Starting phenix.real_space_refine on Sun Feb 18 07:24:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0s_13751/02_2024/7q0s_13751_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0s_13751/02_2024/7q0s_13751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0s_13751/02_2024/7q0s_13751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0s_13751/02_2024/7q0s_13751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0s_13751/02_2024/7q0s_13751_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0s_13751/02_2024/7q0s_13751_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 104 5.16 5 C 13540 2.51 5 N 3628 2.21 5 O 3914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 60": "OD1" <-> "OD2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 60": "OD1" <-> "OD2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "E ASP 331": "OD1" <-> "OD2" Residue "F ASP 331": "OD1" <-> "OD2" Residue "G ASP 331": "OD1" <-> "OD2" Residue "H ASP 331": "OD1" <-> "OD2" 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: 21192 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5002 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5006 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain breaks: 2 Chain: "C" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5006 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain breaks: 2 Chain: "D" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5002 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain breaks: 2 Chain: "E" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "F" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "G" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "H" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.97, per 1000 atoms: 0.61 Number of scatterers: 21192 At special positions: 0 Unit cell: (124.89, 114.03, 140.094, 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 104 16.00 P 6 15.00 O 3914 8.00 N 3628 7.00 C 13540 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: 9.91 Conformation dependent library (CDL) restraints added in 4.4 seconds 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 12 sheets defined 49.9% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.00 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 removed outlier: 4.397A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 76 Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 123 through 137 removed outlier: 3.653A pdb=" N LEU A 126 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU A 127 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS A 137 " --> pdb=" O TRP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 168 Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.992A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 295 through 311 Processing helix chain 'A' and resid 339 through 356 Processing helix chain 'A' and resid 377 through 409 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 422 through 435 Processing helix chain 'A' and resid 455 through 463 Processing helix chain 'A' and resid 493 through 499 removed outlier: 3.532A pdb=" N GLY A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 522 Processing helix chain 'A' and resid 533 through 541 Processing helix chain 'A' and resid 545 through 548 Processing helix chain 'A' and resid 560 through 575 Processing helix chain 'A' and resid 579 through 596 removed outlier: 3.924A pdb=" N LEU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER A 593 " --> pdb=" O THR A 589 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP A 594 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 616 removed outlier: 5.489A pdb=" N ARG A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 58 removed outlier: 4.397A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 76 Processing helix chain 'B' and resid 85 through 96 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 123 through 137 removed outlier: 3.653A pdb=" N LEU B 126 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU B 127 " --> pdb=" O TRP B 124 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS B 130 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS B 137 " --> pdb=" O TRP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 168 Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'B' and resid 208 through 214 removed outlier: 3.992A pdb=" N TYR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 229 through 235 Processing helix chain 'B' and resid 239 through 250 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 295 through 311 Processing helix chain 'B' and resid 339 through 356 Processing helix chain 'B' and resid 377 through 409 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 422 through 435 Processing helix chain 'B' and resid 455 through 463 Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.533A pdb=" N GLY B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 522 Processing helix chain 'B' and resid 533 through 541 Processing helix chain 'B' and resid 545 through 548 Processing helix chain 'B' and resid 560 through 575 Processing helix chain 'B' and resid 579 through 596 removed outlier: 3.924A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER B 593 " --> pdb=" O THR B 589 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP B 594 " --> pdb=" O GLU B 590 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 616 removed outlier: 5.489A pdb=" N ARG B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 58 removed outlier: 4.397A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 76 Processing helix chain 'C' and resid 85 through 96 Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.653A pdb=" N LEU C 126 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU C 127 " --> pdb=" O TRP C 124 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS C 130 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS C 137 " --> pdb=" O TRP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 168 Processing helix chain 'C' and resid 185 through 193 Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.991A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 229 through 235 Processing helix chain 'C' and resid 239 through 250 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 295 through 311 Processing helix chain 'C' and resid 339 through 356 Processing helix chain 'C' and resid 377 through 409 Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 422 through 435 Processing helix chain 'C' and resid 455 through 463 Processing helix chain 'C' and resid 493 through 499 removed outlier: 3.533A pdb=" N GLY C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 522 Processing helix chain 'C' and resid 533 through 541 Processing helix chain 'C' and resid 545 through 548 Processing helix chain 'C' and resid 560 through 575 Processing helix chain 'C' and resid 579 through 596 removed outlier: 3.924A pdb=" N LEU C 592 " --> pdb=" O ARG C 588 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER C 593 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP C 594 " --> pdb=" O GLU C 590 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 616 removed outlier: 5.488A pdb=" N ARG C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 58 removed outlier: 4.397A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 123 through 137 removed outlier: 3.653A pdb=" N LEU D 126 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU D 127 " --> pdb=" O TRP D 124 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS D 130 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS D 137 " --> pdb=" O TRP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 168 Processing helix chain 'D' and resid 185 through 193 Processing helix chain 'D' and resid 208 through 214 removed outlier: 3.993A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 229 through 235 Processing helix chain 'D' and resid 239 through 250 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 284 through 288 Processing helix chain 'D' and resid 295 through 311 Processing helix chain 'D' and resid 339 through 356 Processing helix chain 'D' and resid 377 through 409 Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 422 through 435 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 493 through 499 removed outlier: 3.532A pdb=" N GLY D 499 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 522 Processing helix chain 'D' and resid 533 through 541 Processing helix chain 'D' and resid 545 through 548 Processing helix chain 'D' and resid 560 through 575 Processing helix chain 'D' and resid 579 through 596 removed outlier: 3.923A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER D 593 " --> pdb=" O THR D 589 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP D 594 " --> pdb=" O GLU D 590 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU D 595 " --> pdb=" O ARG D 591 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 616 removed outlier: 5.488A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 327 Processing helix chain 'E' and resid 338 through 348 removed outlier: 4.540A pdb=" N THR E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 327 Processing helix chain 'F' and resid 338 through 348 removed outlier: 4.539A pdb=" N THR F 347 " --> pdb=" O ARG F 343 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 327 Processing helix chain 'G' and resid 338 through 348 removed outlier: 4.540A pdb=" N THR G 347 " --> pdb=" O ARG G 343 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 327 Processing helix chain 'H' and resid 338 through 348 removed outlier: 4.540A pdb=" N THR H 347 " --> pdb=" O ARG H 343 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR H 348 " --> pdb=" O LYS H 344 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.709A pdb=" N LEU A 113 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N PHE A 63 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 29 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL A 65 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N HIS A 174 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE A 30 " --> pdb=" O HIS A 174 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 176 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 32 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS A 178 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 254 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR A 204 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR A 256 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 323 through 329 removed outlier: 6.319A pdb=" N THR A 361 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE A 326 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL A 363 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE A 328 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE A 365 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 526 through 529 Processing sheet with id= D, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.709A pdb=" N LEU B 113 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N PHE B 63 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 29 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL B 65 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU B 31 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N HIS B 174 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE B 30 " --> pdb=" O HIS B 174 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 176 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL B 32 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS B 178 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 254 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR B 204 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR B 256 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 323 through 329 removed outlier: 6.319A pdb=" N THR B 361 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE B 326 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 363 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE B 328 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE B 365 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 526 through 529 Processing sheet with id= G, first strand: chain 'C' and resid 77 through 79 removed outlier: 3.709A pdb=" N LEU C 113 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N PHE C 63 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 29 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL C 65 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N HIS C 174 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N PHE C 30 " --> pdb=" O HIS C 174 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 176 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL C 32 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS C 178 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 254 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR C 204 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR C 256 " --> pdb=" O THR C 204 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 323 through 329 removed outlier: 6.319A pdb=" N THR C 361 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE C 326 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL C 363 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE C 328 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE C 365 " --> pdb=" O ILE C 328 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 526 through 529 Processing sheet with id= J, first strand: chain 'D' and resid 77 through 79 removed outlier: 3.709A pdb=" N LEU D 113 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N PHE D 63 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU D 29 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL D 65 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU D 31 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS D 174 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE D 30 " --> pdb=" O HIS D 174 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL D 176 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL D 32 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS D 178 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL D 254 " --> pdb=" O PHE D 202 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR D 204 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR D 256 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 323 through 329 removed outlier: 6.318A pdb=" N THR D 361 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE D 326 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL D 363 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE D 328 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE D 365 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 526 through 529 880 hydrogen bonds defined for protein. 2532 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: 6.53 Time building geometry restraints manager: 10.56 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: 6881 1.34 - 1.46: 4033 1.46 - 1.58: 10658 1.58 - 1.69: 12 1.69 - 1.81: 156 Bond restraints: 21740 Sorted by residual: bond pdb=" O6 G6P A 801 " pdb=" P G6P A 801 " ideal model delta sigma weight residual 1.722 1.646 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" O6 G6P C 801 " pdb=" P G6P C 801 " ideal model delta sigma weight residual 1.722 1.647 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O6 G6P B 801 " pdb=" P G6P B 801 " ideal model delta sigma weight residual 1.722 1.647 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O6 G6P D 801 " pdb=" P G6P D 801 " ideal model delta sigma weight residual 1.722 1.647 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C1 G6P C 801 " pdb=" O5 G6P C 801 " ideal model delta sigma weight residual 1.401 1.462 -0.061 2.00e-02 2.50e+03 9.41e+00 ... (remaining 21735 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.52: 552 106.52 - 113.38: 11385 113.38 - 120.25: 8180 120.25 - 127.11: 9073 127.11 - 133.97: 268 Bond angle restraints: 29458 Sorted by residual: angle pdb=" N ILE D 238 " pdb=" CA ILE D 238 " pdb=" C ILE D 238 " ideal model delta sigma weight residual 111.77 107.00 4.77 1.04e+00 9.25e-01 2.10e+01 angle pdb=" N ILE C 238 " pdb=" CA ILE C 238 " pdb=" C ILE C 238 " ideal model delta sigma weight residual 111.77 107.01 4.76 1.04e+00 9.25e-01 2.09e+01 angle pdb=" N ILE B 238 " pdb=" CA ILE B 238 " pdb=" C ILE B 238 " ideal model delta sigma weight residual 111.77 107.02 4.75 1.04e+00 9.25e-01 2.09e+01 angle pdb=" N ILE A 238 " pdb=" CA ILE A 238 " pdb=" C ILE A 238 " ideal model delta sigma weight residual 111.77 107.05 4.72 1.04e+00 9.25e-01 2.06e+01 angle pdb=" N GLU E 326 " pdb=" CA GLU E 326 " pdb=" CB GLU E 326 " ideal model delta sigma weight residual 110.16 115.64 -5.48 1.48e+00 4.57e-01 1.37e+01 ... (remaining 29453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.68: 12231 28.68 - 57.37: 502 57.37 - 86.05: 59 86.05 - 114.73: 40 114.73 - 143.41: 20 Dihedral angle restraints: 12852 sinusoidal: 5252 harmonic: 7600 Sorted by residual: dihedral pdb=" C3 G6P C 801 " pdb=" C1 G6P C 801 " pdb=" C2 G6P C 801 " pdb=" O1 G6P C 801 " ideal model delta sinusoidal sigma weight residual 74.65 -68.76 143.41 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C3 G6P B 801 " pdb=" C1 G6P B 801 " pdb=" C2 G6P B 801 " pdb=" O1 G6P B 801 " ideal model delta sinusoidal sigma weight residual 74.65 -68.76 143.41 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C3 G6P D 801 " pdb=" C1 G6P D 801 " pdb=" C2 G6P D 801 " pdb=" O1 G6P D 801 " ideal model delta sinusoidal sigma weight residual 74.65 -68.74 143.39 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 12849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 3124 1.020 - 2.039: 0 2.039 - 3.059: 0 3.059 - 4.079: 0 4.079 - 5.099: 16 Chirality restraints: 3140 Sorted by residual: chirality pdb=" C5 G6P C 801 " pdb=" C4 G6P C 801 " pdb=" C6 G6P C 801 " pdb=" O5 G6P C 801 " both_signs ideal model delta sigma weight residual False -2.51 2.59 -5.10 2.00e-01 2.50e+01 6.50e+02 chirality pdb=" C5 G6P D 801 " pdb=" C4 G6P D 801 " pdb=" C6 G6P D 801 " pdb=" O5 G6P D 801 " both_signs ideal model delta sigma weight residual False -2.51 2.58 -5.10 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C5 G6P A 801 " pdb=" C4 G6P A 801 " pdb=" C6 G6P A 801 " pdb=" O5 G6P A 801 " both_signs ideal model delta sigma weight residual False -2.51 2.58 -5.10 2.00e-01 2.50e+01 6.49e+02 ... (remaining 3137 not shown) Planarity restraints: 3792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 433 " 0.009 2.00e-02 2.50e+03 1.72e-02 5.17e+00 pdb=" CG PHE B 433 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE B 433 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 433 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE B 433 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 433 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 433 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 433 " -0.009 2.00e-02 2.50e+03 1.71e-02 5.11e+00 pdb=" CG PHE C 433 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE C 433 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 433 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE C 433 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 433 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 433 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 433 " 0.009 2.00e-02 2.50e+03 1.71e-02 5.10e+00 pdb=" CG PHE D 433 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE D 433 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE D 433 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE D 433 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 433 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 433 " -0.001 2.00e-02 2.50e+03 ... (remaining 3789 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1980 2.74 - 3.28: 21382 3.28 - 3.82: 35588 3.82 - 4.36: 40664 4.36 - 4.90: 70827 Nonbonded interactions: 170441 Sorted by model distance: nonbonded pdb=" O TYR E 332 " pdb=" OG SER E 337 " model vdw 2.203 2.440 nonbonded pdb=" O TYR G 332 " pdb=" OG SER G 337 " model vdw 2.204 2.440 nonbonded pdb=" O TYR H 332 " pdb=" OG SER H 337 " model vdw 2.204 2.440 nonbonded pdb=" O TYR F 332 " pdb=" OG SER F 337 " model vdw 2.204 2.440 nonbonded pdb=" OG SER E 318 " pdb=" OE1 GLU E 319 " model vdw 2.244 2.440 ... (remaining 170436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 640 or resid 642 or resid 801)) selection = (chain 'B' and (resid 13 through 640 or resid 642 or resid 801)) selection = (chain 'C' and (resid 13 through 640 or resid 642 or resid 801)) selection = (chain 'D' and (resid 13 through 640 or resid 642 or resid 801)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.710 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: 6.760 Check model and map are aligned: 0.310 Set scattering table: 0.210 Process input model: 64.510 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.190 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21740 Z= 0.218 Angle : 0.634 9.094 29458 Z= 0.344 Chirality : 0.344 5.099 3140 Planarity : 0.004 0.050 3792 Dihedral : 18.143 143.415 7956 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.25 % Allowed : 1.56 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2576 helix: 1.53 (0.15), residues: 1320 sheet: -0.37 (0.27), residues: 360 loop : -0.97 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 58 HIS 0.007 0.001 HIS B 610 PHE 0.038 0.001 PHE B 433 TYR 0.023 0.002 TYR D 68 ARG 0.005 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 351 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8101 (t80) cc_final: 0.7754 (t80) REVERT: A 611 MET cc_start: 0.8864 (mmt) cc_final: 0.8612 (mmt) REVERT: B 88 LYS cc_start: 0.9004 (mmpt) cc_final: 0.8566 (mmmt) REVERT: B 303 ARG cc_start: 0.6505 (ttt180) cc_final: 0.6271 (ttt180) REVERT: C 68 TYR cc_start: 0.8075 (t80) cc_final: 0.7789 (t80) REVERT: C 88 LYS cc_start: 0.8980 (mmpt) cc_final: 0.8487 (mmmt) REVERT: D 35 GLU cc_start: 0.7356 (pt0) cc_final: 0.7147 (pt0) REVERT: D 68 TYR cc_start: 0.8094 (t80) cc_final: 0.7723 (t80) REVERT: D 76 GLN cc_start: 0.7437 (pt0) cc_final: 0.7212 (pt0) REVERT: D 88 LYS cc_start: 0.9017 (mmpt) cc_final: 0.8466 (mmmt) REVERT: D 611 MET cc_start: 0.8902 (mmt) cc_final: 0.8656 (mmt) outliers start: 28 outliers final: 8 residues processed: 357 average time/residue: 0.3326 time to fit residues: 184.8200 Evaluate side-chains 266 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 258 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 531 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 109 optimal weight: 0.0070 chunk 67 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 236 optimal weight: 0.5980 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS B 76 GLN ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 HIS C 76 GLN ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 HIS D 138 ASN ** D 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 HIS E 340 ASN F 340 ASN G 340 ASN H 340 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21740 Z= 0.241 Angle : 0.576 8.007 29458 Z= 0.289 Chirality : 0.043 0.197 3140 Planarity : 0.004 0.056 3792 Dihedral : 5.084 56.785 2982 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.34 % Allowed : 8.37 % Favored : 90.29 % 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: 0.82 (0.17), residues: 2576 helix: 1.88 (0.15), residues: 1278 sheet: -0.51 (0.28), residues: 292 loop : -0.87 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 182 HIS 0.006 0.001 HIS B 610 PHE 0.025 0.002 PHE B 433 TYR 0.018 0.002 TYR B 68 ARG 0.007 0.001 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 311 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.5317 (t60) cc_final: 0.5064 (t-100) REVERT: A 94 MET cc_start: 0.8051 (mmt) cc_final: 0.7013 (mmm) REVERT: A 303 ARG cc_start: 0.7032 (ttt180) cc_final: 0.6769 (ttt180) REVERT: A 505 PHE cc_start: 0.8195 (m-80) cc_final: 0.7941 (m-80) REVERT: A 522 MET cc_start: 0.8608 (tpp) cc_final: 0.8081 (mtp) REVERT: B 88 LYS cc_start: 0.9003 (mmpt) cc_final: 0.8558 (mmmt) REVERT: B 94 MET cc_start: 0.8053 (mmt) cc_final: 0.6978 (mmm) REVERT: B 522 MET cc_start: 0.8652 (tpp) cc_final: 0.8155 (mtp) REVERT: C 22 PHE cc_start: 0.6061 (t80) cc_final: 0.5699 (t80) REVERT: C 88 LYS cc_start: 0.9006 (mmpt) cc_final: 0.8422 (mmmt) REVERT: C 94 MET cc_start: 0.8050 (mmt) cc_final: 0.7007 (mmm) REVERT: C 244 MET cc_start: 0.8672 (ptp) cc_final: 0.8291 (ptp) REVERT: C 303 ARG cc_start: 0.6962 (ttt180) cc_final: 0.6621 (ttt180) REVERT: C 522 MET cc_start: 0.8686 (tpp) cc_final: 0.8222 (mtp) REVERT: C 611 MET cc_start: 0.8846 (mmt) cc_final: 0.8482 (mmp) REVERT: D 35 GLU cc_start: 0.7261 (pt0) cc_final: 0.6993 (pt0) REVERT: D 88 LYS cc_start: 0.9005 (mmpt) cc_final: 0.8408 (mmmt) REVERT: D 94 MET cc_start: 0.8059 (mmt) cc_final: 0.7032 (mmm) REVERT: D 303 ARG cc_start: 0.6961 (ttt180) cc_final: 0.6714 (ttt180) REVERT: D 505 PHE cc_start: 0.8197 (m-80) cc_final: 0.7960 (m-80) REVERT: D 522 MET cc_start: 0.8665 (tpp) cc_final: 0.8133 (mtp) REVERT: F 343 ARG cc_start: 0.8305 (ptp-170) cc_final: 0.8057 (ptt-90) REVERT: F 347 THR cc_start: 0.9144 (p) cc_final: 0.8855 (t) outliers start: 30 outliers final: 22 residues processed: 330 average time/residue: 0.3405 time to fit residues: 175.1904 Evaluate side-chains 288 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 266 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain G residue 332 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 196 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 255 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS B 76 GLN B 138 ASN ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 138 ASN ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 HIS D 76 GLN ** D 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 HIS E 340 ASN G 340 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21740 Z= 0.170 Angle : 0.496 8.273 29458 Z= 0.252 Chirality : 0.040 0.149 3140 Planarity : 0.003 0.030 3792 Dihedral : 4.723 52.613 2970 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.83 % Allowed : 12.82 % Favored : 85.35 % 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: 0.82 (0.17), residues: 2576 helix: 1.84 (0.15), residues: 1292 sheet: -0.57 (0.27), residues: 290 loop : -0.83 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.002 0.001 HIS C 180 PHE 0.016 0.001 PHE B 505 TYR 0.018 0.001 TYR B 493 ARG 0.005 0.000 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 304 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.5210 (t60) cc_final: 0.4925 (t-100) REVERT: A 94 MET cc_start: 0.8045 (mmt) cc_final: 0.7704 (mmt) REVERT: A 188 LEU cc_start: 0.8587 (tt) cc_final: 0.8341 (tt) REVERT: A 303 ARG cc_start: 0.7043 (ttt180) cc_final: 0.6661 (ttt180) REVERT: A 613 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8531 (tp) REVERT: B 94 MET cc_start: 0.8063 (mmt) cc_final: 0.7667 (mmt) REVERT: B 188 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8384 (tp) REVERT: B 457 LEU cc_start: 0.8921 (mt) cc_final: 0.8720 (mt) REVERT: B 522 MET cc_start: 0.8678 (tpp) cc_final: 0.8152 (mtp) REVERT: C 94 MET cc_start: 0.8061 (mmt) cc_final: 0.7682 (mmt) REVERT: C 244 MET cc_start: 0.8562 (ptp) cc_final: 0.8216 (ptp) REVERT: C 303 ARG cc_start: 0.7097 (ttt180) cc_final: 0.6695 (ttt180) REVERT: D 22 PHE cc_start: 0.5907 (t80) cc_final: 0.5706 (t80) REVERT: D 88 LYS cc_start: 0.9108 (mmpt) cc_final: 0.8513 (mmmt) REVERT: D 94 MET cc_start: 0.8055 (mmt) cc_final: 0.7715 (mmt) REVERT: F 333 MET cc_start: 0.9086 (mmt) cc_final: 0.8633 (mpp) outliers start: 41 outliers final: 27 residues processed: 323 average time/residue: 0.3071 time to fit residues: 156.2121 Evaluate side-chains 292 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 263 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain G residue 332 TYR Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 237 optimal weight: 3.9990 chunk 251 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 178 HIS B 76 GLN B 178 HIS B 240 HIS ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS D 178 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 21740 Z= 0.366 Angle : 0.628 8.045 29458 Z= 0.323 Chirality : 0.044 0.150 3140 Planarity : 0.004 0.039 3792 Dihedral : 5.545 58.960 2970 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.76 % Allowed : 14.47 % Favored : 82.77 % 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: 0.14 (0.16), residues: 2576 helix: 1.50 (0.14), residues: 1290 sheet: -1.02 (0.25), residues: 316 loop : -1.44 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 182 HIS 0.008 0.002 HIS D 180 PHE 0.020 0.002 PHE C 375 TYR 0.015 0.002 TYR A 102 ARG 0.006 0.001 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 278 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.5365 (t60) cc_final: 0.5062 (t-100) REVERT: A 22 PHE cc_start: 0.6523 (t80) cc_final: 0.5825 (t80) REVERT: A 88 LYS cc_start: 0.9062 (mmpt) cc_final: 0.8551 (mmtt) REVERT: A 94 MET cc_start: 0.8388 (mmt) cc_final: 0.7941 (mmt) REVERT: A 265 GLU cc_start: 0.7872 (pt0) cc_final: 0.7629 (pt0) REVERT: A 303 ARG cc_start: 0.7016 (ttt180) cc_final: 0.6689 (ttm-80) REVERT: A 416 MET cc_start: 0.7952 (tpp) cc_final: 0.7573 (tpp) REVERT: A 522 MET cc_start: 0.8755 (tpp) cc_final: 0.8404 (mtp) REVERT: B 94 MET cc_start: 0.8385 (mmt) cc_final: 0.7935 (mmt) REVERT: B 265 GLU cc_start: 0.7948 (pt0) cc_final: 0.7741 (pt0) REVERT: B 416 MET cc_start: 0.7849 (tpp) cc_final: 0.7474 (tpp) REVERT: B 522 MET cc_start: 0.8734 (tpp) cc_final: 0.8466 (mtp) REVERT: C 31 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: C 94 MET cc_start: 0.8375 (mmt) cc_final: 0.7942 (mmt) REVERT: C 303 ARG cc_start: 0.7016 (ttt180) cc_final: 0.6761 (ttm-80) REVERT: C 522 MET cc_start: 0.8769 (tpp) cc_final: 0.8425 (mtp) REVERT: D 22 PHE cc_start: 0.6360 (t80) cc_final: 0.5999 (t80) REVERT: D 88 LYS cc_start: 0.9067 (mmpt) cc_final: 0.8554 (mmtt) REVERT: D 94 MET cc_start: 0.8362 (mmt) cc_final: 0.7918 (mmt) REVERT: D 303 ARG cc_start: 0.7003 (ttt180) cc_final: 0.6724 (ttm-80) REVERT: D 522 MET cc_start: 0.8757 (tpp) cc_final: 0.8388 (mtp) REVERT: F 333 MET cc_start: 0.9184 (mmt) cc_final: 0.8639 (pmm) REVERT: H 333 MET cc_start: 0.9226 (mmt) cc_final: 0.8512 (pmm) outliers start: 62 outliers final: 52 residues processed: 319 average time/residue: 0.3257 time to fit residues: 161.5141 Evaluate side-chains 303 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 250 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain E residue 325 TRP Chi-restraints excluded: chain F residue 325 TRP Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain G residue 325 TRP Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain H residue 325 TRP Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 0 optimal weight: 10.9990 chunk 128 optimal weight: 0.9980 chunk 225 optimal weight: 0.6980 chunk 63 optimal weight: 0.0970 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 223 ASN B 76 GLN B 223 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN D 223 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21740 Z= 0.173 Angle : 0.509 7.662 29458 Z= 0.259 Chirality : 0.040 0.146 3140 Planarity : 0.003 0.035 3792 Dihedral : 5.126 57.719 2970 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.67 % Allowed : 16.34 % Favored : 80.99 % 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: 0.52 (0.17), residues: 2576 helix: 1.81 (0.15), residues: 1286 sheet: -0.94 (0.24), residues: 318 loop : -1.22 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 134 HIS 0.003 0.001 HIS B 180 PHE 0.015 0.001 PHE B 505 TYR 0.014 0.001 TYR C 493 ARG 0.004 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 293 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.5269 (t60) cc_final: 0.5021 (t-100) REVERT: A 22 PHE cc_start: 0.6471 (t80) cc_final: 0.6269 (t80) REVERT: A 94 MET cc_start: 0.8247 (mmt) cc_final: 0.7791 (mmt) REVERT: A 306 GLU cc_start: 0.8435 (tp30) cc_final: 0.8050 (mm-30) REVERT: A 416 MET cc_start: 0.7754 (tpp) cc_final: 0.7312 (tpp) REVERT: A 590 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6998 (mt-10) REVERT: B 94 MET cc_start: 0.8242 (mmt) cc_final: 0.7751 (mmt) REVERT: B 265 GLU cc_start: 0.7921 (pt0) cc_final: 0.7628 (pt0) REVERT: B 306 GLU cc_start: 0.8493 (tp30) cc_final: 0.8062 (mm-30) REVERT: C 94 MET cc_start: 0.8242 (mmt) cc_final: 0.7782 (mmt) REVERT: D 22 PHE cc_start: 0.6410 (t80) cc_final: 0.6050 (t80) REVERT: D 94 MET cc_start: 0.8184 (mmt) cc_final: 0.7737 (mmt) REVERT: D 306 GLU cc_start: 0.8429 (tp30) cc_final: 0.8036 (mm-30) REVERT: D 590 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6959 (mt-10) REVERT: F 333 MET cc_start: 0.9109 (mmt) cc_final: 0.8681 (pmm) outliers start: 60 outliers final: 45 residues processed: 330 average time/residue: 0.3422 time to fit residues: 174.9292 Evaluate side-chains 302 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 257 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 548 TYR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain E residue 325 TRP Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain F residue 325 TRP Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 325 TRP Chi-restraints excluded: chain G residue 332 TYR Chi-restraints excluded: chain H residue 325 TRP Chi-restraints excluded: chain H residue 332 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 21740 Z= 0.534 Angle : 0.752 10.172 29458 Z= 0.387 Chirality : 0.048 0.173 3140 Planarity : 0.005 0.046 3792 Dihedral : 5.928 59.139 2970 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 94.99 % Rotamer: Outliers : 3.65 % Allowed : 17.19 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2576 helix: 1.01 (0.14), residues: 1286 sheet: -1.45 (0.26), residues: 304 loop : -1.94 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 182 HIS 0.015 0.003 HIS A 180 PHE 0.022 0.003 PHE C 496 TYR 0.018 0.002 TYR A 493 ARG 0.011 0.001 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 264 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.5308 (t60) cc_final: 0.5031 (t-100) REVERT: A 22 PHE cc_start: 0.6854 (t80) cc_final: 0.6288 (t80) REVERT: A 88 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8575 (mmtt) REVERT: A 94 MET cc_start: 0.8565 (mmt) cc_final: 0.8063 (mmt) REVERT: A 282 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8478 (pp) REVERT: A 306 GLU cc_start: 0.8472 (tp30) cc_final: 0.8222 (mm-30) REVERT: A 522 MET cc_start: 0.8767 (tpp) cc_final: 0.8477 (mtp) REVERT: B 94 MET cc_start: 0.8522 (mmt) cc_final: 0.8024 (mmt) REVERT: B 265 GLU cc_start: 0.7996 (pt0) cc_final: 0.7731 (pt0) REVERT: B 306 GLU cc_start: 0.8624 (tp30) cc_final: 0.8366 (mm-30) REVERT: B 333 GLU cc_start: 0.8704 (mp0) cc_final: 0.8478 (mp0) REVERT: B 522 MET cc_start: 0.8759 (tpp) cc_final: 0.8416 (mtp) REVERT: C 94 MET cc_start: 0.8545 (mmt) cc_final: 0.8047 (mmt) REVERT: C 522 MET cc_start: 0.8751 (tpp) cc_final: 0.8444 (mtp) REVERT: D 35 GLU cc_start: 0.7030 (pt0) cc_final: 0.6813 (pt0) REVERT: D 94 MET cc_start: 0.8532 (mmt) cc_final: 0.8038 (mmt) REVERT: D 282 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8524 (pp) REVERT: D 306 GLU cc_start: 0.8463 (tp30) cc_final: 0.8211 (mm-30) REVERT: D 333 GLU cc_start: 0.8768 (mp0) cc_final: 0.8543 (mp0) REVERT: D 522 MET cc_start: 0.8775 (tpp) cc_final: 0.8429 (mtp) REVERT: F 333 MET cc_start: 0.9127 (mmt) cc_final: 0.8672 (pmm) outliers start: 82 outliers final: 72 residues processed: 328 average time/residue: 0.3336 time to fit residues: 171.1360 Evaluate side-chains 318 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 244 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 481 PHE Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain E residue 325 TRP Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain F residue 325 TRP Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain G residue 325 TRP Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain H residue 325 TRP Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 250 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21740 Z= 0.173 Angle : 0.528 8.348 29458 Z= 0.270 Chirality : 0.040 0.138 3140 Planarity : 0.003 0.036 3792 Dihedral : 5.305 58.770 2970 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.63 % Allowed : 18.17 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2576 helix: 1.73 (0.15), residues: 1258 sheet: -1.52 (0.24), residues: 334 loop : -1.38 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 182 HIS 0.005 0.001 HIS A 240 PHE 0.013 0.001 PHE A 334 TYR 0.008 0.001 TYR A 493 ARG 0.005 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 295 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.5219 (t60) cc_final: 0.4979 (t-100) REVERT: A 22 PHE cc_start: 0.6717 (t80) cc_final: 0.6204 (t80) REVERT: A 88 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8516 (mmtt) REVERT: A 94 MET cc_start: 0.8284 (mmt) cc_final: 0.8020 (mmt) REVERT: A 306 GLU cc_start: 0.8406 (tp30) cc_final: 0.8076 (mm-30) REVERT: A 416 MET cc_start: 0.7910 (tpp) cc_final: 0.7389 (tpp) REVERT: A 538 MET cc_start: 0.8624 (mmm) cc_final: 0.7907 (mpp) REVERT: A 590 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7063 (mt-10) REVERT: B 94 MET cc_start: 0.8279 (mmt) cc_final: 0.7928 (mmt) REVERT: B 240 HIS cc_start: 0.8637 (p-80) cc_final: 0.8392 (p-80) REVERT: B 265 GLU cc_start: 0.7821 (pt0) cc_final: 0.7612 (pt0) REVERT: B 306 GLU cc_start: 0.8499 (tp30) cc_final: 0.8223 (mm-30) REVERT: B 606 MET cc_start: 0.7130 (ttp) cc_final: 0.6890 (ttm) REVERT: C 88 LYS cc_start: 0.9391 (mtpt) cc_final: 0.9024 (mtmm) REVERT: C 94 MET cc_start: 0.8315 (mmt) cc_final: 0.8044 (mmt) REVERT: C 306 GLU cc_start: 0.8426 (tp30) cc_final: 0.8022 (mm-30) REVERT: D 22 PHE cc_start: 0.6434 (t80) cc_final: 0.6172 (t80) REVERT: D 94 MET cc_start: 0.8248 (mmt) cc_final: 0.8007 (mmt) REVERT: D 293 PHE cc_start: 0.2594 (m-10) cc_final: 0.2391 (m-10) REVERT: D 306 GLU cc_start: 0.8383 (tp30) cc_final: 0.8054 (mm-30) REVERT: D 590 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7016 (mt-10) REVERT: F 343 ARG cc_start: 0.8610 (ptp-170) cc_final: 0.8310 (ptt-90) outliers start: 59 outliers final: 52 residues processed: 337 average time/residue: 0.3272 time to fit residues: 169.8612 Evaluate side-chains 320 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 268 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 548 TYR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 481 PHE Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 548 TYR Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 159 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 HIS ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21740 Z= 0.224 Angle : 0.566 8.723 29458 Z= 0.283 Chirality : 0.041 0.138 3140 Planarity : 0.003 0.045 3792 Dihedral : 5.296 58.633 2970 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.76 % Allowed : 18.92 % Favored : 78.32 % 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: 0.24 (0.17), residues: 2576 helix: 1.72 (0.15), residues: 1270 sheet: -1.50 (0.25), residues: 336 loop : -1.34 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 182 HIS 0.007 0.001 HIS A 541 PHE 0.024 0.001 PHE B 334 TYR 0.027 0.001 TYR A 62 ARG 0.008 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 273 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.5265 (t60) cc_final: 0.4979 (t-100) REVERT: A 22 PHE cc_start: 0.6609 (t80) cc_final: 0.6120 (t80) REVERT: A 88 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8529 (mmtt) REVERT: A 94 MET cc_start: 0.8375 (mmt) cc_final: 0.7726 (mmt) REVERT: A 306 GLU cc_start: 0.8408 (tp30) cc_final: 0.8073 (mm-30) REVERT: A 538 MET cc_start: 0.8634 (mmm) cc_final: 0.7925 (mpp) REVERT: A 590 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7131 (mt-10) REVERT: B 94 MET cc_start: 0.8330 (mmt) cc_final: 0.7796 (mmt) REVERT: B 240 HIS cc_start: 0.8704 (p-80) cc_final: 0.8461 (p90) REVERT: B 303 ARG cc_start: 0.6792 (ttt180) cc_final: 0.6488 (ttt180) REVERT: B 306 GLU cc_start: 0.8508 (tp30) cc_final: 0.8203 (mm-30) REVERT: B 522 MET cc_start: 0.8736 (tpp) cc_final: 0.8327 (mtp) REVERT: B 590 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7068 (mt-10) REVERT: C 88 LYS cc_start: 0.9419 (mtpt) cc_final: 0.8949 (mtmm) REVERT: C 94 MET cc_start: 0.8398 (mmt) cc_final: 0.7748 (mmt) REVERT: C 240 HIS cc_start: 0.8706 (p-80) cc_final: 0.8432 (p-80) REVERT: C 306 GLU cc_start: 0.8441 (tp30) cc_final: 0.8093 (mm-30) REVERT: D 88 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8559 (mmtt) REVERT: D 94 MET cc_start: 0.8332 (mmt) cc_final: 0.7678 (mmt) REVERT: D 306 GLU cc_start: 0.8382 (tp30) cc_final: 0.8035 (mm-30) REVERT: D 590 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7109 (mt-10) REVERT: F 343 ARG cc_start: 0.8607 (ptp-170) cc_final: 0.8201 (ptt-90) outliers start: 62 outliers final: 60 residues processed: 320 average time/residue: 0.3325 time to fit residues: 164.9951 Evaluate side-chains 318 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 258 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 548 TYR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 481 PHE Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 548 TYR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain G residue 325 TRP Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 219 optimal weight: 0.0980 chunk 233 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 101 optimal weight: 0.0870 chunk 183 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 220 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21740 Z= 0.227 Angle : 0.562 8.521 29458 Z= 0.281 Chirality : 0.041 0.141 3140 Planarity : 0.003 0.048 3792 Dihedral : 5.147 57.350 2970 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.94 % Allowed : 18.61 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2576 helix: 1.65 (0.15), residues: 1278 sheet: -1.54 (0.24), residues: 336 loop : -1.29 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 58 HIS 0.006 0.001 HIS D 541 PHE 0.022 0.001 PHE A 334 TYR 0.021 0.001 TYR A 62 ARG 0.009 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 264 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.5253 (t60) cc_final: 0.5002 (t-100) REVERT: A 22 PHE cc_start: 0.6515 (t80) cc_final: 0.5996 (t80) REVERT: A 94 MET cc_start: 0.8299 (mmt) cc_final: 0.7867 (mmt) REVERT: A 306 GLU cc_start: 0.8388 (tp30) cc_final: 0.8024 (mm-30) REVERT: A 590 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7116 (mt-10) REVERT: B 94 MET cc_start: 0.8361 (mmt) cc_final: 0.7830 (mmt) REVERT: B 240 HIS cc_start: 0.8686 (p-80) cc_final: 0.8475 (p-80) REVERT: B 303 ARG cc_start: 0.6819 (ttt180) cc_final: 0.6444 (ttt180) REVERT: B 306 GLU cc_start: 0.8497 (tp30) cc_final: 0.8185 (mm-30) REVERT: B 522 MET cc_start: 0.8709 (tpp) cc_final: 0.8276 (mtp) REVERT: B 590 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7079 (mt-10) REVERT: C 88 LYS cc_start: 0.9418 (mtpt) cc_final: 0.9022 (mtmm) REVERT: C 94 MET cc_start: 0.8322 (mmt) cc_final: 0.7876 (mmt) REVERT: C 240 HIS cc_start: 0.8693 (p-80) cc_final: 0.8407 (p-80) REVERT: C 306 GLU cc_start: 0.8404 (tp30) cc_final: 0.8037 (mm-30) REVERT: C 522 MET cc_start: 0.8645 (tpp) cc_final: 0.8264 (mtp) REVERT: C 590 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7067 (mt-10) REVERT: D 22 PHE cc_start: 0.6474 (t80) cc_final: 0.6198 (t80) REVERT: D 31 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: D 88 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8498 (mmtt) REVERT: D 94 MET cc_start: 0.8258 (mmt) cc_final: 0.7828 (mmt) REVERT: D 306 GLU cc_start: 0.8340 (tp30) cc_final: 0.7993 (mm-30) REVERT: D 522 MET cc_start: 0.8694 (tpp) cc_final: 0.8249 (mtp) REVERT: D 590 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7030 (mt-10) REVERT: F 343 ARG cc_start: 0.8621 (ptp-170) cc_final: 0.8074 (ptt-90) outliers start: 66 outliers final: 63 residues processed: 313 average time/residue: 0.3248 time to fit residues: 158.9010 Evaluate side-chains 319 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 255 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 548 TYR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 481 PHE Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 548 TYR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain H residue 340 ASN Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.7980 chunk 246 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 259 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21740 Z= 0.216 Angle : 0.561 8.866 29458 Z= 0.280 Chirality : 0.041 0.145 3140 Planarity : 0.003 0.048 3792 Dihedral : 5.039 58.395 2970 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.07 % Allowed : 18.52 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2576 helix: 1.69 (0.15), residues: 1282 sheet: -1.50 (0.24), residues: 336 loop : -1.21 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 182 HIS 0.006 0.001 HIS D 541 PHE 0.026 0.001 PHE C 334 TYR 0.020 0.001 TYR A 62 ARG 0.009 0.000 ARG H 343 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 259 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.5247 (t60) cc_final: 0.5045 (t-100) REVERT: A 22 PHE cc_start: 0.6448 (t80) cc_final: 0.5925 (t80) REVERT: A 88 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8454 (mmtt) REVERT: A 94 MET cc_start: 0.8318 (mmt) cc_final: 0.7843 (mmt) REVERT: A 244 MET cc_start: 0.8784 (ptp) cc_final: 0.8468 (ptp) REVERT: A 306 GLU cc_start: 0.8403 (tp30) cc_final: 0.8019 (mm-30) REVERT: A 538 MET cc_start: 0.8654 (mmm) cc_final: 0.7969 (mpp) REVERT: A 590 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7141 (mt-10) REVERT: B 94 MET cc_start: 0.8350 (mmt) cc_final: 0.7869 (mmt) REVERT: B 240 HIS cc_start: 0.8660 (p-80) cc_final: 0.8321 (p-80) REVERT: B 303 ARG cc_start: 0.6834 (ttt180) cc_final: 0.6493 (ttt180) REVERT: B 306 GLU cc_start: 0.8486 (tp30) cc_final: 0.8167 (mm-30) REVERT: B 522 MET cc_start: 0.8749 (tpp) cc_final: 0.8311 (mtp) REVERT: B 590 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7081 (mt-10) REVERT: C 88 LYS cc_start: 0.9405 (mtpt) cc_final: 0.9172 (mmtt) REVERT: C 94 MET cc_start: 0.8315 (mmt) cc_final: 0.7883 (mmt) REVERT: C 240 HIS cc_start: 0.8668 (p-80) cc_final: 0.8367 (p-80) REVERT: C 522 MET cc_start: 0.8649 (tpp) cc_final: 0.8273 (mtp) REVERT: C 590 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7056 (mt-10) REVERT: D 22 PHE cc_start: 0.6550 (t80) cc_final: 0.6289 (t80) REVERT: D 31 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8420 (tt0) REVERT: D 88 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8448 (mmtt) REVERT: D 94 MET cc_start: 0.8272 (mmt) cc_final: 0.7815 (mmt) REVERT: D 522 MET cc_start: 0.8699 (tpp) cc_final: 0.8243 (mtp) REVERT: D 590 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7092 (mt-10) REVERT: F 343 ARG cc_start: 0.8608 (ptp-170) cc_final: 0.8081 (ptt-90) outliers start: 69 outliers final: 64 residues processed: 309 average time/residue: 0.3166 time to fit residues: 152.0252 Evaluate side-chains 319 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 254 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 548 TYR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 481 PHE Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 548 TYR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain H residue 340 ASN Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.7980 chunk 219 optimal weight: 0.4980 chunk 63 optimal weight: 0.1980 chunk 190 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 206 optimal weight: 0.3980 chunk 86 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.127186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101027 restraints weight = 41377.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.102858 restraints weight = 28745.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.103379 restraints weight = 23158.145| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21740 Z= 0.144 Angle : 0.532 8.910 29458 Z= 0.263 Chirality : 0.040 0.137 3140 Planarity : 0.003 0.033 3792 Dihedral : 4.786 58.065 2970 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.23 % Allowed : 19.32 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2576 helix: 1.89 (0.15), residues: 1278 sheet: -1.18 (0.24), residues: 324 loop : -1.01 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 58 HIS 0.005 0.001 HIS D 541 PHE 0.015 0.001 PHE A 334 TYR 0.023 0.001 TYR D 62 ARG 0.007 0.000 ARG H 343 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3962.98 seconds wall clock time: 74 minutes 3.34 seconds (4443.34 seconds total)