=" CG GLN A 411 " ideal model delta sigma weight residual 114.10 120.25 -6.15 2.00e+00 2.50e-01 9.47e+00 ... (remaining 23839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9606 17.92 - 35.83: 834 35.83 - 53.75: 76 53.75 - 71.67: 24 71.67 - 89.59: 28 Dihedral angle restraints: 10568 sinusoidal: 4240 harmonic: 6328 Sorted by residual: dihedral pdb=" CA ARG J 76 " pdb=" CB ARG J 76 " pdb=" CG ARG J 76 " pdb=" CD ARG J 76 " ideal model delta sinusoidal sigma weight residual -60.00 -111.88 51.88 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" CA ARG G 76 " pdb=" CB ARG G 76 " pdb=" CG ARG G 76 " pdb=" CD ARG G 76 " ideal model delta sinusoidal sigma weight residual -60.00 -111.88 51.88 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" CA ARG A 76 " pdb=" CB ARG A 76 " pdb=" CG ARG A 76 " pdb=" CD ARG A 76 " ideal model delta sinusoidal sigma weight residual -60.00 -111.86 51.86 3 1.50e+01 4.44e-03 9.06e+00 ... (remaining 10565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1673 0.033 - 0.065: 639 0.065 - 0.098: 149 0.098 - 0.131: 140 0.131 - 0.163: 23 Chirality restraints: 2624 Sorted by residual: chirality pdb=" CA MET B 602 " pdb=" N MET B 602 " pdb=" C MET B 602 " pdb=" CB MET B 602 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA MET E 602 " pdb=" N MET E 602 " pdb=" C MET E 602 " pdb=" CB MET E 602 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA MET K 602 " pdb=" N MET K 602 " pdb=" C MET K 602 " pdb=" CB MET K 602 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 2621 not shown) Planarity restraints: 3212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 321 " 0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO D 322 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 321 " 0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO G 322 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO G 322 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO G 322 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 321 " 0.064 5.00e-02 4.00e+02 9.57e-02 1.47e+01 pdb=" N PRO A 322 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.053 5.00e-02 4.00e+02 ... (remaining 3209 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 817 2.73 - 3.27: 16561 3.27 - 3.81: 26493 3.81 - 4.36: 29713 4.36 - 4.90: 53526 Nonbonded interactions: 127110 Sorted by model distance: nonbonded pdb=" OE2 GLU G 514 " pdb=" OH TYR G 543 " model vdw 2.185 2.440 nonbonded pdb=" OE2 GLU D 514 " pdb=" OH TYR D 543 " model vdw 2.185 2.440 nonbonded pdb=" OE2 GLU J 514 " pdb=" OH TYR J 543 " model vdw 2.185 2.440 nonbonded pdb=" OE2 GLU A 514 " pdb=" OH TYR A 543 " model vdw 2.185 2.440 nonbonded pdb=" OD2 ASP A 540 " pdb=" OH TYR A 550 " model vdw 2.253 2.440 ... (remaining 127105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.850 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 47.120 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.003 0.057 17588 Z= 0.173 Angle : 0.632 7.812 23844 Z= 0.349 Chirality : 0.044 0.163 2624 Planarity : 0.005 0.096 3212 Dihedral : 13.785 89.586 6488 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 2184 helix: 2.13 (0.20), residues: 744 sheet: 0.46 (0.24), residues: 524 loop : -0.31 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 516 HIS 0.001 0.000 HIS G 101 PHE 0.016 0.001 PHE D 466 TYR 0.009 0.001 TYR D 539 ARG 0.008 0.000 ARG G 541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.929 Fit side-chains REVERT: A 218 ASP cc_start: 0.8155 (m-30) cc_final: 0.7638 (m-30) REVERT: A 376 MET cc_start: 0.9021 (tpp) cc_final: 0.8648 (tpp) REVERT: B 591 ARG cc_start: 0.7830 (ptm160) cc_final: 0.7581 (pmt170) REVERT: B 600 ASN cc_start: 0.8866 (m110) cc_final: 0.8634 (m110) REVERT: D 218 ASP cc_start: 0.8157 (m-30) cc_final: 0.7641 (m-30) REVERT: D 376 MET cc_start: 0.9011 (tpp) cc_final: 0.8643 (tpp) REVERT: E 591 ARG cc_start: 0.7830 (ptm160) cc_final: 0.7582 (pmt170) REVERT: E 600 ASN cc_start: 0.8864 (m110) cc_final: 0.8633 (m110) REVERT: G 218 ASP cc_start: 0.8147 (m-30) cc_final: 0.7633 (m-30) REVERT: G 376 MET cc_start: 0.9015 (tpp) cc_final: 0.8646 (tpp) REVERT: H 591 ARG cc_start: 0.7825 (ptm160) cc_final: 0.7586 (pmt170) REVERT: H 600 ASN cc_start: 0.8869 (m110) cc_final: 0.8640 (m110) REVERT: J 218 ASP cc_start: 0.8153 (m-30) cc_final: 0.7635 (m-30) REVERT: J 376 MET cc_start: 0.9014 (tpp) cc_final: 0.8645 (tpp) REVERT: K 591 ARG cc_start: 0.7831 (ptm160) cc_final: 0.7584 (pmt170) REVERT: K 600 ASN cc_start: 0.8858 (m110) cc_final: 0.8629 (m110) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2647 time to fit residues: 47.8174 Evaluate side-chains 88 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 128 optimal weight: 0.0670 chunk 199 optimal weight: 6.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17588 Z= 0.167 Angle : 0.483 6.098 23844 Z= 0.249 Chirality : 0.041 0.156 2624 Planarity : 0.004 0.048 3212 Dihedral : 3.311 11.348 2388 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.31 % Allowed : 3.28 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.19), residues: 2184 helix: 2.14 (0.20), residues: 780 sheet: 0.18 (0.24), residues: 508 loop : -0.41 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 516 HIS 0.002 0.001 HIS G 101 PHE 0.011 0.001 PHE D 404 TYR 0.004 0.001 TYR G 284 ARG 0.002 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 2.100 Fit side-chains REVERT: A 527 LEU cc_start: 0.9339 (tt) cc_final: 0.9137 (tt) REVERT: B 591 ARG cc_start: 0.7851 (ptm160) cc_final: 0.7616 (pmt170) REVERT: E 591 ARG cc_start: 0.7850 (ptm160) cc_final: 0.7605 (pmt170) REVERT: G 527 LEU cc_start: 0.9324 (tt) cc_final: 0.9113 (tt) REVERT: H 591 ARG cc_start: 0.7846 (ptm160) cc_final: 0.7610 (pmt170) REVERT: J 527 LEU cc_start: 0.9321 (tt) cc_final: 0.9111 (tt) REVERT: K 591 ARG cc_start: 0.7854 (ptm160) cc_final: 0.7619 (pmt170) outliers start: 24 outliers final: 16 residues processed: 100 average time/residue: 0.2734 time to fit residues: 44.1408 Evaluate side-chains 95 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 557 CYS Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 557 CYS Chi-restraints excluded: chain K residue 596 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 601 ASN E 601 ASN H 601 ASN K 601 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17588 Z= 0.310 Angle : 0.552 6.580 23844 Z= 0.284 Chirality : 0.043 0.184 2624 Planarity : 0.004 0.045 3212 Dihedral : 3.822 16.840 2388 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.97 % Allowed : 5.73 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 2184 helix: 2.08 (0.20), residues: 752 sheet: -0.47 (0.22), residues: 520 loop : -0.45 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 105 HIS 0.004 0.001 HIS A 255 PHE 0.014 0.002 PHE D 515 TYR 0.010 0.002 TYR D 284 ARG 0.007 0.000 ARG D 532 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 90 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 591 ARG cc_start: 0.7992 (ptm160) cc_final: 0.7558 (pmt170) REVERT: E 591 ARG cc_start: 0.7989 (ptm160) cc_final: 0.7555 (pmt170) REVERT: H 591 ARG cc_start: 0.7985 (ptm160) cc_final: 0.7561 (pmt170) REVERT: K 591 ARG cc_start: 0.7991 (ptm160) cc_final: 0.7561 (pmt170) outliers start: 36 outliers final: 28 residues processed: 110 average time/residue: 0.3166 time to fit residues: 53.4002 Evaluate side-chains 112 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 595 ASN Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 557 CYS Chi-restraints excluded: chain H residue 595 ASN Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 557 CYS Chi-restraints excluded: chain K residue 595 ASN Chi-restraints excluded: chain K residue 596 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 95 optimal weight: 0.0040 chunk 134 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 overall best weight: 4.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 480 GLN G 480 GLN J 480 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17588 Z= 0.266 Angle : 0.511 7.087 23844 Z= 0.261 Chirality : 0.042 0.147 2624 Planarity : 0.003 0.044 3212 Dihedral : 3.702 14.260 2388 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.97 % Allowed : 7.59 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 2184 helix: 2.05 (0.20), residues: 748 sheet: -0.39 (0.23), residues: 500 loop : -0.50 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 105 HIS 0.002 0.001 HIS J 255 PHE 0.008 0.001 PHE D 515 TYR 0.008 0.001 TYR J 284 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8219 (tp) REVERT: A 408 MET cc_start: 0.8063 (mmt) cc_final: 0.7768 (mmp) REVERT: A 411 GLN cc_start: 0.6974 (tt0) cc_final: 0.6735 (tm-30) REVERT: B 591 ARG cc_start: 0.7992 (ptm160) cc_final: 0.7623 (pmt170) REVERT: D 407 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8225 (tp) REVERT: D 408 MET cc_start: 0.8077 (mmt) cc_final: 0.7782 (mmp) REVERT: D 411 GLN cc_start: 0.6956 (tt0) cc_final: 0.6752 (tm-30) REVERT: E 591 ARG cc_start: 0.7985 (ptm160) cc_final: 0.7621 (pmt170) REVERT: G 407 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8244 (tp) REVERT: G 408 MET cc_start: 0.8106 (mmt) cc_final: 0.7809 (mmp) REVERT: H 591 ARG cc_start: 0.7981 (ptm160) cc_final: 0.7626 (pmt170) REVERT: J 407 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8236 (tp) REVERT: J 408 MET cc_start: 0.8088 (mmt) cc_final: 0.7791 (mmp) REVERT: J 411 GLN cc_start: 0.6968 (tt0) cc_final: 0.6766 (tm-30) REVERT: K 591 ARG cc_start: 0.7991 (ptm160) cc_final: 0.7625 (pmt170) outliers start: 36 outliers final: 28 residues processed: 104 average time/residue: 0.3204 time to fit residues: 50.9413 Evaluate side-chains 119 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 87 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 595 ASN Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 557 CYS Chi-restraints excluded: chain H residue 595 ASN Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 557 CYS Chi-restraints excluded: chain K residue 595 ASN Chi-restraints excluded: chain K residue 596 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 190 optimal weight: 0.1980 chunk 53 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17588 Z= 0.136 Angle : 0.453 6.526 23844 Z= 0.226 Chirality : 0.041 0.134 2624 Planarity : 0.003 0.042 3212 Dihedral : 3.302 13.548 2388 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.86 % Allowed : 9.28 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 2184 helix: 2.29 (0.20), residues: 744 sheet: -0.26 (0.24), residues: 500 loop : -0.43 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 384 HIS 0.001 0.000 HIS G 255 PHE 0.009 0.001 PHE A 296 TYR 0.005 0.001 TYR G 166 ARG 0.001 0.000 ARG D 541 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 92 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 TYR cc_start: 0.7806 (t80) cc_final: 0.7447 (t80) REVERT: A 527 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8757 (tt) REVERT: B 591 ARG cc_start: 0.7963 (ptm160) cc_final: 0.7638 (pmt170) REVERT: D 519 TYR cc_start: 0.7761 (t80) cc_final: 0.7462 (t80) REVERT: E 591 ARG cc_start: 0.7960 (ptm160) cc_final: 0.7639 (pmt170) REVERT: G 519 TYR cc_start: 0.7803 (t80) cc_final: 0.7441 (t80) REVERT: G 527 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8760 (tt) REVERT: H 591 ARG cc_start: 0.7955 (ptm160) cc_final: 0.7641 (pmt170) REVERT: J 519 TYR cc_start: 0.7763 (t80) cc_final: 0.7454 (t80) REVERT: J 527 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8755 (tt) REVERT: J 580 MET cc_start: 0.8466 (pmm) cc_final: 0.7689 (pmm) REVERT: K 591 ARG cc_start: 0.7962 (ptm160) cc_final: 0.7641 (pmt170) outliers start: 34 outliers final: 24 residues processed: 114 average time/residue: 0.3113 time to fit residues: 54.2986 Evaluate side-chains 115 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 595 ASN Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 557 CYS Chi-restraints excluded: chain H residue 595 ASN Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 557 CYS Chi-restraints excluded: chain K residue 595 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 chunk 176 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17588 Z= 0.256 Angle : 0.498 6.793 23844 Z= 0.253 Chirality : 0.041 0.136 2624 Planarity : 0.003 0.040 3212 Dihedral : 3.555 13.777 2388 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.80 % Allowed : 9.99 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 2184 helix: 2.20 (0.20), residues: 748 sheet: -0.48 (0.23), residues: 520 loop : -0.54 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 105 HIS 0.002 0.001 HIS D 255 PHE 0.009 0.001 PHE J 167 TYR 0.008 0.001 TYR G 284 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 TYR cc_start: 0.7833 (t80) cc_final: 0.7446 (t80) REVERT: A 527 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8824 (tt) REVERT: A 580 MET cc_start: 0.8226 (pmm) cc_final: 0.7940 (pmm) REVERT: B 591 ARG cc_start: 0.7978 (ptm160) cc_final: 0.7593 (pmt170) REVERT: D 519 TYR cc_start: 0.7833 (t80) cc_final: 0.7449 (t80) REVERT: D 580 MET cc_start: 0.8219 (pmm) cc_final: 0.7936 (pmm) REVERT: E 591 ARG cc_start: 0.7980 (ptm160) cc_final: 0.7594 (pmt170) REVERT: G 519 TYR cc_start: 0.7831 (t80) cc_final: 0.7442 (t80) REVERT: G 527 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8822 (tt) REVERT: G 580 MET cc_start: 0.8217 (pmm) cc_final: 0.7929 (pmm) REVERT: H 591 ARG cc_start: 0.7971 (ptm160) cc_final: 0.7596 (pmt170) REVERT: J 519 TYR cc_start: 0.7833 (t80) cc_final: 0.7445 (t80) REVERT: J 527 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8820 (tt) REVERT: K 591 ARG cc_start: 0.7978 (ptm160) cc_final: 0.7595 (pmt170) outliers start: 33 outliers final: 26 residues processed: 111 average time/residue: 0.3200 time to fit residues: 54.4528 Evaluate side-chains 117 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 595 ASN Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 557 CYS Chi-restraints excluded: chain H residue 595 ASN Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 557 CYS Chi-restraints excluded: chain K residue 595 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 132 optimal weight: 0.0030 chunk 129 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17588 Z= 0.126 Angle : 0.456 7.202 23844 Z= 0.223 Chirality : 0.040 0.133 2624 Planarity : 0.003 0.039 3212 Dihedral : 3.233 12.330 2388 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.64 % Allowed : 10.97 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 2184 helix: 2.34 (0.20), residues: 744 sheet: -0.29 (0.24), residues: 500 loop : -0.44 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 384 HIS 0.001 0.001 HIS G 255 PHE 0.008 0.001 PHE D 296 TYR 0.005 0.001 TYR A 166 ARG 0.001 0.000 ARG J 541 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 96 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 TYR cc_start: 0.7753 (t80) cc_final: 0.7455 (t80) REVERT: A 527 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8744 (tt) REVERT: B 591 ARG cc_start: 0.7983 (ptm160) cc_final: 0.7643 (pmt170) REVERT: D 519 TYR cc_start: 0.7754 (t80) cc_final: 0.7457 (t80) REVERT: E 591 ARG cc_start: 0.7984 (ptm160) cc_final: 0.7644 (pmt170) REVERT: G 519 TYR cc_start: 0.7751 (t80) cc_final: 0.7450 (t80) REVERT: G 527 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8743 (tt) REVERT: H 591 ARG cc_start: 0.7974 (ptm160) cc_final: 0.7645 (pmt170) REVERT: J 519 TYR cc_start: 0.7754 (t80) cc_final: 0.7451 (t80) REVERT: J 527 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8740 (tt) REVERT: J 580 MET cc_start: 0.8382 (pmm) cc_final: 0.7738 (pmm) REVERT: K 591 ARG cc_start: 0.7982 (ptm160) cc_final: 0.7646 (pmt170) outliers start: 30 outliers final: 26 residues processed: 112 average time/residue: 0.3487 time to fit residues: 57.2283 Evaluate side-chains 119 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 595 ASN Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 557 CYS Chi-restraints excluded: chain H residue 595 ASN Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 557 CYS Chi-restraints excluded: chain K residue 595 ASN Chi-restraints excluded: chain K residue 596 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.1980 chunk 84 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17588 Z= 0.199 Angle : 0.475 8.876 23844 Z= 0.235 Chirality : 0.040 0.135 2624 Planarity : 0.003 0.038 3212 Dihedral : 3.351 14.844 2388 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.07 % Allowed : 11.24 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.19), residues: 2184 helix: 2.34 (0.20), residues: 744 sheet: -0.44 (0.23), residues: 520 loop : -0.50 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 105 HIS 0.002 0.001 HIS G 255 PHE 0.011 0.001 PHE D 404 TYR 0.006 0.001 TYR G 284 ARG 0.005 0.000 ARG A 541 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 90 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 TYR cc_start: 0.7811 (t80) cc_final: 0.7383 (t80) REVERT: A 527 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8782 (tt) REVERT: B 591 ARG cc_start: 0.7979 (ptm160) cc_final: 0.7594 (pmt170) REVERT: D 519 TYR cc_start: 0.7813 (t80) cc_final: 0.7386 (t80) REVERT: E 591 ARG cc_start: 0.7981 (ptm160) cc_final: 0.7595 (pmt170) REVERT: G 519 TYR cc_start: 0.7807 (t80) cc_final: 0.7379 (t80) REVERT: G 527 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8784 (tt) REVERT: H 591 ARG cc_start: 0.7971 (ptm160) cc_final: 0.7597 (pmt170) REVERT: J 519 TYR cc_start: 0.7814 (t80) cc_final: 0.7383 (t80) REVERT: J 527 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8783 (tt) REVERT: K 591 ARG cc_start: 0.8138 (ptm160) cc_final: 0.7754 (pmt170) outliers start: 38 outliers final: 27 residues processed: 113 average time/residue: 0.3240 time to fit residues: 54.3668 Evaluate side-chains 118 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 595 ASN Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 557 CYS Chi-restraints excluded: chain H residue 595 ASN Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 557 CYS Chi-restraints excluded: chain K residue 595 ASN Chi-restraints excluded: chain K residue 596 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17588 Z= 0.244 Angle : 0.510 8.982 23844 Z= 0.253 Chirality : 0.041 0.137 2624 Planarity : 0.003 0.041 3212 Dihedral : 3.573 14.261 2388 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.75 % Allowed : 11.68 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 2184 helix: 2.17 (0.20), residues: 748 sheet: -0.53 (0.23), residues: 520 loop : -0.55 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.002 0.001 HIS D 255 PHE 0.010 0.001 PHE G 404 TYR 0.007 0.001 TYR G 284 ARG 0.004 0.000 ARG G 541 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 88 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8101 (mmt) cc_final: 0.7745 (mmt) REVERT: A 519 TYR cc_start: 0.7821 (t80) cc_final: 0.7417 (t80) REVERT: A 527 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8802 (tt) REVERT: A 580 MET cc_start: 0.8276 (pmm) cc_final: 0.7971 (pmm) REVERT: B 591 ARG cc_start: 0.8140 (ptm160) cc_final: 0.7742 (pmt170) REVERT: D 519 TYR cc_start: 0.7823 (t80) cc_final: 0.7429 (t80) REVERT: D 580 MET cc_start: 0.8270 (pmm) cc_final: 0.7966 (pmm) REVERT: E 591 ARG cc_start: 0.8141 (ptm160) cc_final: 0.7742 (pmt170) REVERT: G 519 TYR cc_start: 0.7818 (t80) cc_final: 0.7414 (t80) REVERT: G 527 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8801 (tt) REVERT: G 580 MET cc_start: 0.8272 (pmm) cc_final: 0.7963 (pmm) REVERT: H 591 ARG cc_start: 0.8135 (ptm160) cc_final: 0.7747 (pmt170) REVERT: J 519 TYR cc_start: 0.7821 (t80) cc_final: 0.7419 (t80) REVERT: J 527 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8804 (tt) REVERT: J 580 MET cc_start: 0.8264 (pmm) cc_final: 0.7960 (pmm) REVERT: K 591 ARG cc_start: 0.8145 (ptm160) cc_final: 0.7747 (pmt170) outliers start: 32 outliers final: 29 residues processed: 105 average time/residue: 0.3796 time to fit residues: 58.8165 Evaluate side-chains 120 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 88 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 595 ASN Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 557 CYS Chi-restraints excluded: chain H residue 595 ASN Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 541 ARG Chi-restraints excluded: chain J residue 557 CYS Chi-restraints excluded: chain K residue 595 ASN Chi-restraints excluded: chain K residue 596 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 219 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 134 optimal weight: 0.1980 chunk 107 optimal weight: 0.1980 chunk 138 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17588 Z= 0.117 Angle : 0.465 8.917 23844 Z= 0.223 Chirality : 0.041 0.133 2624 Planarity : 0.003 0.038 3212 Dihedral : 3.168 14.291 2388 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.26 % Allowed : 12.17 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 2184 helix: 2.33 (0.20), residues: 744 sheet: -0.27 (0.24), residues: 500 loop : -0.44 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 384 HIS 0.001 0.000 HIS D 255 PHE 0.009 0.001 PHE G 404 TYR 0.006 0.001 TYR A 166 ARG 0.006 0.000 ARG G 541 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8143 (mmt) cc_final: 0.7838 (mmt) REVERT: A 519 TYR cc_start: 0.7684 (t80) cc_final: 0.7483 (t80) REVERT: A 527 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8742 (tt) REVERT: A 580 MET cc_start: 0.8401 (pmm) cc_final: 0.7673 (pmm) REVERT: B 591 ARG cc_start: 0.8062 (ptm160) cc_final: 0.7684 (pmt170) REVERT: C 624 GLN cc_start: 0.8820 (pm20) cc_final: 0.8576 (pp30) REVERT: D 408 MET cc_start: 0.8152 (mmt) cc_final: 0.7845 (mmt) REVERT: D 580 MET cc_start: 0.8393 (pmm) cc_final: 0.7665 (pmm) REVERT: E 591 ARG cc_start: 0.8064 (ptm160) cc_final: 0.7684 (pmt170) REVERT: F 624 GLN cc_start: 0.8820 (pm20) cc_final: 0.8577 (pp30) REVERT: G 369 MET cc_start: 0.7373 (pmm) cc_final: 0.6301 (ppp) REVERT: G 408 MET cc_start: 0.8106 (mmt) cc_final: 0.7740 (mmt) REVERT: G 519 TYR cc_start: 0.7680 (t80) cc_final: 0.7478 (t80) REVERT: G 527 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8745 (tt) REVERT: G 580 MET cc_start: 0.8392 (pmm) cc_final: 0.7661 (pmm) REVERT: H 591 ARG cc_start: 0.8054 (ptm160) cc_final: 0.7686 (pmt170) REVERT: I 624 GLN cc_start: 0.8817 (pm20) cc_final: 0.8572 (pp30) REVERT: J 408 MET cc_start: 0.8163 (mmt) cc_final: 0.7857 (mmt) REVERT: J 519 TYR cc_start: 0.7682 (t80) cc_final: 0.7481 (t80) REVERT: J 527 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8744 (tt) REVERT: J 580 MET cc_start: 0.8392 (pmm) cc_final: 0.7739 (pmm) REVERT: K 591 ARG cc_start: 0.8060 (ptm160) cc_final: 0.7686 (pmt170) REVERT: L 624 GLN cc_start: 0.8825 (pm20) cc_final: 0.8577 (pp30) outliers start: 23 outliers final: 20 residues processed: 113 average time/residue: 0.3346 time to fit residues: 56.5325 Evaluate side-chains 114 residues out of total 1832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain E residue 595 ASN Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 595 ASN Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 541 ARG Chi-restraints excluded: chain K residue 595 ASN Chi-restraints excluded: chain K residue 596 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 9.9990 chunk 53 optimal weight: 0.0670 chunk 160 optimal weight: 10.0000 chunk 25 optimal weight: 0.0040 chunk 48 optimal weight: 8.9990 chunk 174 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 179 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 overall best weight: 1.7134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 GLN ** 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 = 0.3595 r_free = 0.3595 target = 0.090669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.067752 restraints weight = 48092.105| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 4.88 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17588 Z= 0.135 Angle : 0.459 9.007 23844 Z= 0.222 Chirality : 0.040 0.133 2624 Planarity : 0.003 0.037 3212 Dihedral : 3.144 14.051 2388 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.42 % Allowed : 12.45 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 2184 helix: 2.38 (0.20), residues: 744 sheet: -0.29 (0.24), residues: 500 loop : -0.43 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 384 HIS 0.001 0.000 HIS A 255 PHE 0.010 0.001 PHE G 404 TYR 0.009 0.001 TYR D 519 ARG 0.005 0.000 ARG G 541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2498.87 seconds wall clock time: 47 minutes 3.32 seconds (2823.32 seconds total)