Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 9 17:01:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhz_26520/10_2023/7uhz_26520_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhz_26520/10_2023/7uhz_26520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhz_26520/10_2023/7uhz_26520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhz_26520/10_2023/7uhz_26520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhz_26520/10_2023/7uhz_26520_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhz_26520/10_2023/7uhz_26520_neut.pdb" } resolution = 3.3 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= 0.001 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 93 5.16 5 C 12180 2.51 5 N 3333 2.21 5 O 3693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 10": "OE1" <-> "OE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 10": "OE1" <-> "OE2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ASP 30": "OD1" <-> "OD2" Residue "L PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 84": "OD1" <-> "OD2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "M ASP 1": "OD1" <-> "OD2" Residue "M ARG 24": "NH1" <-> "NH2" Residue "M ASP 30": "OD1" <-> "OD2" Residue "M PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 84": "OD1" <-> "OD2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "N ASP 1": "OD1" <-> "OD2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ASP 30": "OD1" <-> "OD2" Residue "N PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 84": "OD1" <-> "OD2" Residue "N GLU 97": "OE1" <-> "OE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 277": "OD1" <-> "OD2" Residue "B PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 687": "OE1" <-> "OE2" Residue "B TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 219": "OE1" <-> "OE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 687": "OE1" <-> "OE2" Residue "C TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 19299 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "I" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "J" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "N" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "A" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4658 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Chain: "B" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4658 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Chain: "C" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4658 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Time building chain proxies: 9.94, per 1000 atoms: 0.52 Number of scatterers: 19299 At special positions: 0 Unit cell: (98.175, 103.125, 204.6, 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 93 16.00 O 3693 8.00 N 3333 7.00 C 12180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.02 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.02 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.02 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.03 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: 8.04 Conformation dependent library (CDL) restraints added in 2.8 seconds 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4530 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 19.3% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.130A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.514A pdb=" N ARG H 64 " --> pdb=" O GLU H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.130A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.513A pdb=" N ARG I 64 " --> pdb=" O GLU I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'J' and resid 28 through 32 removed outlier: 4.129A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.513A pdb=" N ARG J 64 " --> pdb=" O GLU J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 410 through 429 removed outlier: 4.190A pdb=" N GLY A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 546 removed outlier: 4.296A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.804A pdb=" N ILE A 664 " --> pdb=" O ARG A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 701 through 717 removed outlier: 4.772A pdb=" N ASP A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 714 " --> pdb=" O GLN A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 410 through 429 removed outlier: 4.191A pdb=" N GLY B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 546 removed outlier: 4.295A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.804A pdb=" N ILE B 664 " --> pdb=" O ARG B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 701 through 717 removed outlier: 4.772A pdb=" N ASP B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 714 " --> pdb=" O GLN B 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 410 through 429 removed outlier: 4.190A pdb=" N GLY C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 546 removed outlier: 4.295A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 660 through 664 removed outlier: 3.804A pdb=" N ILE C 664 " --> pdb=" O ARG C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 697 Processing helix chain 'C' and resid 701 through 717 removed outlier: 4.772A pdb=" N ASP C 713 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU C 714 " --> pdb=" O GLN C 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 105 through 106 Processing sheet with id=AA3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 105 through 106 Processing sheet with id=AA5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 105 through 106 Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.515A pdb=" N ILE L 52 " --> pdb=" O TRP L 39 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLN L 41 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU L 50 " --> pdb=" O GLN L 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.672A pdb=" N ASP L 74 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AB1, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.514A pdb=" N ILE M 52 " --> pdb=" O TRP M 39 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN M 41 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU M 50 " --> pdb=" O GLN M 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 19 through 24 removed outlier: 3.672A pdb=" N ASP M 74 " --> pdb=" O SER M 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 30 through 31 Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.514A pdb=" N ILE N 52 " --> pdb=" O TRP N 39 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN N 41 " --> pdb=" O LEU N 50 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU N 50 " --> pdb=" O GLN N 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 19 through 24 removed outlier: 3.673A pdb=" N ASP N 74 " --> pdb=" O SER N 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 30 through 31 Processing sheet with id=AB7, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.312A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 559 through 563 removed outlier: 7.728A pdb=" N VAL C 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLN A 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 145 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 366 through 368 current: chain 'A' and resid 448 through 457 Processing sheet with id=AC1, first strand: chain 'A' and resid 157 through 175 removed outlier: 4.756A pdb=" N TRP A 174 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE A 182 " --> pdb=" O TRP A 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 180 through 190 current: chain 'A' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 294 through 295 current: chain 'A' and resid 343 through 346 Processing sheet with id=AC2, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AC3, first strand: chain 'A' and resid 213 through 214 Processing sheet with id=AC4, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AC5, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AC6, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AC7, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.674A pdb=" N PHE A 641 " --> pdb=" O VAL A 648 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 665 through 667 removed outlier: 3.696A pdb=" N THR A 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.312A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 145 through 152 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 366 through 368 current: chain 'B' and resid 448 through 457 Processing sheet with id=AD2, first strand: chain 'B' and resid 157 through 175 removed outlier: 4.755A pdb=" N TRP B 174 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE B 182 " --> pdb=" O TRP B 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 180 through 190 current: chain 'B' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 294 through 295 current: chain 'B' and resid 343 through 346 Processing sheet with id=AD3, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AD4, first strand: chain 'B' and resid 213 through 214 Processing sheet with id=AD5, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AD6, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AD7, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AD8, first strand: chain 'B' and resid 638 through 643 removed outlier: 3.674A pdb=" N PHE B 641 " --> pdb=" O VAL B 648 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 665 through 667 removed outlier: 3.618A pdb=" N THR B 665 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.311A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 145 through 152 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 366 through 368 current: chain 'C' and resid 448 through 457 Processing sheet with id=AE3, first strand: chain 'C' and resid 157 through 175 removed outlier: 4.756A pdb=" N TRP C 174 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE C 182 " --> pdb=" O TRP C 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 180 through 190 current: chain 'C' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 294 through 295 current: chain 'C' and resid 343 through 346 Processing sheet with id=AE4, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AE5, first strand: chain 'C' and resid 213 through 214 Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE7, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AE8, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AE9, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.675A pdb=" N PHE C 641 " --> pdb=" O VAL C 648 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1461 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: 7.17 Time building geometry restraints manager: 8.63 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: 6360 1.34 - 1.46: 4972 1.46 - 1.58: 8303 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 19779 Sorted by residual: bond pdb=" C CYS A 133 " pdb=" N PRO A 134 " ideal model delta sigma weight residual 1.332 1.365 -0.034 1.26e-02 6.30e+03 7.18e+00 bond pdb=" C CYS B 133 " pdb=" N PRO B 134 " ideal model delta sigma weight residual 1.332 1.365 -0.034 1.26e-02 6.30e+03 7.18e+00 bond pdb=" C CYS C 133 " pdb=" N PRO C 134 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.26e-02 6.30e+03 6.97e+00 bond pdb=" CA SER C 209 " pdb=" C SER C 209 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.41e-02 5.03e+03 6.34e+00 bond pdb=" CA SER A 209 " pdb=" C SER A 209 " ideal model delta sigma weight residual 1.523 1.488 0.035 1.41e-02 5.03e+03 6.19e+00 ... (remaining 19774 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.30: 393 105.30 - 112.48: 9945 112.48 - 119.67: 6039 119.67 - 126.85: 10202 126.85 - 134.04: 283 Bond angle restraints: 26862 Sorted by residual: angle pdb=" N ILE B 154 " pdb=" CA ILE B 154 " pdb=" C ILE B 154 " ideal model delta sigma weight residual 112.90 107.77 5.13 9.60e-01 1.09e+00 2.85e+01 angle pdb=" N ILE A 154 " pdb=" CA ILE A 154 " pdb=" C ILE A 154 " ideal model delta sigma weight residual 112.90 107.78 5.12 9.60e-01 1.09e+00 2.84e+01 angle pdb=" N ILE C 154 " pdb=" CA ILE C 154 " pdb=" C ILE C 154 " ideal model delta sigma weight residual 112.90 107.83 5.07 9.60e-01 1.09e+00 2.78e+01 angle pdb=" C VAL A 705 " pdb=" N GLN A 706 " pdb=" CA GLN A 706 " ideal model delta sigma weight residual 122.06 112.29 9.77 1.86e+00 2.89e-01 2.76e+01 angle pdb=" C VAL B 705 " pdb=" N GLN B 706 " pdb=" CA GLN B 706 " ideal model delta sigma weight residual 122.06 112.34 9.72 1.86e+00 2.89e-01 2.73e+01 ... (remaining 26857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 10752 17.70 - 35.40: 840 35.40 - 53.10: 111 53.10 - 70.80: 48 70.80 - 88.50: 12 Dihedral angle restraints: 11763 sinusoidal: 4695 harmonic: 7068 Sorted by residual: dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 529 " pdb=" CB CYS B 529 " ideal model delta sinusoidal sigma weight residual 93.00 146.58 -53.58 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 529 " pdb=" CB CYS C 529 " ideal model delta sinusoidal sigma weight residual 93.00 146.56 -53.56 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 529 " pdb=" CB CYS A 529 " ideal model delta sinusoidal sigma weight residual 93.00 146.55 -53.55 1 1.00e+01 1.00e-02 3.90e+01 ... (remaining 11760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2080 0.042 - 0.084: 545 0.084 - 0.126: 229 0.126 - 0.168: 38 0.168 - 0.209: 9 Chirality restraints: 2901 Sorted by residual: chirality pdb=" CB THR C 241 " pdb=" CA THR C 241 " pdb=" OG1 THR C 241 " pdb=" CG2 THR C 241 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB THR A 241 " pdb=" CA THR A 241 " pdb=" OG1 THR A 241 " pdb=" CG2 THR A 241 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB THR B 241 " pdb=" CA THR B 241 " pdb=" OG1 THR B 241 " pdb=" CG2 THR B 241 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2898 not shown) Planarity restraints: 3498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 534 " -0.016 2.00e-02 2.50e+03 1.76e-02 4.64e+00 pdb=" CG HIS C 534 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS C 534 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS C 534 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS C 534 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 534 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 534 " -0.016 2.00e-02 2.50e+03 1.76e-02 4.63e+00 pdb=" CG HIS A 534 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS A 534 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS A 534 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS A 534 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 534 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 534 " -0.016 2.00e-02 2.50e+03 1.75e-02 4.61e+00 pdb=" CG HIS B 534 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS B 534 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 534 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS B 534 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 534 " -0.003 2.00e-02 2.50e+03 ... (remaining 3495 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 369 2.61 - 3.18: 18064 3.18 - 3.75: 31481 3.75 - 4.33: 43854 4.33 - 4.90: 72226 Nonbonded interactions: 165994 Sorted by model distance: nonbonded pdb=" ND2 ASN H 58 " pdb=" O SER A 590 " model vdw 2.033 2.520 nonbonded pdb=" O THR A 143 " pdb=" OH TYR A 452 " model vdw 2.096 2.440 nonbonded pdb=" O THR C 143 " pdb=" OH TYR C 452 " model vdw 2.096 2.440 nonbonded pdb=" O THR B 143 " pdb=" OH TYR B 452 " model vdw 2.096 2.440 nonbonded pdb=" NZ LYS A 253 " pdb=" OD1 ASN A 255 " model vdw 2.108 2.520 ... (remaining 165989 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' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 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: 19.490 Check model and map are aligned: 0.320 Set scattering table: 0.170 Process input model: 52.260 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.005 0.065 19779 Z= 0.339 Angle : 0.775 9.772 26862 Z= 0.451 Chirality : 0.046 0.209 2901 Planarity : 0.004 0.034 3498 Dihedral : 13.196 88.496 7170 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.49 (0.17), residues: 2391 helix: -1.02 (0.26), residues: 333 sheet: -1.17 (0.19), residues: 777 loop : -0.74 (0.16), residues: 1281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.3244 time to fit residues: 178.7734 Evaluate side-chains 244 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 chunk 100 optimal weight: 0.0030 chunk 62 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 0.1980 chunk 217 optimal weight: 5.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82AHIS I 82AHIS ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 HIS ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 HIS ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS A 507 GLN B 438 GLN B 507 GLN B 534 HIS C 343 ASN C 710 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19779 Z= 0.202 Angle : 0.635 9.295 26862 Z= 0.331 Chirality : 0.045 0.221 2901 Planarity : 0.004 0.048 3498 Dihedral : 5.067 23.530 2697 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.77 % Allowed : 8.51 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.12 (0.17), residues: 2391 helix: -0.19 (0.27), residues: 300 sheet: -0.97 (0.18), residues: 921 loop : -0.54 (0.18), residues: 1170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 295 time to evaluate : 2.232 Fit side-chains outliers start: 37 outliers final: 21 residues processed: 311 average time/residue: 0.3014 time to fit residues: 145.6045 Evaluate side-chains 253 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 2.455 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1856 time to fit residues: 10.3181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 194 optimal weight: 0.2980 chunk 216 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 175 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN ** C 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19779 Z= 0.199 Angle : 0.584 13.101 26862 Z= 0.305 Chirality : 0.043 0.219 2901 Planarity : 0.004 0.043 3498 Dihedral : 4.822 21.564 2697 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.01 % Allowed : 10.28 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.03 (0.17), residues: 2391 helix: -0.10 (0.26), residues: 318 sheet: -0.97 (0.18), residues: 924 loop : -0.42 (0.18), residues: 1149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 277 time to evaluate : 2.129 Fit side-chains outliers start: 42 outliers final: 17 residues processed: 302 average time/residue: 0.3012 time to fit residues: 141.4218 Evaluate side-chains 249 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 232 time to evaluate : 2.001 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1826 time to fit residues: 8.4905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.0470 chunk 164 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 231 optimal weight: 0.0980 chunk 114 optimal weight: 0.5980 chunk 207 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 433 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 HIS ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19779 Z= 0.174 Angle : 0.578 10.501 26862 Z= 0.297 Chirality : 0.043 0.194 2901 Planarity : 0.004 0.045 3498 Dihedral : 4.630 22.677 2697 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.72 % Allowed : 12.10 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.87 (0.17), residues: 2391 helix: 0.14 (0.26), residues: 318 sheet: -0.85 (0.18), residues: 897 loop : -0.38 (0.18), residues: 1176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 264 time to evaluate : 2.256 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 17 residues processed: 279 average time/residue: 0.3071 time to fit residues: 133.9534 Evaluate side-chains 244 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 227 time to evaluate : 2.257 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1977 time to fit residues: 9.0493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 172 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 58 optimal weight: 0.0470 overall best weight: 2.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 35 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 343 ASN B 433 HIS ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 19779 Z= 0.400 Angle : 0.659 10.007 26862 Z= 0.345 Chirality : 0.046 0.222 2901 Planarity : 0.005 0.046 3498 Dihedral : 4.927 26.364 2697 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.77 % Allowed : 13.92 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.02 (0.17), residues: 2391 helix: 0.01 (0.27), residues: 321 sheet: -1.09 (0.18), residues: 858 loop : -0.38 (0.18), residues: 1212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 242 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 20 residues processed: 262 average time/residue: 0.2976 time to fit residues: 122.5178 Evaluate side-chains 250 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 230 time to evaluate : 2.248 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1826 time to fit residues: 9.7661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.4980 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 232 optimal weight: 0.5980 chunk 192 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19779 Z= 0.191 Angle : 0.596 9.545 26862 Z= 0.306 Chirality : 0.043 0.225 2901 Planarity : 0.004 0.049 3498 Dihedral : 4.643 20.188 2697 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.24 % Allowed : 14.49 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2391 helix: 0.24 (0.27), residues: 321 sheet: -0.84 (0.18), residues: 837 loop : -0.36 (0.18), residues: 1233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 259 time to evaluate : 2.248 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 273 average time/residue: 0.3064 time to fit residues: 130.6587 Evaluate side-chains 247 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 231 time to evaluate : 2.079 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1975 time to fit residues: 8.3689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 195 optimal weight: 0.0030 chunk 129 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 19779 Z= 0.372 Angle : 0.650 12.206 26862 Z= 0.337 Chirality : 0.044 0.246 2901 Planarity : 0.004 0.048 3498 Dihedral : 4.825 21.054 2697 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.56 % Favored : 95.40 % Rotamer: Outliers : 1.00 % Allowed : 16.07 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.91 (0.17), residues: 2391 helix: -0.15 (0.27), residues: 339 sheet: -0.96 (0.18), residues: 837 loop : -0.30 (0.18), residues: 1215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 243 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 255 average time/residue: 0.3143 time to fit residues: 124.7167 Evaluate side-chains 241 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 230 time to evaluate : 2.137 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1861 time to fit residues: 6.7629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19779 Z= 0.208 Angle : 0.619 11.709 26862 Z= 0.317 Chirality : 0.043 0.234 2901 Planarity : 0.004 0.048 3498 Dihedral : 4.679 21.917 2697 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.91 % Allowed : 16.79 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.17), residues: 2391 helix: -0.26 (0.27), residues: 357 sheet: -0.90 (0.18), residues: 849 loop : -0.17 (0.18), residues: 1185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 247 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 257 average time/residue: 0.3296 time to fit residues: 132.4611 Evaluate side-chains 240 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 3.079 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2328 time to fit residues: 8.1298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.9980 chunk 221 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 203 optimal weight: 0.6980 chunk 214 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19779 Z= 0.216 Angle : 0.614 9.753 26862 Z= 0.315 Chirality : 0.043 0.214 2901 Planarity : 0.004 0.044 3498 Dihedral : 4.614 20.750 2697 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.91 % Allowed : 16.79 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2391 helix: -0.25 (0.26), residues: 357 sheet: -0.86 (0.18), residues: 849 loop : -0.15 (0.19), residues: 1185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 257 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 265 average time/residue: 0.3283 time to fit residues: 133.5981 Evaluate side-chains 244 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 236 time to evaluate : 2.273 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1961 time to fit residues: 5.9154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 10.0000 chunk 227 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 chunk 220 optimal weight: 0.1980 chunk 190 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 147 optimal weight: 0.0010 chunk 116 optimal weight: 4.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 HIS ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19779 Z= 0.220 Angle : 0.626 9.898 26862 Z= 0.320 Chirality : 0.043 0.228 2901 Planarity : 0.004 0.045 3498 Dihedral : 4.572 20.406 2697 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.19 % Allowed : 17.79 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.73 (0.17), residues: 2391 helix: -0.27 (0.26), residues: 357 sheet: -0.87 (0.18), residues: 849 loop : -0.06 (0.19), residues: 1185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 246 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 247 average time/residue: 0.3253 time to fit residues: 123.9511 Evaluate side-chains 238 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 2.180 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3103 time to fit residues: 4.2817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 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 = 0.3556 r_free = 0.3556 target = 0.089997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.073555 restraints weight = 53580.630| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.13 r_work: 0.3095 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19779 Z= 0.425 Angle : 0.689 11.286 26862 Z= 0.360 Chirality : 0.045 0.247 2901 Planarity : 0.004 0.043 3498 Dihedral : 4.863 21.318 2697 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.48 % Allowed : 18.17 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2391 helix: -0.30 (0.27), residues: 339 sheet: -1.04 (0.18), residues: 876 loop : -0.20 (0.19), residues: 1176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3998.57 seconds wall clock time: 74 minutes 12.35 seconds (4452.35 seconds total)