Starting phenix.real_space_refine on Fri Nov 17 21:25:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5t_31466/11_2023/7f5t_31466.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5t_31466/11_2023/7f5t_31466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5t_31466/11_2023/7f5t_31466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5t_31466/11_2023/7f5t_31466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5t_31466/11_2023/7f5t_31466.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5t_31466/11_2023/7f5t_31466.pdb" } resolution = 4.1 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12800 2.51 5 N 3620 2.21 5 O 3904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ASP 548": "OD1" <-> "OD2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A ASP 690": "OD1" <-> "OD2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ASP 548": "OD1" <-> "OD2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B ASP 690": "OD1" <-> "OD2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 411": "NH1" <-> "NH2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C ASP 548": "OD1" <-> "OD2" Residue "C ARG 551": "NH1" <-> "NH2" Residue "C ARG 576": "NH1" <-> "NH2" Residue "C ARG 625": "NH1" <-> "NH2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C ASP 690": "OD1" <-> "OD2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ARG 411": "NH1" <-> "NH2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D ASP 548": "OD1" <-> "OD2" Residue "D ARG 551": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D ARG 625": "NH1" <-> "NH2" Residue "D GLU 669": "OE1" <-> "OE2" Residue "D ASP 690": "OD1" <-> "OD2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D ARG 766": "NH1" <-> "NH2" Residue "B GLU 801": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 20436 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5099 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5099 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5099 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5099 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 11.03, per 1000 atoms: 0.54 Number of scatterers: 20436 At special positions: 0 Unit cell: (193.98, 107.06, 94.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3904 8.00 N 3620 7.00 C 12800 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 4.1 seconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5024 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 20 sheets defined 51.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 removed outlier: 3.795A pdb=" N LYS A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 removed outlier: 4.016A pdb=" N ILE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 77 through 95 removed outlier: 4.124A pdb=" N LEU A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 95 " --> pdb=" O CYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.691A pdb=" N SER A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 163 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.762A pdb=" N TYR A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 180' Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 207 through 210 Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.851A pdb=" N SER A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 349 through 363 Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.776A pdb=" N ILE A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 415 through 433 Processing helix chain 'A' and resid 471 through 483 removed outlier: 4.014A pdb=" N GLN A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 512 Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 609 through 612 Processing helix chain 'A' and resid 614 through 627 Processing helix chain 'A' and resid 633 through 640 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 710 through 714 Processing helix chain 'A' and resid 716 through 720 Processing helix chain 'A' and resid 740 through 744 Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'B' and resid 49 through 55 removed outlier: 3.795A pdb=" N LYS B 54 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 removed outlier: 4.016A pdb=" N ILE B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 69' Processing helix chain 'B' and resid 77 through 95 removed outlier: 4.124A pdb=" N LEU B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 95 " --> pdb=" O CYS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.692A pdb=" N SER B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 163 Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.762A pdb=" N TYR B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 180 " --> pdb=" O PRO B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 175 through 180' Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 207 through 210 Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.851A pdb=" N SER B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 349 through 363 Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 384 through 403 removed outlier: 3.776A pdb=" N ILE B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 415 through 433 Processing helix chain 'B' and resid 471 through 483 removed outlier: 4.014A pdb=" N GLN B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 512 Processing helix chain 'B' and resid 527 through 534 Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 609 through 612 Processing helix chain 'B' and resid 614 through 627 Processing helix chain 'B' and resid 633 through 640 Processing helix chain 'B' and resid 666 through 678 Processing helix chain 'B' and resid 689 through 700 Processing helix chain 'B' and resid 710 through 714 Processing helix chain 'B' and resid 716 through 720 Processing helix chain 'B' and resid 740 through 744 Processing helix chain 'B' and resid 757 through 761 Processing helix chain 'C' and resid 49 through 55 removed outlier: 3.794A pdb=" N LYS C 54 " --> pdb=" O SER C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 removed outlier: 4.016A pdb=" N ILE C 68 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 69' Processing helix chain 'C' and resid 77 through 95 removed outlier: 4.124A pdb=" N LEU C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 95 " --> pdb=" O CYS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 115 through 122 removed outlier: 3.691A pdb=" N SER C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 163 Processing helix chain 'C' and resid 175 through 180 removed outlier: 3.763A pdb=" N TYR C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 180 " --> pdb=" O PRO C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 175 through 180' Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 207 through 210 Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.852A pdb=" N SER C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'C' and resid 321 through 328 Processing helix chain 'C' and resid 349 through 363 Processing helix chain 'C' and resid 368 through 384 Processing helix chain 'C' and resid 384 through 403 removed outlier: 3.777A pdb=" N ILE C 388 " --> pdb=" O ARG C 384 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 Processing helix chain 'C' and resid 415 through 433 Processing helix chain 'C' and resid 471 through 483 removed outlier: 4.015A pdb=" N GLN C 475 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 512 Processing helix chain 'C' and resid 527 through 534 Processing helix chain 'C' and resid 546 through 557 Processing helix chain 'C' and resid 579 through 592 Processing helix chain 'C' and resid 609 through 612 Processing helix chain 'C' and resid 614 through 627 Processing helix chain 'C' and resid 633 through 640 Processing helix chain 'C' and resid 666 through 678 Processing helix chain 'C' and resid 689 through 700 Processing helix chain 'C' and resid 710 through 714 Processing helix chain 'C' and resid 716 through 720 Processing helix chain 'C' and resid 740 through 744 Processing helix chain 'C' and resid 757 through 761 Processing helix chain 'D' and resid 49 through 55 removed outlier: 3.794A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 removed outlier: 4.016A pdb=" N ILE D 68 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 69' Processing helix chain 'D' and resid 77 through 95 removed outlier: 4.125A pdb=" N LEU D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY D 95 " --> pdb=" O CYS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 114 Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.692A pdb=" N SER D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 163 Processing helix chain 'D' and resid 175 through 180 removed outlier: 3.762A pdb=" N TYR D 179 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN D 180 " --> pdb=" O PRO D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 175 through 180' Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 233 through 245 removed outlier: 3.851A pdb=" N SER D 237 " --> pdb=" O ASN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 349 through 363 Processing helix chain 'D' and resid 368 through 384 Processing helix chain 'D' and resid 384 through 403 removed outlier: 3.776A pdb=" N ILE D 388 " --> pdb=" O ARG D 384 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 Processing helix chain 'D' and resid 415 through 433 Processing helix chain 'D' and resid 471 through 483 removed outlier: 4.015A pdb=" N GLN D 475 " --> pdb=" O ASP D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 512 Processing helix chain 'D' and resid 527 through 534 Processing helix chain 'D' and resid 546 through 557 Processing helix chain 'D' and resid 579 through 592 Processing helix chain 'D' and resid 609 through 612 Processing helix chain 'D' and resid 614 through 627 Processing helix chain 'D' and resid 633 through 640 Processing helix chain 'D' and resid 666 through 678 Processing helix chain 'D' and resid 689 through 700 Processing helix chain 'D' and resid 710 through 714 Processing helix chain 'D' and resid 716 through 720 Processing helix chain 'D' and resid 740 through 744 Processing helix chain 'D' and resid 757 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 98 removed outlier: 6.840A pdb=" N ARG A 58 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE A 250 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 60 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL A 312 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 336 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 173 removed outlier: 3.933A pdb=" N ALA A 169 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 771 through 772 removed outlier: 3.517A pdb=" N ARG A 442 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU A 451 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 751 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N VAL C 705 " --> pdb=" O THR A 746 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP A 748 " --> pdb=" O VAL C 705 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N HIS C 707 " --> pdb=" O TRP A 748 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU A 750 " --> pdb=" O HIS C 707 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASP C 683 " --> pdb=" O PHE C 706 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL C 572 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS C 607 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE C 574 " --> pdb=" O HIS C 607 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU C 604 " --> pdb=" O GLU C 662 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL C 664 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE C 606 " --> pdb=" O VAL C 664 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 488 removed outlier: 6.646A pdb=" N LEU A 462 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A 461 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE A 542 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 463 " --> pdb=" O ILE A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 660 through 664 removed outlier: 6.007A pdb=" N LEU A 604 " --> pdb=" O GLU A 662 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL A 664 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE A 606 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL A 572 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS A 607 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE A 574 " --> pdb=" O HIS A 607 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP A 683 " --> pdb=" O PHE A 706 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 751 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU C 451 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 442 " --> pdb=" O GLN C 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 726 through 728 removed outlier: 3.826A pdb=" N GLY A 726 " --> pdb=" O VAL A 738 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 98 removed outlier: 6.840A pdb=" N ARG B 58 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE B 250 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL B 60 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 312 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 336 " --> pdb=" O VAL B 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 167 through 173 removed outlier: 3.932A pdb=" N ALA B 169 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 771 through 772 removed outlier: 3.517A pdb=" N ARG B 442 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU B 451 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B 751 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N VAL D 705 " --> pdb=" O THR B 746 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP B 748 " --> pdb=" O VAL D 705 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N HIS D 707 " --> pdb=" O TRP B 748 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU B 750 " --> pdb=" O HIS D 707 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP D 683 " --> pdb=" O PHE D 706 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL D 572 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS D 607 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE D 574 " --> pdb=" O HIS D 607 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU D 604 " --> pdb=" O GLU D 662 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL D 664 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE D 606 " --> pdb=" O VAL D 664 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 487 through 488 removed outlier: 6.645A pdb=" N LEU B 462 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL B 461 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE B 542 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU B 463 " --> pdb=" O ILE B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 660 through 664 removed outlier: 6.007A pdb=" N LEU B 604 " --> pdb=" O GLU B 662 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 664 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE B 606 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL B 572 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS B 607 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE B 574 " --> pdb=" O HIS B 607 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP B 683 " --> pdb=" O PHE B 706 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 751 " --> pdb=" O GLU D 451 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU D 451 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 442 " --> pdb=" O GLN D 454 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 726 through 728 removed outlier: 3.827A pdb=" N GLY B 726 " --> pdb=" O VAL B 738 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 97 through 98 removed outlier: 6.840A pdb=" N ARG C 58 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE C 250 " --> pdb=" O ARG C 58 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL C 60 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL C 312 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 336 " --> pdb=" O VAL C 312 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 167 through 173 removed outlier: 3.933A pdb=" N ALA C 169 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 487 through 488 removed outlier: 6.646A pdb=" N LEU C 462 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL C 461 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE C 542 " --> pdb=" O VAL C 461 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU C 463 " --> pdb=" O ILE C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 726 through 728 removed outlier: 3.827A pdb=" N GLY C 726 " --> pdb=" O VAL C 738 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.841A pdb=" N ARG D 58 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE D 250 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL D 60 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL D 312 " --> pdb=" O PHE D 336 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 336 " --> pdb=" O VAL D 312 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 167 through 173 removed outlier: 3.933A pdb=" N ALA D 169 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 487 through 488 removed outlier: 6.646A pdb=" N LEU D 462 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL D 461 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE D 542 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU D 463 " --> pdb=" O ILE D 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 726 through 728 removed outlier: 3.826A pdb=" N GLY D 726 " --> pdb=" O VAL D 738 " (cutoff:3.500A) 976 hydrogen bonds defined for protein. 2724 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: 8.01 Time building geometry restraints manager: 10.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6350 1.33 - 1.45: 2720 1.45 - 1.57: 11474 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 20728 Sorted by residual: bond pdb=" CA LEU B 53 " pdb=" C LEU B 53 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.56e-02 4.11e+03 1.29e+01 bond pdb=" CA LEU D 53 " pdb=" C LEU D 53 " ideal model delta sigma weight residual 1.523 1.468 0.056 1.56e-02 4.11e+03 1.27e+01 bond pdb=" CA LEU A 53 " pdb=" C LEU A 53 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.56e-02 4.11e+03 1.25e+01 bond pdb=" CA LEU C 53 " pdb=" C LEU C 53 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.56e-02 4.11e+03 1.24e+01 bond pdb=" CA VAL D 346 " pdb=" CB VAL D 346 " ideal model delta sigma weight residual 1.540 1.517 0.023 7.70e-03 1.69e+04 8.74e+00 ... (remaining 20723 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.66: 555 106.66 - 113.49: 12228 113.49 - 120.32: 7169 120.32 - 127.15: 7896 127.15 - 133.98: 188 Bond angle restraints: 28036 Sorted by residual: angle pdb=" C ALA D 345 " pdb=" N VAL D 346 " pdb=" CA VAL D 346 " ideal model delta sigma weight residual 123.33 118.63 4.70 8.70e-01 1.32e+00 2.91e+01 angle pdb=" C ALA C 345 " pdb=" N VAL C 346 " pdb=" CA VAL C 346 " ideal model delta sigma weight residual 123.33 118.64 4.69 8.70e-01 1.32e+00 2.91e+01 angle pdb=" C ALA A 345 " pdb=" N VAL A 346 " pdb=" CA VAL A 346 " ideal model delta sigma weight residual 123.33 118.65 4.68 8.70e-01 1.32e+00 2.90e+01 angle pdb=" C ALA B 345 " pdb=" N VAL B 346 " pdb=" CA VAL B 346 " ideal model delta sigma weight residual 123.33 118.67 4.66 8.70e-01 1.32e+00 2.87e+01 angle pdb=" N ALA A 691 " pdb=" CA ALA A 691 " pdb=" C ALA A 691 " ideal model delta sigma weight residual 111.03 105.16 5.87 1.11e+00 8.12e-01 2.80e+01 ... (remaining 28031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 11333 17.73 - 35.45: 1040 35.45 - 53.18: 243 53.18 - 70.90: 36 70.90 - 88.63: 28 Dihedral angle restraints: 12680 sinusoidal: 4932 harmonic: 7748 Sorted by residual: dihedral pdb=" CA ASN B 344 " pdb=" C ASN B 344 " pdb=" N ALA B 345 " pdb=" CA ALA B 345 " ideal model delta harmonic sigma weight residual -180.00 -150.82 -29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ASN A 344 " pdb=" C ASN A 344 " pdb=" N ALA A 345 " pdb=" CA ALA A 345 " ideal model delta harmonic sigma weight residual -180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ASN C 344 " pdb=" C ASN C 344 " pdb=" N ALA C 345 " pdb=" CA ALA C 345 " ideal model delta harmonic sigma weight residual 180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 12677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2196 0.038 - 0.076: 793 0.076 - 0.113: 277 0.113 - 0.151: 34 0.151 - 0.189: 8 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CA LEU B 53 " pdb=" N LEU B 53 " pdb=" C LEU B 53 " pdb=" CB LEU B 53 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA LEU D 53 " pdb=" N LEU D 53 " pdb=" C LEU D 53 " pdb=" CB LEU D 53 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CA LEU C 53 " pdb=" N LEU C 53 " pdb=" C LEU C 53 " pdb=" CB LEU C 53 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 3305 not shown) Planarity restraints: 3632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 597 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ALA B 597 " -0.034 2.00e-02 2.50e+03 pdb=" O ALA B 597 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS B 598 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 597 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C ALA C 597 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA C 597 " -0.013 2.00e-02 2.50e+03 pdb=" N CYS C 598 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 597 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C ALA A 597 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA A 597 " -0.013 2.00e-02 2.50e+03 pdb=" N CYS A 598 " -0.011 2.00e-02 2.50e+03 ... (remaining 3629 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1288 2.69 - 3.24: 24453 3.24 - 3.80: 34306 3.80 - 4.35: 41978 4.35 - 4.90: 66489 Nonbonded interactions: 168514 Sorted by model distance: nonbonded pdb=" O ASN D 354 " pdb=" OG1 THR D 357 " model vdw 2.141 2.440 nonbonded pdb=" O ASN A 354 " pdb=" OG1 THR A 357 " model vdw 2.141 2.440 nonbonded pdb=" O ASN B 354 " pdb=" OG1 THR B 357 " model vdw 2.142 2.440 nonbonded pdb=" O ASN C 354 " pdb=" OG1 THR C 357 " model vdw 2.142 2.440 nonbonded pdb=" O ALA C 399 " pdb=" OG SER C 402 " model vdw 2.204 2.440 ... (remaining 168509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 6.580 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 59.550 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.007 0.056 20728 Z= 0.483 Angle : 0.886 7.118 28036 Z= 0.535 Chirality : 0.043 0.189 3308 Planarity : 0.004 0.041 3632 Dihedral : 15.070 88.631 7656 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.25 % Favored : 86.30 % Rotamer: Outliers : 3.48 % Allowed : 7.14 % Favored : 89.38 % 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: -5.03 (0.13), residues: 2664 helix: -2.50 (0.12), residues: 1136 sheet: -4.18 (0.18), residues: 428 loop : -3.78 (0.16), residues: 1100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 275 time to evaluate : 2.504 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 19 residues processed: 329 average time/residue: 0.3451 time to fit residues: 170.3215 Evaluate side-chains 208 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 189 time to evaluate : 2.445 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2248 time to fit residues: 10.6716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 3.9990 chunk 203 optimal weight: 0.2980 chunk 112 optimal weight: 30.0000 chunk 69 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 363 GLN A 369 GLN A 607 HIS A 652 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 363 GLN B 369 GLN B 607 HIS B 652 HIS C 150 GLN C 363 GLN C 369 GLN C 607 HIS C 652 HIS D 363 GLN D 369 GLN D 607 HIS D 652 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20728 Z= 0.180 Angle : 0.629 13.256 28036 Z= 0.324 Chirality : 0.043 0.257 3308 Planarity : 0.004 0.045 3632 Dihedral : 5.209 28.329 2872 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.83 % Favored : 92.87 % Rotamer: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.15), residues: 2664 helix: -0.58 (0.14), residues: 1184 sheet: -3.22 (0.20), residues: 448 loop : -2.95 (0.18), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 2.330 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.3600 time to fit residues: 145.4907 Evaluate side-chains 191 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.267 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 67 optimal weight: 30.0000 chunk 243 optimal weight: 7.9990 chunk 263 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 241 optimal weight: 30.0000 chunk 83 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 392 ASN A 637 ASN A 707 HIS ** B 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN C 392 ASN D 204 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20728 Z= 0.249 Angle : 0.635 12.668 28036 Z= 0.330 Chirality : 0.042 0.211 3308 Planarity : 0.004 0.053 3632 Dihedral : 5.176 27.795 2872 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.94 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.16), residues: 2664 helix: 0.07 (0.15), residues: 1188 sheet: -2.81 (0.20), residues: 472 loop : -2.80 (0.18), residues: 1004 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.700 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 outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.3387 time to fit residues: 116.3167 Evaluate side-chains 167 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 20.0000 chunk 183 optimal weight: 30.0000 chunk 126 optimal weight: 5.9990 chunk 26 optimal weight: 0.2980 chunk 116 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 259 optimal weight: 30.0000 chunk 127 optimal weight: 5.9990 chunk 231 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN B 559 HIS B 637 ASN B 707 HIS C 150 GLN C 637 ASN C 707 HIS D 559 HIS D 637 ASN D 707 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20728 Z= 0.186 Angle : 0.592 15.756 28036 Z= 0.300 Chirality : 0.042 0.235 3308 Planarity : 0.004 0.048 3632 Dihedral : 4.869 28.307 2872 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.79 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: -1.51 (0.16), residues: 2664 helix: 0.69 (0.15), residues: 1192 sheet: -2.23 (0.21), residues: 472 loop : -2.45 (0.19), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.546 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 outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3339 time to fit residues: 109.7186 Evaluate side-chains 171 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.304 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 192 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 chunk 221 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 392 ASN B 185 ASN C 185 ASN C 392 ASN D 185 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20728 Z= 0.254 Angle : 0.632 16.042 28036 Z= 0.322 Chirality : 0.042 0.273 3308 Planarity : 0.004 0.059 3632 Dihedral : 5.004 29.770 2872 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.77 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2664 helix: 0.72 (0.15), residues: 1224 sheet: -2.05 (0.21), residues: 472 loop : -2.64 (0.19), residues: 968 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.3358 time to fit residues: 110.0105 Evaluate side-chains 159 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 152 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 259 optimal weight: 30.0000 chunk 215 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 136 optimal weight: 0.0020 overall best weight: 5.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 454 GLN A 559 HIS C 392 ASN C 454 GLN C 559 HIS D 204 ASN D 454 GLN D 556 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20728 Z= 0.247 Angle : 0.618 10.733 28036 Z= 0.318 Chirality : 0.042 0.254 3308 Planarity : 0.004 0.056 3632 Dihedral : 5.029 30.652 2872 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.85 % Favored : 92.00 % Rotamer: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2664 helix: 0.78 (0.15), residues: 1200 sheet: -1.79 (0.22), residues: 472 loop : -2.46 (0.19), residues: 992 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 2.533 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 outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.3244 time to fit residues: 106.5844 Evaluate side-chains 162 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.433 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 258 optimal weight: 20.0000 chunk 161 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN C 392 ASN D 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20728 Z= 0.204 Angle : 0.590 10.292 28036 Z= 0.300 Chirality : 0.041 0.180 3308 Planarity : 0.004 0.055 3632 Dihedral : 4.930 30.907 2872 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.21 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.98 (0.17), residues: 2664 helix: 1.04 (0.15), residues: 1200 sheet: -1.48 (0.23), residues: 460 loop : -2.36 (0.19), residues: 1004 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.486 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3314 time to fit residues: 108.9068 Evaluate side-chains 168 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.476 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 203 optimal weight: 0.0970 chunk 234 optimal weight: 7.9990 overall best weight: 3.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN B 150 GLN C 392 ASN D 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20728 Z= 0.186 Angle : 0.583 12.652 28036 Z= 0.293 Chirality : 0.042 0.263 3308 Planarity : 0.004 0.064 3632 Dihedral : 4.801 31.057 2872 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.47 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.69 (0.17), residues: 2664 helix: 1.20 (0.15), residues: 1192 sheet: -1.32 (0.23), residues: 460 loop : -2.08 (0.20), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.464 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 outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.3292 time to fit residues: 110.3608 Evaluate side-chains 166 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 20.0000 chunk 225 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 104 optimal weight: 0.0070 chunk 189 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 overall best weight: 6.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN B 621 ASN C 392 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20728 Z= 0.258 Angle : 0.642 10.262 28036 Z= 0.326 Chirality : 0.042 0.188 3308 Planarity : 0.005 0.069 3632 Dihedral : 5.040 32.459 2872 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.92 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.16), residues: 2664 helix: 0.78 (0.15), residues: 1232 sheet: -1.35 (0.24), residues: 448 loop : -2.43 (0.19), residues: 984 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.487 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 outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.3271 time to fit residues: 107.5326 Evaluate side-chains 161 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 6.9990 chunk 155 optimal weight: 30.0000 chunk 120 optimal weight: 5.9990 chunk 176 optimal weight: 0.0070 chunk 266 optimal weight: 30.0000 chunk 245 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 overall best weight: 2.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN C 392 ASN D 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20728 Z= 0.165 Angle : 0.597 11.228 28036 Z= 0.294 Chirality : 0.042 0.164 3308 Planarity : 0.004 0.055 3632 Dihedral : 4.751 31.185 2872 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.42 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2664 helix: 1.07 (0.15), residues: 1232 sheet: -1.07 (0.25), residues: 448 loop : -2.27 (0.19), residues: 984 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 3.323 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 outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.3323 time to fit residues: 112.2845 Evaluate side-chains 164 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.387 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 10.0000 chunk 65 optimal weight: 50.0000 chunk 196 optimal weight: 30.0000 chunk 31 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN D 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.039583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.030343 restraints weight = 183701.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.030948 restraints weight = 132487.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.031508 restraints weight = 106735.498| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20728 Z= 0.162 Angle : 0.588 10.223 28036 Z= 0.290 Chirality : 0.042 0.179 3308 Planarity : 0.004 0.056 3632 Dihedral : 4.596 30.190 2872 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.27 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2664 helix: 1.10 (0.15), residues: 1240 sheet: -0.95 (0.25), residues: 448 loop : -2.13 (0.20), residues: 976 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.20 seconds wall clock time: 67 minutes 3.90 seconds (4023.90 seconds total)