Starting phenix.real_space_refine on Sat Feb 17 18:57:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0n_24110/02_2024/7n0n_24110.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0n_24110/02_2024/7n0n_24110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0n_24110/02_2024/7n0n_24110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0n_24110/02_2024/7n0n_24110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0n_24110/02_2024/7n0n_24110.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0n_24110/02_2024/7n0n_24110.pdb" } resolution = 4.15 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= 0.041 sd= 0.120 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12888 2.51 5 N 3276 2.21 5 O 3356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 680": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B GLU 599": "OE1" <-> "OE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 680": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C ARG 317": "NH1" <-> "NH2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "C ARG 535": "NH1" <-> "NH2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C GLU 670": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 680": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D ARG 459": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D GLU 599": "OE1" <-> "OE2" Residue "D GLU 670": "OE1" <-> "OE2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D ARG 680": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 706": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19632 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4908 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 593} Chain breaks: 4 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 4908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4908 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 593} Chain breaks: 4 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 117 Chain: "C" Number of atoms: 4908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4908 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 593} Chain breaks: 4 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 117 Chain: "D" Number of atoms: 4908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4908 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 593} Chain breaks: 4 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 117 Time building chain proxies: 10.06, per 1000 atoms: 0.51 Number of scatterers: 19632 At special positions: 0 Unit cell: (140.17, 140.17, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3356 8.00 N 3276 7.00 C 12888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.29 Conformation dependent library (CDL) restraints added in 3.2 seconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 8 sheets defined 63.0% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.540A pdb=" N GLY A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 removed outlier: 3.544A pdb=" N TYR A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 4.072A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.508A pdb=" N LEU A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.559A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.784A pdb=" N GLU A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.565A pdb=" N SER A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.643A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 414 removed outlier: 3.511A pdb=" N LEU A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 470 through 492 Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.694A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 519 through 527 removed outlier: 3.973A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 560 removed outlier: 3.787A pdb=" N ASP A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 606 removed outlier: 5.423A pdb=" N GLU A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 651 removed outlier: 3.744A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 674 removed outlier: 3.817A pdb=" N TRP A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 719 Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.540A pdb=" N GLY B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 removed outlier: 3.545A pdb=" N TYR B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 4.072A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.508A pdb=" N LEU B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.559A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.785A pdb=" N GLU B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.565A pdb=" N SER B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.642A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 374 " --> pdb=" O HIS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 414 removed outlier: 3.510A pdb=" N LEU B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN B 414 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 470 through 492 Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.694A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 Processing helix chain 'B' and resid 519 through 527 removed outlier: 3.973A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 560 removed outlier: 3.787A pdb=" N ASP B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 606 removed outlier: 5.424A pdb=" N GLU B 599 " --> pdb=" O ASP B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 651 removed outlier: 3.743A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 674 removed outlier: 3.817A pdb=" N TRP B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 719 Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.540A pdb=" N GLY C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 103 removed outlier: 3.543A pdb=" N TYR C 98 " --> pdb=" O GLY C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 removed outlier: 4.072A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.507A pdb=" N LEU C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.559A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.784A pdb=" N GLU C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.565A pdb=" N SER C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.643A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 374 " --> pdb=" O HIS C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 414 removed outlier: 3.511A pdb=" N LEU C 381 " --> pdb=" O PRO C 377 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 412 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN C 414 " --> pdb=" O VAL C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'C' and resid 470 through 492 Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.694A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 519 through 527 removed outlier: 3.974A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 560 removed outlier: 3.787A pdb=" N ASP C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 547 " --> pdb=" O VAL C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 606 removed outlier: 5.424A pdb=" N GLU C 599 " --> pdb=" O ASP C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 651 removed outlier: 3.743A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 649 " --> pdb=" O MET C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 674 removed outlier: 3.817A pdb=" N TRP C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 719 Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.540A pdb=" N GLY D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 removed outlier: 3.544A pdb=" N TYR D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 4.072A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.509A pdb=" N LEU D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.559A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.784A pdb=" N GLU D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.565A pdb=" N SER D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.643A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 374 " --> pdb=" O HIS D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 414 removed outlier: 3.511A pdb=" N LEU D 381 " --> pdb=" O PRO D 377 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR D 412 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN D 414 " --> pdb=" O VAL D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 461 through 465 Processing helix chain 'D' and resid 470 through 492 Processing helix chain 'D' and resid 496 through 511 removed outlier: 3.694A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 518 Processing helix chain 'D' and resid 519 through 527 removed outlier: 3.974A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 560 removed outlier: 3.787A pdb=" N ASP D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE D 547 " --> pdb=" O VAL D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 606 removed outlier: 5.423A pdb=" N GLU D 599 " --> pdb=" O ASP D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 651 removed outlier: 3.743A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D 649 " --> pdb=" O MET D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 674 removed outlier: 3.816A pdb=" N TRP D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.904A pdb=" N HIS A 165 " --> pdb=" O CYS A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 341 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 707 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.905A pdb=" N HIS B 165 " --> pdb=" O CYS B 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 341 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 707 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.904A pdb=" N HIS C 165 " --> pdb=" O CYS C 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.979A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 341 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 707 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 156 through 157 removed outlier: 3.905A pdb=" N HIS D 165 " --> pdb=" O CYS D 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER D 341 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 707 " --> pdb=" O SER D 341 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.57 Time building geometry restraints manager: 7.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5972 1.34 - 1.46: 3821 1.46 - 1.57: 10167 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 20132 Sorted by residual: bond pdb=" SD MET C 404 " pdb=" CE MET C 404 " ideal model delta sigma weight residual 1.791 1.741 0.050 2.50e-02 1.60e+03 4.02e+00 bond pdb=" SD MET A 404 " pdb=" CE MET A 404 " ideal model delta sigma weight residual 1.791 1.741 0.050 2.50e-02 1.60e+03 3.96e+00 bond pdb=" SD MET B 404 " pdb=" CE MET B 404 " ideal model delta sigma weight residual 1.791 1.742 0.049 2.50e-02 1.60e+03 3.92e+00 bond pdb=" SD MET D 404 " pdb=" CE MET D 404 " ideal model delta sigma weight residual 1.791 1.742 0.049 2.50e-02 1.60e+03 3.87e+00 bond pdb=" CB MET B 404 " pdb=" CG MET B 404 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.80e+00 ... (remaining 20127 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.64: 312 104.64 - 112.49: 10479 112.49 - 120.35: 8844 120.35 - 128.20: 7490 128.20 - 136.06: 243 Bond angle restraints: 27368 Sorted by residual: angle pdb=" N VAL D 649 " pdb=" CA VAL D 649 " pdb=" C VAL D 649 " ideal model delta sigma weight residual 112.96 107.16 5.80 1.00e+00 1.00e+00 3.37e+01 angle pdb=" N VAL B 649 " pdb=" CA VAL B 649 " pdb=" C VAL B 649 " ideal model delta sigma weight residual 112.96 107.16 5.80 1.00e+00 1.00e+00 3.37e+01 angle pdb=" N VAL A 649 " pdb=" CA VAL A 649 " pdb=" C VAL A 649 " ideal model delta sigma weight residual 112.96 107.17 5.79 1.00e+00 1.00e+00 3.35e+01 angle pdb=" N VAL C 649 " pdb=" CA VAL C 649 " pdb=" C VAL C 649 " ideal model delta sigma weight residual 112.96 107.19 5.77 1.00e+00 1.00e+00 3.32e+01 angle pdb=" N VAL D 691 " pdb=" CA VAL D 691 " pdb=" C VAL D 691 " ideal model delta sigma weight residual 113.71 109.88 3.83 9.50e-01 1.11e+00 1.63e+01 ... (remaining 27363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 10326 16.45 - 32.90: 1142 32.90 - 49.36: 252 49.36 - 65.81: 28 65.81 - 82.26: 28 Dihedral angle restraints: 11776 sinusoidal: 4564 harmonic: 7212 Sorted by residual: dihedral pdb=" CA ILE C 529 " pdb=" C ILE C 529 " pdb=" N GLN C 530 " pdb=" CA GLN C 530 " ideal model delta harmonic sigma weight residual -180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ILE A 529 " pdb=" C ILE A 529 " pdb=" N GLN A 530 " pdb=" CA GLN A 530 " ideal model delta harmonic sigma weight residual -180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ILE D 529 " pdb=" C ILE D 529 " pdb=" N GLN D 530 " pdb=" CA GLN D 530 " ideal model delta harmonic sigma weight residual -180.00 -158.24 -21.76 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 11773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2437 0.060 - 0.121: 582 0.121 - 0.181: 89 0.181 - 0.241: 22 0.241 - 0.302: 6 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CB VAL C 348 " pdb=" CA VAL C 348 " pdb=" CG1 VAL C 348 " pdb=" CG2 VAL C 348 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB VAL B 348 " pdb=" CA VAL B 348 " pdb=" CG1 VAL B 348 " pdb=" CG2 VAL B 348 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB VAL A 348 " pdb=" CA VAL A 348 " pdb=" CG1 VAL A 348 " pdb=" CG2 VAL A 348 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 3133 not shown) Planarity restraints: 3372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 88 " 0.011 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C VAL B 88 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL B 88 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO B 89 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 88 " -0.011 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C VAL A 88 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL A 88 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO A 89 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 88 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C VAL C 88 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL C 88 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO C 89 " 0.012 2.00e-02 2.50e+03 ... (remaining 3369 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4227 2.77 - 3.31: 18939 3.31 - 3.84: 33203 3.84 - 4.37: 35196 4.37 - 4.90: 58979 Nonbonded interactions: 150544 Sorted by model distance: nonbonded pdb=" OG SER A 557 " pdb=" O ALA D 411 " model vdw 2.243 2.440 nonbonded pdb=" O LEU C 513 " pdb=" OG1 THR C 516 " model vdw 2.270 2.440 nonbonded pdb=" O LEU A 513 " pdb=" OG1 THR A 516 " model vdw 2.271 2.440 nonbonded pdb=" O LEU B 513 " pdb=" OG1 THR B 516 " model vdw 2.271 2.440 nonbonded pdb=" O LEU D 513 " pdb=" OG1 THR D 516 " model vdw 2.271 2.440 ... (remaining 150539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 4.720 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 48.850 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 0.052 20132 Z= 0.402 Angle : 1.013 11.420 27368 Z= 0.513 Chirality : 0.056 0.302 3136 Planarity : 0.006 0.039 3372 Dihedral : 14.980 82.262 7104 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.38 % Allowed : 1.35 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.21 (0.14), residues: 2428 helix: -1.05 (0.12), residues: 1456 sheet: -2.58 (0.72), residues: 40 loop : -1.93 (0.17), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 677 HIS 0.011 0.002 HIS D 313 PHE 0.021 0.003 PHE D 472 TYR 0.010 0.002 TYR D 471 ARG 0.006 0.001 ARG D 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 2.287 Fit side-chains REVERT: A 271 TYR cc_start: 0.8717 (t80) cc_final: 0.8371 (t80) REVERT: A 277 MET cc_start: 0.8831 (tpt) cc_final: 0.8494 (mmm) REVERT: A 372 MET cc_start: 0.8903 (tpp) cc_final: 0.8701 (tpp) REVERT: A 636 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9106 (mp) REVERT: B 270 MET cc_start: 0.8753 (tpt) cc_final: 0.8551 (tpp) REVERT: B 715 TRP cc_start: 0.8563 (t60) cc_final: 0.8046 (t60) REVERT: C 715 TRP cc_start: 0.8541 (t60) cc_final: 0.7956 (t60) REVERT: D 270 MET cc_start: 0.8768 (tpt) cc_final: 0.8544 (tpp) REVERT: D 607 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7255 (tmm) REVERT: D 715 TRP cc_start: 0.8539 (t60) cc_final: 0.7846 (t60) outliers start: 8 outliers final: 0 residues processed: 145 average time/residue: 0.2469 time to fit residues: 61.3355 Evaluate side-chains 120 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 116 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 259 ASN B 316 GLN C 259 ASN D 259 ASN D 316 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 20132 Z= 0.302 Angle : 0.642 6.874 27368 Z= 0.324 Chirality : 0.039 0.124 3136 Planarity : 0.004 0.028 3372 Dihedral : 5.134 19.411 2656 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.19 % Allowed : 6.49 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.67 (0.16), residues: 2428 helix: 0.35 (0.13), residues: 1480 sheet: -2.64 (0.83), residues: 40 loop : -1.62 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 677 HIS 0.007 0.001 HIS D 313 PHE 0.014 0.002 PHE C 311 TYR 0.009 0.001 TYR D 471 ARG 0.003 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 2.316 Fit side-chains REVERT: A 271 TYR cc_start: 0.8462 (t80) cc_final: 0.8135 (t80) REVERT: B 270 MET cc_start: 0.8834 (tpt) cc_final: 0.8596 (tpp) REVERT: B 715 TRP cc_start: 0.8586 (t60) cc_final: 0.8080 (t60) REVERT: C 271 TYR cc_start: 0.8576 (t80) cc_final: 0.8244 (t80) REVERT: C 715 TRP cc_start: 0.8606 (t60) cc_final: 0.8104 (t60) REVERT: D 270 MET cc_start: 0.8840 (tpt) cc_final: 0.8598 (tpp) REVERT: D 715 TRP cc_start: 0.8580 (t60) cc_final: 0.8043 (t60) outliers start: 4 outliers final: 4 residues processed: 132 average time/residue: 0.2614 time to fit residues: 58.9032 Evaluate side-chains 109 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 0.1980 chunk 184 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 221 optimal weight: 9.9990 chunk 239 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 316 GLN B 259 ASN C 259 ASN C 316 GLN D 259 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20132 Z= 0.125 Angle : 0.517 7.814 27368 Z= 0.252 Chirality : 0.036 0.124 3136 Planarity : 0.003 0.025 3372 Dihedral : 4.391 17.437 2656 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.12 (0.17), residues: 2428 helix: 0.91 (0.13), residues: 1504 sheet: -2.64 (0.85), residues: 40 loop : -1.69 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 715 HIS 0.005 0.001 HIS C 313 PHE 0.013 0.001 PHE A 601 TYR 0.006 0.001 TYR C 471 ARG 0.003 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.362 Fit side-chains REVERT: A 271 TYR cc_start: 0.8487 (t80) cc_final: 0.8255 (t80) REVERT: A 308 ILE cc_start: 0.9110 (tp) cc_final: 0.8710 (tp) REVERT: A 372 MET cc_start: 0.8834 (tpp) cc_final: 0.8436 (tpp) REVERT: A 715 TRP cc_start: 0.8329 (t60) cc_final: 0.7971 (t60) REVERT: B 271 TYR cc_start: 0.8598 (t80) cc_final: 0.8298 (t80) REVERT: B 715 TRP cc_start: 0.8512 (t60) cc_final: 0.8292 (t60) REVERT: C 271 TYR cc_start: 0.8497 (t80) cc_final: 0.8271 (t80) REVERT: C 607 MET cc_start: 0.7399 (ttp) cc_final: 0.6916 (tmm) REVERT: C 715 TRP cc_start: 0.8520 (t60) cc_final: 0.8314 (t60) REVERT: D 271 TYR cc_start: 0.8600 (t80) cc_final: 0.8260 (t80) REVERT: D 715 TRP cc_start: 0.8466 (t60) cc_final: 0.8263 (t60) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2838 time to fit residues: 75.6125 Evaluate side-chains 119 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 30.0000 chunk 166 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 24 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 222 optimal weight: 8.9990 chunk 235 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 259 ASN C 259 ASN D 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20132 Z= 0.211 Angle : 0.558 7.397 27368 Z= 0.274 Chirality : 0.037 0.124 3136 Planarity : 0.003 0.023 3372 Dihedral : 4.395 17.962 2656 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2428 helix: 1.24 (0.14), residues: 1480 sheet: -2.82 (0.85), residues: 40 loop : -1.45 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 677 HIS 0.005 0.001 HIS C 313 PHE 0.014 0.001 PHE B 362 TYR 0.007 0.001 TYR A 515 ARG 0.002 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.227 Fit side-chains REVERT: A 271 TYR cc_start: 0.8550 (t80) cc_final: 0.8338 (t80) REVERT: A 715 TRP cc_start: 0.8492 (t60) cc_final: 0.7836 (t60) REVERT: B 271 TYR cc_start: 0.8491 (t80) cc_final: 0.8216 (t80) REVERT: B 715 TRP cc_start: 0.8579 (t60) cc_final: 0.8229 (t60) REVERT: C 271 TYR cc_start: 0.8561 (t80) cc_final: 0.8324 (t80) REVERT: C 715 TRP cc_start: 0.8564 (t60) cc_final: 0.8228 (t60) REVERT: D 271 TYR cc_start: 0.8492 (t80) cc_final: 0.8214 (t80) REVERT: D 715 TRP cc_start: 0.8570 (t60) cc_final: 0.8227 (t60) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2818 time to fit residues: 60.9942 Evaluate side-chains 106 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 175 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 316 GLN C 259 ASN D 316 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20132 Z= 0.217 Angle : 0.569 9.750 27368 Z= 0.277 Chirality : 0.037 0.134 3136 Planarity : 0.003 0.025 3372 Dihedral : 4.344 19.669 2656 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.48 (0.17), residues: 2428 helix: 1.40 (0.14), residues: 1480 sheet: -3.11 (0.83), residues: 40 loop : -1.36 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 677 HIS 0.005 0.001 HIS C 313 PHE 0.012 0.001 PHE B 540 TYR 0.008 0.001 TYR A 515 ARG 0.002 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.267 Fit side-chains REVERT: A 271 TYR cc_start: 0.8512 (t80) cc_final: 0.8291 (t80) REVERT: A 715 TRP cc_start: 0.8559 (t60) cc_final: 0.7913 (t60) REVERT: B 271 TYR cc_start: 0.8503 (t80) cc_final: 0.8264 (t80) REVERT: B 715 TRP cc_start: 0.8599 (t60) cc_final: 0.8192 (t60) REVERT: C 271 TYR cc_start: 0.8540 (t80) cc_final: 0.8303 (t80) REVERT: C 715 TRP cc_start: 0.8586 (t60) cc_final: 0.8189 (t60) REVERT: D 271 TYR cc_start: 0.8514 (t80) cc_final: 0.8267 (t80) REVERT: D 715 TRP cc_start: 0.8587 (t60) cc_final: 0.8188 (t60) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2618 time to fit residues: 60.5898 Evaluate side-chains 108 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 138 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 0.0170 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN C 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20132 Z= 0.155 Angle : 0.517 7.519 27368 Z= 0.250 Chirality : 0.036 0.117 3136 Planarity : 0.002 0.023 3372 Dihedral : 4.115 17.535 2656 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.61 (0.17), residues: 2428 helix: 1.51 (0.14), residues: 1484 sheet: -3.21 (0.83), residues: 40 loop : -1.32 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 386 HIS 0.004 0.001 HIS C 313 PHE 0.010 0.001 PHE A 362 TYR 0.007 0.001 TYR A 497 ARG 0.002 0.000 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.135 Fit side-chains REVERT: A 715 TRP cc_start: 0.8553 (t60) cc_final: 0.7964 (t60) REVERT: B 271 TYR cc_start: 0.8567 (t80) cc_final: 0.8343 (t80) REVERT: B 715 TRP cc_start: 0.8572 (t60) cc_final: 0.8204 (t60) REVERT: C 271 TYR cc_start: 0.8453 (t80) cc_final: 0.8103 (t80) REVERT: C 715 TRP cc_start: 0.8584 (t60) cc_final: 0.8233 (t60) REVERT: D 271 TYR cc_start: 0.8545 (t80) cc_final: 0.8321 (t80) REVERT: D 715 TRP cc_start: 0.8601 (t60) cc_final: 0.8231 (t60) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2467 time to fit residues: 58.8639 Evaluate side-chains 107 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 133 optimal weight: 0.1980 chunk 198 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 chunk 147 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN B 263 ASN C 263 ASN D 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20132 Z= 0.144 Angle : 0.513 7.475 27368 Z= 0.246 Chirality : 0.036 0.174 3136 Planarity : 0.002 0.023 3372 Dihedral : 3.997 17.487 2656 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2428 helix: 1.64 (0.14), residues: 1480 sheet: -3.25 (0.83), residues: 40 loop : -1.30 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 657 HIS 0.004 0.001 HIS B 313 PHE 0.013 0.001 PHE A 601 TYR 0.012 0.001 TYR A 271 ARG 0.002 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.278 Fit side-chains REVERT: A 715 TRP cc_start: 0.8577 (t60) cc_final: 0.8097 (t60) REVERT: B 271 TYR cc_start: 0.8458 (t80) cc_final: 0.8139 (t80) REVERT: B 641 LEU cc_start: 0.9373 (mm) cc_final: 0.9131 (pp) REVERT: B 715 TRP cc_start: 0.8585 (t60) cc_final: 0.8209 (t60) REVERT: C 271 TYR cc_start: 0.8446 (t80) cc_final: 0.8195 (t80) REVERT: C 641 LEU cc_start: 0.9381 (mm) cc_final: 0.9149 (pp) REVERT: C 715 TRP cc_start: 0.8585 (t60) cc_final: 0.8269 (t60) REVERT: D 271 TYR cc_start: 0.8507 (t80) cc_final: 0.8203 (t80) REVERT: D 641 LEU cc_start: 0.9385 (mm) cc_final: 0.9155 (pp) REVERT: D 715 TRP cc_start: 0.8585 (t60) cc_final: 0.8216 (t60) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2550 time to fit residues: 63.2680 Evaluate side-chains 116 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.4980 chunk 93 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 45 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN C 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20132 Z= 0.317 Angle : 0.652 6.927 27368 Z= 0.323 Chirality : 0.040 0.153 3136 Planarity : 0.003 0.026 3372 Dihedral : 4.508 19.619 2656 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.47 (0.17), residues: 2428 helix: 1.28 (0.13), residues: 1504 sheet: -3.45 (0.77), residues: 40 loop : -1.18 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 677 HIS 0.006 0.001 HIS A 234 PHE 0.018 0.002 PHE B 456 TYR 0.012 0.001 TYR A 497 ARG 0.004 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.515 Fit side-chains REVERT: A 640 MET cc_start: 0.8250 (tpt) cc_final: 0.7942 (ttt) REVERT: A 715 TRP cc_start: 0.8659 (t60) cc_final: 0.8371 (t60) REVERT: B 271 TYR cc_start: 0.8543 (t80) cc_final: 0.8246 (t80) REVERT: B 715 TRP cc_start: 0.8720 (t60) cc_final: 0.8259 (t60) REVERT: C 271 TYR cc_start: 0.8510 (t80) cc_final: 0.8224 (t80) REVERT: C 715 TRP cc_start: 0.8706 (t60) cc_final: 0.8252 (t60) REVERT: D 271 TYR cc_start: 0.8512 (t80) cc_final: 0.8239 (t80) REVERT: D 715 TRP cc_start: 0.8718 (t60) cc_final: 0.8252 (t60) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2518 time to fit residues: 55.0355 Evaluate side-chains 102 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 6.9990 chunk 225 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 chunk 198 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20132 Z= 0.166 Angle : 0.561 7.520 27368 Z= 0.267 Chirality : 0.038 0.172 3136 Planarity : 0.003 0.021 3372 Dihedral : 4.201 18.567 2656 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.66 (0.17), residues: 2428 helix: 1.47 (0.14), residues: 1504 sheet: -3.41 (0.79), residues: 40 loop : -1.19 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 386 HIS 0.005 0.001 HIS B 438 PHE 0.020 0.001 PHE C 491 TYR 0.008 0.001 TYR A 271 ARG 0.002 0.000 ARG D 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.268 Fit side-chains REVERT: A 270 MET cc_start: 0.8786 (mmm) cc_final: 0.8357 (tmm) REVERT: A 640 MET cc_start: 0.8125 (tpt) cc_final: 0.7788 (ttt) REVERT: A 715 TRP cc_start: 0.8639 (t60) cc_final: 0.8099 (t60) REVERT: B 271 TYR cc_start: 0.8544 (t80) cc_final: 0.8316 (t80) REVERT: B 640 MET cc_start: 0.8222 (tpt) cc_final: 0.8021 (ttt) REVERT: B 715 TRP cc_start: 0.8572 (t60) cc_final: 0.8244 (t60) REVERT: C 271 TYR cc_start: 0.8541 (t80) cc_final: 0.8307 (t80) REVERT: C 640 MET cc_start: 0.8188 (tpt) cc_final: 0.7985 (ttt) REVERT: C 715 TRP cc_start: 0.8599 (t60) cc_final: 0.8282 (t60) REVERT: D 271 TYR cc_start: 0.8541 (t80) cc_final: 0.8326 (t80) REVERT: D 640 MET cc_start: 0.8178 (tpt) cc_final: 0.7972 (ttt) REVERT: D 715 TRP cc_start: 0.8567 (t60) cc_final: 0.8248 (t60) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2563 time to fit residues: 61.1271 Evaluate side-chains 109 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 243 optimal weight: 3.9990 chunk 223 optimal weight: 9.9990 chunk 193 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20132 Z= 0.243 Angle : 0.603 7.019 27368 Z= 0.294 Chirality : 0.038 0.129 3136 Planarity : 0.003 0.024 3372 Dihedral : 4.343 19.850 2656 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2428 helix: 1.40 (0.13), residues: 1508 sheet: -3.55 (0.76), residues: 40 loop : -1.19 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 677 HIS 0.005 0.001 HIS C 438 PHE 0.017 0.001 PHE C 491 TYR 0.011 0.001 TYR B 515 ARG 0.003 0.000 ARG A 458 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.226 Fit side-chains REVERT: A 270 MET cc_start: 0.8853 (mmm) cc_final: 0.8451 (tmm) REVERT: A 640 MET cc_start: 0.8161 (tpt) cc_final: 0.7709 (tpt) REVERT: A 715 TRP cc_start: 0.8652 (t60) cc_final: 0.8107 (t60) REVERT: B 271 TYR cc_start: 0.8657 (t80) cc_final: 0.8425 (t80) REVERT: B 641 LEU cc_start: 0.9374 (mm) cc_final: 0.9164 (pp) REVERT: B 715 TRP cc_start: 0.8676 (t60) cc_final: 0.8293 (t60) REVERT: C 271 TYR cc_start: 0.8652 (t80) cc_final: 0.8415 (t80) REVERT: C 715 TRP cc_start: 0.8670 (t60) cc_final: 0.8287 (t60) REVERT: D 271 TYR cc_start: 0.8645 (t80) cc_final: 0.8414 (t80) REVERT: D 715 TRP cc_start: 0.8676 (t60) cc_final: 0.8285 (t60) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2660 time to fit residues: 60.5197 Evaluate side-chains 111 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 28 optimal weight: 0.0070 chunk 53 optimal weight: 9.9990 chunk 193 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 overall best weight: 1.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.065286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.056365 restraints weight = 109031.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057667 restraints weight = 66226.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058530 restraints weight = 45485.276| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20132 Z= 0.149 Angle : 0.552 7.639 27368 Z= 0.261 Chirality : 0.037 0.175 3136 Planarity : 0.003 0.024 3372 Dihedral : 4.071 18.321 2656 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.76 (0.17), residues: 2428 helix: 1.60 (0.14), residues: 1504 sheet: -3.55 (0.80), residues: 40 loop : -1.24 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 657 HIS 0.005 0.001 HIS D 438 PHE 0.015 0.001 PHE D 491 TYR 0.008 0.001 TYR A 271 ARG 0.002 0.000 ARG D 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2738.55 seconds wall clock time: 51 minutes 56.26 seconds (3116.26 seconds total)