Starting phenix.real_space_refine on Sat Feb 17 18:47:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6q_25724/02_2024/7t6q_25724_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6q_25724/02_2024/7t6q_25724.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6q_25724/02_2024/7t6q_25724_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6q_25724/02_2024/7t6q_25724_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6q_25724/02_2024/7t6q_25724_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6q_25724/02_2024/7t6q_25724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6q_25724/02_2024/7t6q_25724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6q_25724/02_2024/7t6q_25724_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6q_25724/02_2024/7t6q_25724_updated.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= 0.007 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 140 5.16 5 C 12648 2.51 5 N 3284 2.21 5 O 3516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 489": "OD1" <-> "OD2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 357": "OD1" <-> "OD2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 489": "OD1" <-> "OD2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 489": "OD1" <-> "OD2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 309": "OE1" <-> "OE2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 357": "OD1" <-> "OD2" Residue "D TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 489": "OD1" <-> "OD2" Residue "D ASP 516": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19600 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.69, per 1000 atoms: 0.49 Number of scatterers: 19600 At special positions: 0 Unit cell: (121.9, 122.96, 120.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 12 15.00 O 3516 8.00 N 3284 7.00 C 12648 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.93 Conformation dependent library (CDL) restraints added in 3.4 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 119 helices and 8 sheets defined 55.7% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'A' and resid 31 through 46 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 59 through 66 removed outlier: 4.189A pdb=" N ILE A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.074A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 107 " --> pdb=" O GLU A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.876A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.861A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 302 through 305 removed outlier: 3.622A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 305' Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 325 through 347 removed outlier: 3.580A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 removed outlier: 3.642A pdb=" N GLY A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.941A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 423 through 445 removed outlier: 3.664A pdb=" N ILE A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 469 removed outlier: 4.127A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 removed outlier: 3.594A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 501 through 513 removed outlier: 3.631A pdb=" N THR A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 553 through 565 removed outlier: 3.764A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 605 removed outlier: 4.175A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 46 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 59 through 66 removed outlier: 4.041A pdb=" N ILE B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 103 through 107 removed outlier: 4.066A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 107 " --> pdb=" O GLU B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 107' Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 253 through 263 removed outlier: 4.003A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 284 No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 302 through 305 removed outlier: 3.606A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 305' Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 325 through 348 removed outlier: 3.522A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.642A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.954A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 423 through 445 removed outlier: 3.616A pdb=" N ILE B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 469 removed outlier: 4.191A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 488 removed outlier: 3.797A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 501 through 513 removed outlier: 3.504A pdb=" N THR B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 553 through 565 removed outlier: 3.785A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 562 " --> pdb=" O THR B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 605 removed outlier: 4.169A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 46 Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 59 through 66 removed outlier: 4.117A pdb=" N ILE C 63 " --> pdb=" O ARG C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.085A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 107' Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 243 through 250 Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.743A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 284 No H-bonds generated for 'chain 'C' and resid 281 through 284' Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 302 through 305 removed outlier: 3.663A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 302 through 305' Processing helix chain 'C' and resid 314 through 323 Processing helix chain 'C' and resid 325 through 348 removed outlier: 3.531A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 removed outlier: 3.611A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 412 through 415 No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 423 through 444 removed outlier: 3.674A pdb=" N ILE C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 469 removed outlier: 4.028A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N MET C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 488 removed outlier: 4.189A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 497 Processing helix chain 'C' and resid 501 through 513 removed outlier: 3.593A pdb=" N THR C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 553 through 565 removed outlier: 3.808A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 562 " --> pdb=" O THR C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 605 removed outlier: 4.095A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 59 through 66 removed outlier: 4.307A pdb=" N ILE D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 103 through 107 removed outlier: 4.072A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 107' Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.977A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 284 No H-bonds generated for 'chain 'D' and resid 281 through 284' Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 302 through 305 removed outlier: 3.632A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 302 through 305' Processing helix chain 'D' and resid 314 through 323 Processing helix chain 'D' and resid 325 through 348 removed outlier: 3.582A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 removed outlier: 3.654A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.963A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 423 through 445 removed outlier: 3.681A pdb=" N ILE D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 469 removed outlier: 4.083A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS D 463 " --> pdb=" O VAL D 459 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 497 removed outlier: 3.689A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N CYS D 494 " --> pdb=" O LEU D 490 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 513 removed outlier: 3.539A pdb=" N THR D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 553 through 565 removed outlier: 3.755A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 562 " --> pdb=" O THR D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 605 removed outlier: 4.071A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 630 through 634 removed outlier: 3.624A pdb=" N TRP A 268 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 352 through 354 Processing sheet with id= C, first strand: chain 'B' and resid 630 through 634 removed outlier: 3.576A pdb=" N TRP B 268 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 352 through 354 Processing sheet with id= E, first strand: chain 'C' and resid 630 through 634 removed outlier: 3.599A pdb=" N TRP C 268 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 352 through 354 Processing sheet with id= G, first strand: chain 'D' and resid 630 through 634 removed outlier: 3.598A pdb=" N TRP D 268 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 352 through 354 813 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.21 Time building geometry restraints manager: 7.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3116 1.31 - 1.44: 5435 1.44 - 1.56: 11252 1.56 - 1.69: 17 1.69 - 1.82: 228 Bond restraints: 20048 Sorted by residual: bond pdb=" C VAL C 452 " pdb=" N PRO C 453 " ideal model delta sigma weight residual 1.336 1.366 -0.031 1.23e-02 6.61e+03 6.26e+00 bond pdb=" CB PHE D 478 " pdb=" CG PHE D 478 " ideal model delta sigma weight residual 1.502 1.549 -0.047 2.30e-02 1.89e+03 4.25e+00 bond pdb=" C ARG B 326 " pdb=" N PRO B 327 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.20e-02 6.94e+03 4.03e+00 bond pdb=" C ARG A 326 " pdb=" N PRO A 327 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.20e-02 6.94e+03 3.93e+00 bond pdb=" C ARG D 326 " pdb=" N PRO D 327 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.20e-02 6.94e+03 3.91e+00 ... (remaining 20043 not shown) Histogram of bond angle deviations from ideal: 96.04 - 104.35: 345 104.35 - 112.65: 10012 112.65 - 120.95: 10904 120.95 - 129.26: 5788 129.26 - 137.56: 175 Bond angle restraints: 27224 Sorted by residual: angle pdb=" C GLU C 515 " pdb=" N ASP C 516 " pdb=" CA ASP C 516 " ideal model delta sigma weight residual 121.61 136.10 -14.49 1.39e+00 5.18e-01 1.09e+02 angle pdb=" N MET C 491 " pdb=" CA MET C 491 " pdb=" C MET C 491 " ideal model delta sigma weight residual 114.04 104.66 9.38 1.24e+00 6.50e-01 5.72e+01 angle pdb=" N MET A 491 " pdb=" CA MET A 491 " pdb=" C MET A 491 " ideal model delta sigma weight residual 114.56 105.44 9.12 1.27e+00 6.20e-01 5.15e+01 angle pdb=" N MET B 491 " pdb=" CA MET B 491 " pdb=" C MET B 491 " ideal model delta sigma weight residual 114.04 105.29 8.75 1.24e+00 6.50e-01 4.98e+01 angle pdb=" N ILE B 307 " pdb=" CA ILE B 307 " pdb=" C ILE B 307 " ideal model delta sigma weight residual 113.22 105.65 7.57 1.23e+00 6.61e-01 3.79e+01 ... (remaining 27219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 10514 17.76 - 35.52: 1191 35.52 - 53.28: 147 53.28 - 71.03: 40 71.03 - 88.79: 28 Dihedral angle restraints: 11920 sinusoidal: 4840 harmonic: 7080 Sorted by residual: dihedral pdb=" CA ILE B 202 " pdb=" C ILE B 202 " pdb=" N LEU B 203 " pdb=" CA LEU B 203 " ideal model delta harmonic sigma weight residual 180.00 149.31 30.69 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA ILE D 202 " pdb=" C ILE D 202 " pdb=" N LEU D 203 " pdb=" CA LEU D 203 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ILE A 202 " pdb=" C ILE A 202 " pdb=" N LEU A 203 " pdb=" CA LEU A 203 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 11917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2435 0.067 - 0.134: 542 0.134 - 0.201: 93 0.201 - 0.268: 18 0.268 - 0.335: 12 Chirality restraints: 3100 Sorted by residual: chirality pdb=" CB VAL C 297 " pdb=" CA VAL C 297 " pdb=" CG1 VAL C 297 " pdb=" CG2 VAL C 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB VAL A 297 " pdb=" CA VAL A 297 " pdb=" CG1 VAL A 297 " pdb=" CG2 VAL A 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB VAL D 297 " pdb=" CA VAL D 297 " pdb=" CG1 VAL D 297 " pdb=" CG2 VAL D 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 3097 not shown) Planarity restraints: 3424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 574 " 0.026 2.00e-02 2.50e+03 2.78e-02 1.35e+01 pdb=" CG PHE B 574 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE B 574 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE B 574 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 574 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 574 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE B 574 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 432 " -0.014 2.00e-02 2.50e+03 2.52e-02 1.27e+01 pdb=" CG TYR B 432 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR B 432 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 432 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 432 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 432 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 432 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 432 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 456 " -0.026 2.00e-02 2.50e+03 2.50e-02 1.09e+01 pdb=" CG PHE A 456 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 456 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 456 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 456 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 456 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 456 " -0.008 2.00e-02 2.50e+03 ... (remaining 3421 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5129 2.81 - 3.33: 17984 3.33 - 3.85: 33466 3.85 - 4.38: 37805 4.38 - 4.90: 64282 Nonbonded interactions: 158666 Sorted by model distance: nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.282 2.440 nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.285 2.440 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.287 2.440 nonbonded pdb=" O PRO A 544 " pdb=" OH TYR A 555 " model vdw 2.289 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" OD1 ASN B 635 " model vdw 2.306 2.440 ... (remaining 158661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.650 Check model and map are aligned: 0.270 Set scattering table: 0.230 Process input model: 50.830 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 20048 Z= 0.370 Angle : 1.295 19.707 27224 Z= 0.649 Chirality : 0.062 0.335 3100 Planarity : 0.009 0.090 3424 Dihedral : 15.174 88.794 7344 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.13), residues: 2408 helix: -2.51 (0.10), residues: 1480 sheet: 0.12 (0.77), residues: 56 loop : -2.57 (0.17), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 29 HIS 0.010 0.002 HIS C 201 PHE 0.060 0.003 PHE B 574 TYR 0.059 0.003 TYR B 432 ARG 0.019 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 2.318 Fit side-chains revert: symmetry clash REVERT: A 432 TYR cc_start: 0.8338 (t80) cc_final: 0.7739 (t80) REVERT: A 584 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.7208 (ttt180) REVERT: B 592 LEU cc_start: 0.8456 (mt) cc_final: 0.8219 (mt) REVERT: C 588 GLU cc_start: 0.7711 (pp20) cc_final: 0.7191 (pt0) REVERT: D 570 MET cc_start: 0.7821 (tpp) cc_final: 0.7474 (ttt) REVERT: D 584 ARG cc_start: 0.7488 (ttp-110) cc_final: 0.7162 (ttt180) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.2988 time to fit residues: 169.9858 Evaluate side-chains 254 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 217 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 HIS A 518 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN B 519 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 HIS C 519 ASN D 157 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN D 519 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20048 Z= 0.162 Angle : 0.631 11.567 27224 Z= 0.299 Chirality : 0.039 0.171 3100 Planarity : 0.005 0.051 3424 Dihedral : 5.975 59.952 2752 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.48 % Allowed : 9.26 % Favored : 89.27 % 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: -2.37 (0.15), residues: 2408 helix: -1.12 (0.12), residues: 1524 sheet: 0.19 (0.75), residues: 56 loop : -2.38 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 29 HIS 0.004 0.001 HIS C 201 PHE 0.024 0.001 PHE D 574 TYR 0.024 0.001 TYR B 432 ARG 0.004 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 276 time to evaluate : 2.345 Fit side-chains REVERT: A 584 ARG cc_start: 0.7495 (ttp-110) cc_final: 0.7289 (ttt180) REVERT: B 592 LEU cc_start: 0.8603 (mt) cc_final: 0.8371 (mt) REVERT: C 592 LEU cc_start: 0.8647 (mt) cc_final: 0.8234 (mt) REVERT: D 255 MET cc_start: 0.8166 (tpp) cc_final: 0.7861 (mmm) REVERT: D 584 ARG cc_start: 0.7480 (ttp-110) cc_final: 0.7173 (ttt180) outliers start: 31 outliers final: 22 residues processed: 291 average time/residue: 0.3110 time to fit residues: 143.8200 Evaluate side-chains 271 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 249 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 514 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 157 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20048 Z= 0.231 Angle : 0.640 13.543 27224 Z= 0.304 Chirality : 0.040 0.173 3100 Planarity : 0.004 0.046 3424 Dihedral : 5.722 59.662 2752 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.86 % Allowed : 13.31 % Favored : 83.83 % 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: -1.53 (0.16), residues: 2408 helix: -0.42 (0.13), residues: 1524 sheet: 0.29 (0.77), residues: 56 loop : -2.12 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 29 HIS 0.005 0.001 HIS C 582 PHE 0.024 0.002 PHE D 574 TYR 0.016 0.002 TYR D 216 ARG 0.003 0.000 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 247 time to evaluate : 2.260 Fit side-chains REVERT: A 83 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8496 (tt) REVERT: A 157 HIS cc_start: 0.6398 (OUTLIER) cc_final: 0.5746 (m90) REVERT: A 164 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: A 592 LEU cc_start: 0.8718 (mt) cc_final: 0.8410 (mt) REVERT: B 157 HIS cc_start: 0.6570 (OUTLIER) cc_final: 0.5849 (m90) REVERT: B 164 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: B 368 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6473 (pp) REVERT: B 447 MET cc_start: 0.7474 (ptt) cc_final: 0.7187 (ptt) REVERT: B 555 TYR cc_start: 0.6707 (t80) cc_final: 0.6431 (t80) REVERT: B 592 LEU cc_start: 0.8684 (mt) cc_final: 0.8366 (mt) REVERT: C 157 HIS cc_start: 0.6481 (OUTLIER) cc_final: 0.5836 (m90) REVERT: C 164 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: C 260 MET cc_start: 0.7374 (mmt) cc_final: 0.6915 (mmt) REVERT: D 157 HIS cc_start: 0.6529 (OUTLIER) cc_final: 0.5837 (m90) REVERT: D 164 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: D 345 THR cc_start: 0.9053 (t) cc_final: 0.8847 (t) REVERT: D 584 ARG cc_start: 0.7600 (ttp-110) cc_final: 0.7284 (ttt180) outliers start: 60 outliers final: 31 residues processed: 289 average time/residue: 0.3182 time to fit residues: 144.3826 Evaluate side-chains 263 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 222 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 585 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20048 Z= 0.171 Angle : 0.606 13.635 27224 Z= 0.284 Chirality : 0.039 0.165 3100 Planarity : 0.004 0.046 3424 Dihedral : 5.541 58.027 2752 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.53 % Allowed : 14.89 % Favored : 82.59 % 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 (0.17), residues: 2408 helix: -0.03 (0.13), residues: 1524 sheet: 0.32 (0.77), residues: 56 loop : -1.94 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 29 HIS 0.007 0.001 HIS A 157 PHE 0.023 0.001 PHE B 574 TYR 0.018 0.001 TYR A 432 ARG 0.001 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 241 time to evaluate : 2.394 Fit side-chains REVERT: A 570 MET cc_start: 0.7810 (mtp) cc_final: 0.7519 (mtt) REVERT: A 592 LEU cc_start: 0.8701 (mt) cc_final: 0.8459 (mt) REVERT: B 368 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6472 (pp) REVERT: B 447 MET cc_start: 0.7528 (ptt) cc_final: 0.7244 (ptt) REVERT: B 555 TYR cc_start: 0.6653 (t80) cc_final: 0.6323 (t80) REVERT: B 592 LEU cc_start: 0.8645 (mt) cc_final: 0.8352 (mt) REVERT: C 368 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6742 (pp) REVERT: C 592 LEU cc_start: 0.8593 (mt) cc_final: 0.8367 (mt) REVERT: D 584 ARG cc_start: 0.7596 (ttp-110) cc_final: 0.7283 (ttt180) outliers start: 53 outliers final: 32 residues processed: 275 average time/residue: 0.3011 time to fit residues: 129.6576 Evaluate side-chains 259 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 225 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.2980 chunk 131 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 58 optimal weight: 0.0270 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20048 Z= 0.179 Angle : 0.618 14.804 27224 Z= 0.284 Chirality : 0.039 0.171 3100 Planarity : 0.004 0.045 3424 Dihedral : 5.432 57.641 2752 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.58 % Allowed : 15.60 % Favored : 81.82 % 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 (0.17), residues: 2408 helix: 0.20 (0.14), residues: 1524 sheet: 0.38 (0.77), residues: 56 loop : -1.90 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 29 HIS 0.003 0.001 HIS C 582 PHE 0.024 0.001 PHE C 574 TYR 0.018 0.001 TYR A 432 ARG 0.002 0.000 ARG C 632 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 238 time to evaluate : 2.035 Fit side-chains REVERT: A 570 MET cc_start: 0.7822 (mtp) cc_final: 0.7570 (mtt) REVERT: A 592 LEU cc_start: 0.8667 (mt) cc_final: 0.8366 (mt) REVERT: B 368 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6510 (pp) REVERT: B 447 MET cc_start: 0.7410 (ptt) cc_final: 0.7120 (ptt) REVERT: B 592 LEU cc_start: 0.8686 (mt) cc_final: 0.8363 (mt) REVERT: C 260 MET cc_start: 0.7368 (mmt) cc_final: 0.6857 (mmt) REVERT: C 368 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6761 (pp) REVERT: C 489 ASP cc_start: 0.8004 (m-30) cc_final: 0.7367 (t0) REVERT: D 83 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8539 (tt) REVERT: D 157 HIS cc_start: 0.6596 (OUTLIER) cc_final: 0.5921 (m90) REVERT: D 584 ARG cc_start: 0.7573 (ttp-110) cc_final: 0.7282 (ttt180) outliers start: 54 outliers final: 36 residues processed: 277 average time/residue: 0.2997 time to fit residues: 129.4309 Evaluate side-chains 265 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 225 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 514 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 232 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 157 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20048 Z= 0.226 Angle : 0.649 15.099 27224 Z= 0.300 Chirality : 0.040 0.177 3100 Planarity : 0.004 0.045 3424 Dihedral : 5.506 57.815 2752 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.34 % Allowed : 16.70 % Favored : 79.96 % 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: -0.74 (0.17), residues: 2408 helix: 0.21 (0.14), residues: 1516 sheet: 0.38 (0.77), residues: 56 loop : -1.79 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 29 HIS 0.005 0.001 HIS A 582 PHE 0.023 0.001 PHE C 574 TYR 0.016 0.001 TYR A 432 ARG 0.002 0.000 ARG C 632 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 231 time to evaluate : 2.337 Fit side-chains REVERT: A 157 HIS cc_start: 0.6545 (OUTLIER) cc_final: 0.5893 (m90) REVERT: A 164 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: A 588 GLU cc_start: 0.7346 (pp20) cc_final: 0.6741 (pt0) REVERT: A 592 LEU cc_start: 0.8605 (mt) cc_final: 0.8395 (mt) REVERT: B 51 GLN cc_start: 0.7946 (tp-100) cc_final: 0.7531 (tp-100) REVERT: B 157 HIS cc_start: 0.6665 (OUTLIER) cc_final: 0.5972 (m90) REVERT: B 164 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: B 255 MET cc_start: 0.8467 (mmm) cc_final: 0.8044 (tpt) REVERT: B 368 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6478 (pp) REVERT: B 447 MET cc_start: 0.7435 (ptt) cc_final: 0.7145 (ptt) REVERT: B 592 LEU cc_start: 0.8692 (mt) cc_final: 0.8360 (mt) REVERT: C 83 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8510 (tt) REVERT: C 157 HIS cc_start: 0.6607 (OUTLIER) cc_final: 0.5963 (m90) REVERT: C 164 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: C 260 MET cc_start: 0.7491 (mmt) cc_final: 0.6986 (mmt) REVERT: C 588 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7219 (pt0) REVERT: C 592 LEU cc_start: 0.8656 (mt) cc_final: 0.8344 (mt) REVERT: D 42 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8320 (tm-30) REVERT: D 157 HIS cc_start: 0.6557 (OUTLIER) cc_final: 0.5868 (m90) REVERT: D 164 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: D 584 ARG cc_start: 0.7585 (ttp-110) cc_final: 0.7279 (ttt180) outliers start: 70 outliers final: 44 residues processed: 284 average time/residue: 0.3268 time to fit residues: 146.0050 Evaluate side-chains 282 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 226 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20048 Z= 0.176 Angle : 0.631 14.079 27224 Z= 0.289 Chirality : 0.039 0.166 3100 Planarity : 0.004 0.046 3424 Dihedral : 5.389 58.895 2752 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.05 % Allowed : 17.03 % Favored : 79.91 % 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: -0.54 (0.17), residues: 2408 helix: 0.38 (0.14), residues: 1516 sheet: 0.52 (0.77), residues: 56 loop : -1.74 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 495 HIS 0.003 0.001 HIS A 157 PHE 0.020 0.001 PHE C 574 TYR 0.014 0.001 TYR A 432 ARG 0.002 0.000 ARG C 632 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 234 time to evaluate : 2.140 Fit side-chains REVERT: A 157 HIS cc_start: 0.6504 (OUTLIER) cc_final: 0.5868 (m90) REVERT: A 164 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: A 447 MET cc_start: 0.7361 (ptt) cc_final: 0.7152 (ptt) REVERT: A 588 GLU cc_start: 0.7320 (pp20) cc_final: 0.6748 (pt0) REVERT: A 592 LEU cc_start: 0.8595 (mt) cc_final: 0.8382 (mt) REVERT: B 51 GLN cc_start: 0.7932 (tp-100) cc_final: 0.7531 (tp-100) REVERT: B 157 HIS cc_start: 0.6590 (OUTLIER) cc_final: 0.5920 (m90) REVERT: B 164 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: B 255 MET cc_start: 0.8417 (mmm) cc_final: 0.8097 (tpt) REVERT: B 368 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6475 (pp) REVERT: B 415 TYR cc_start: 0.7017 (t80) cc_final: 0.6725 (t80) REVERT: B 447 MET cc_start: 0.7391 (ptt) cc_final: 0.7103 (ptt) REVERT: B 578 MET cc_start: 0.7243 (mtt) cc_final: 0.6986 (mtt) REVERT: B 588 GLU cc_start: 0.7704 (pp20) cc_final: 0.7361 (pp20) REVERT: B 592 LEU cc_start: 0.8663 (mt) cc_final: 0.8421 (mt) REVERT: C 157 HIS cc_start: 0.6605 (OUTLIER) cc_final: 0.5976 (m90) REVERT: C 164 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6640 (mp0) REVERT: C 260 MET cc_start: 0.7460 (mmt) cc_final: 0.6927 (mmt) REVERT: C 489 ASP cc_start: 0.7898 (m-30) cc_final: 0.7316 (t0) REVERT: C 588 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: C 592 LEU cc_start: 0.8567 (mt) cc_final: 0.8249 (mt) REVERT: D 157 HIS cc_start: 0.6553 (OUTLIER) cc_final: 0.5905 (m90) REVERT: D 164 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: D 481 MET cc_start: 0.7944 (ttp) cc_final: 0.7730 (ptt) REVERT: D 584 ARG cc_start: 0.7563 (ttp-110) cc_final: 0.7278 (ttt180) outliers start: 64 outliers final: 43 residues processed: 281 average time/residue: 0.2903 time to fit residues: 128.0543 Evaluate side-chains 282 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 229 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20048 Z= 0.176 Angle : 0.629 13.803 27224 Z= 0.286 Chirality : 0.039 0.165 3100 Planarity : 0.004 0.046 3424 Dihedral : 5.331 59.222 2752 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.86 % Allowed : 17.18 % Favored : 79.96 % 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: -0.43 (0.17), residues: 2408 helix: 0.52 (0.14), residues: 1492 sheet: 0.70 (0.77), residues: 56 loop : -1.75 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 495 HIS 0.004 0.001 HIS A 157 PHE 0.021 0.001 PHE C 574 TYR 0.013 0.001 TYR A 432 ARG 0.002 0.000 ARG C 632 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 237 time to evaluate : 2.304 Fit side-chains REVERT: A 164 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6602 (mp0) REVERT: A 447 MET cc_start: 0.7382 (ptt) cc_final: 0.7179 (ptt) REVERT: A 588 GLU cc_start: 0.7346 (pp20) cc_final: 0.6748 (pt0) REVERT: A 592 LEU cc_start: 0.8607 (mt) cc_final: 0.8382 (mt) REVERT: B 51 GLN cc_start: 0.7919 (tp-100) cc_final: 0.7242 (tp-100) REVERT: B 164 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6715 (mp0) REVERT: B 255 MET cc_start: 0.8431 (mmm) cc_final: 0.8155 (tpt) REVERT: B 368 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6485 (pp) REVERT: B 447 MET cc_start: 0.7393 (ptt) cc_final: 0.7100 (ptt) REVERT: B 588 GLU cc_start: 0.7631 (pp20) cc_final: 0.7285 (pp20) REVERT: B 592 LEU cc_start: 0.8667 (mt) cc_final: 0.8421 (mt) REVERT: C 164 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: C 260 MET cc_start: 0.7419 (mmt) cc_final: 0.6883 (mmt) REVERT: C 478 PHE cc_start: 0.7528 (m-10) cc_final: 0.7307 (m-10) REVERT: C 489 ASP cc_start: 0.7882 (m-30) cc_final: 0.7346 (t0) REVERT: C 588 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7226 (pt0) REVERT: C 592 LEU cc_start: 0.8572 (mt) cc_final: 0.8233 (mt) REVERT: D 157 HIS cc_start: 0.6507 (OUTLIER) cc_final: 0.5860 (m90) REVERT: D 164 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: D 300 LYS cc_start: 0.8185 (ptpt) cc_final: 0.7895 (pttm) REVERT: D 447 MET cc_start: 0.7269 (ptt) cc_final: 0.7062 (ptt) REVERT: D 584 ARG cc_start: 0.7532 (ttp-110) cc_final: 0.7271 (ttt180) outliers start: 60 outliers final: 42 residues processed: 274 average time/residue: 0.2917 time to fit residues: 125.6028 Evaluate side-chains 280 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 231 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 514 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.6980 chunk 221 optimal weight: 0.3980 chunk 202 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20048 Z= 0.225 Angle : 0.664 15.038 27224 Z= 0.302 Chirality : 0.040 0.171 3100 Planarity : 0.004 0.046 3424 Dihedral : 5.411 59.333 2752 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.62 % Allowed : 17.80 % Favored : 79.58 % 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: -0.39 (0.17), residues: 2408 helix: 0.48 (0.14), residues: 1500 sheet: 0.76 (0.77), residues: 56 loop : -1.62 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 29 HIS 0.005 0.001 HIS C 582 PHE 0.023 0.001 PHE C 574 TYR 0.012 0.001 TYR A 432 ARG 0.002 0.000 ARG C 632 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 231 time to evaluate : 2.195 Fit side-chains REVERT: A 164 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: A 588 GLU cc_start: 0.7369 (pp20) cc_final: 0.6782 (pt0) REVERT: A 592 LEU cc_start: 0.8629 (mt) cc_final: 0.8399 (mt) REVERT: B 51 GLN cc_start: 0.7928 (tp-100) cc_final: 0.7561 (tp-100) REVERT: B 164 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: B 255 MET cc_start: 0.8545 (mmm) cc_final: 0.8230 (tpt) REVERT: B 368 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6476 (pp) REVERT: B 447 MET cc_start: 0.7349 (ptt) cc_final: 0.7052 (ptt) REVERT: B 592 LEU cc_start: 0.8686 (mt) cc_final: 0.8371 (mt) REVERT: B 603 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6753 (ttt) REVERT: C 164 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: C 260 MET cc_start: 0.7523 (mmt) cc_final: 0.7044 (mmt) REVERT: C 588 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7250 (pt0) REVERT: C 592 LEU cc_start: 0.8617 (mt) cc_final: 0.8261 (mt) REVERT: D 157 HIS cc_start: 0.6466 (OUTLIER) cc_final: 0.5813 (m90) REVERT: D 164 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: D 584 ARG cc_start: 0.7586 (ttp-110) cc_final: 0.7290 (ttt180) outliers start: 55 outliers final: 42 residues processed: 264 average time/residue: 0.2980 time to fit residues: 123.1046 Evaluate side-chains 276 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 226 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 chunk 158 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20048 Z= 0.196 Angle : 0.641 13.987 27224 Z= 0.292 Chirality : 0.040 0.168 3100 Planarity : 0.004 0.046 3424 Dihedral : 5.327 57.940 2752 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.48 % Allowed : 17.89 % Favored : 79.63 % 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: -0.30 (0.17), residues: 2408 helix: 0.61 (0.14), residues: 1492 sheet: 0.86 (0.76), residues: 56 loop : -1.69 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 495 HIS 0.004 0.001 HIS C 426 PHE 0.025 0.001 PHE C 574 TYR 0.012 0.001 TYR A 432 ARG 0.002 0.000 ARG C 632 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 231 time to evaluate : 3.115 Fit side-chains REVERT: A 164 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6649 (mp0) REVERT: A 588 GLU cc_start: 0.7513 (pp20) cc_final: 0.6937 (pt0) REVERT: A 592 LEU cc_start: 0.8614 (mt) cc_final: 0.8390 (mt) REVERT: B 51 GLN cc_start: 0.7916 (tp-100) cc_final: 0.7301 (tp-100) REVERT: B 164 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: B 255 MET cc_start: 0.8523 (mmm) cc_final: 0.8228 (tpt) REVERT: B 368 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6485 (pp) REVERT: B 447 MET cc_start: 0.7313 (ptt) cc_final: 0.7019 (ptt) REVERT: B 592 LEU cc_start: 0.8686 (mt) cc_final: 0.8371 (mt) REVERT: B 603 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6723 (ttt) REVERT: C 51 GLN cc_start: 0.7977 (tp-100) cc_final: 0.7323 (tp-100) REVERT: C 164 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: C 260 MET cc_start: 0.7491 (mmt) cc_final: 0.7006 (mmt) REVERT: C 489 ASP cc_start: 0.7905 (m-30) cc_final: 0.7681 (t0) REVERT: C 588 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: C 592 LEU cc_start: 0.8583 (mt) cc_final: 0.8231 (mt) REVERT: D 157 HIS cc_start: 0.6405 (OUTLIER) cc_final: 0.5794 (m90) REVERT: D 164 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: D 584 ARG cc_start: 0.7582 (ttp-110) cc_final: 0.7308 (ttt180) outliers start: 52 outliers final: 40 residues processed: 263 average time/residue: 0.2968 time to fit residues: 122.6912 Evaluate side-chains 275 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 227 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.163180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.138328 restraints weight = 29488.726| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.12 r_work: 0.3583 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20048 Z= 0.214 Angle : 0.654 14.622 27224 Z= 0.298 Chirality : 0.040 0.170 3100 Planarity : 0.004 0.046 3424 Dihedral : 5.318 58.220 2752 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.53 % Allowed : 17.84 % Favored : 79.63 % 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: -0.29 (0.17), residues: 2408 helix: 0.52 (0.14), residues: 1504 sheet: 0.88 (0.75), residues: 56 loop : -1.50 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 29 HIS 0.005 0.001 HIS C 582 PHE 0.025 0.001 PHE C 574 TYR 0.012 0.001 TYR A 432 ARG 0.002 0.000 ARG C 632 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3950.15 seconds wall clock time: 72 minutes 50.17 seconds (4370.17 seconds total)