Starting phenix.real_space_refine on Thu Feb 5 15:49:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qnd_53244/02_2026/9qnd_53244.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qnd_53244/02_2026/9qnd_53244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qnd_53244/02_2026/9qnd_53244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qnd_53244/02_2026/9qnd_53244.map" model { file = "/net/cci-nas-00/data/ceres_data/9qnd_53244/02_2026/9qnd_53244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qnd_53244/02_2026/9qnd_53244.cif" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 168 5.16 5 C 12252 2.51 5 N 2964 2.21 5 O 3084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18468 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "B" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "C" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "D" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "E" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "F" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "G" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "H" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "I" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "J" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "K" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "L" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Time building chain proxies: 3.91, per 1000 atoms: 0.21 Number of scatterers: 18468 At special positions: 0 Unit cell: (102.436, 94.5057, 160.594, 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 168 16.00 O 3084 8.00 N 2964 7.00 C 12252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.04 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 179 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 173 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 168 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 179 " distance=2.04 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 173 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 168 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 179 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 173 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 168 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 179 " distance=2.04 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 168 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 179 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 173 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 168 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 179 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 173 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.63 Conformation dependent library (CDL) restraints added in 894.9 milliseconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 75.7% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.600A pdb=" N GLY A 12 " --> pdb=" O THR A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 24 Processing helix chain 'A' and resid 24 through 44 removed outlier: 4.978A pdb=" N GLU A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 105 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 128 through 157 Processing helix chain 'A' and resid 183 through 217 Processing helix chain 'B' and resid 5 through 12 removed outlier: 3.536A pdb=" N GLY B 12 " --> pdb=" O THR B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 24 Processing helix chain 'B' and resid 24 through 44 removed outlier: 4.958A pdb=" N GLU B 41 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 105 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 128 through 157 Processing helix chain 'B' and resid 183 through 217 Processing helix chain 'C' and resid 5 through 12 removed outlier: 3.604A pdb=" N GLY C 12 " --> pdb=" O THR C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 24 Processing helix chain 'C' and resid 24 through 44 removed outlier: 4.977A pdb=" N GLU C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 105 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 128 through 157 Processing helix chain 'C' and resid 183 through 217 Processing helix chain 'D' and resid 5 through 12 removed outlier: 3.587A pdb=" N GLY D 12 " --> pdb=" O THR D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 24 Processing helix chain 'D' and resid 24 through 44 removed outlier: 4.965A pdb=" N GLU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 105 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 128 through 157 Processing helix chain 'D' and resid 183 through 217 Processing helix chain 'E' and resid 5 through 12 removed outlier: 3.589A pdb=" N GLY E 12 " --> pdb=" O THR E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 24 Processing helix chain 'E' and resid 24 through 44 removed outlier: 4.973A pdb=" N GLU E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 105 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 128 through 157 Processing helix chain 'E' and resid 183 through 217 Processing helix chain 'F' and resid 5 through 12 removed outlier: 3.584A pdb=" N GLY F 12 " --> pdb=" O THR F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 24 Processing helix chain 'F' and resid 24 through 44 removed outlier: 4.950A pdb=" N GLU F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER F 42 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 105 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 128 through 157 Processing helix chain 'F' and resid 183 through 217 Processing helix chain 'G' and resid 5 through 12 removed outlier: 3.583A pdb=" N GLY G 12 " --> pdb=" O THR G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 24 through 44 removed outlier: 4.969A pdb=" N GLU G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 105 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 128 through 157 Processing helix chain 'G' and resid 183 through 217 Processing helix chain 'H' and resid 5 through 12 removed outlier: 3.595A pdb=" N GLY H 12 " --> pdb=" O THR H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 24 Processing helix chain 'H' and resid 24 through 44 removed outlier: 4.974A pdb=" N GLU H 41 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 105 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 128 through 157 Processing helix chain 'H' and resid 183 through 217 Processing helix chain 'I' and resid 5 through 12 removed outlier: 3.582A pdb=" N GLY I 12 " --> pdb=" O THR I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 24 Processing helix chain 'I' and resid 24 through 44 removed outlier: 4.968A pdb=" N GLU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER I 42 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 105 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 128 through 157 Processing helix chain 'I' and resid 183 through 217 Processing helix chain 'J' and resid 5 through 12 removed outlier: 3.576A pdb=" N GLY J 12 " --> pdb=" O THR J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 24 Processing helix chain 'J' and resid 24 through 44 removed outlier: 4.947A pdb=" N GLU J 41 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 105 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 128 through 157 Processing helix chain 'J' and resid 183 through 217 Processing helix chain 'K' and resid 5 through 12 removed outlier: 3.569A pdb=" N GLY K 12 " --> pdb=" O THR K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 24 Processing helix chain 'K' and resid 24 through 44 removed outlier: 4.955A pdb=" N GLU K 41 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER K 42 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 105 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 128 through 157 Processing helix chain 'K' and resid 183 through 217 Processing helix chain 'L' and resid 5 through 12 removed outlier: 3.590A pdb=" N GLY L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 24 Processing helix chain 'L' and resid 24 through 44 removed outlier: 4.967A pdb=" N GLU L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER L 42 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 105 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 128 through 157 Processing helix chain 'L' and resid 183 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.826A pdb=" N ILE A 52 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.811A pdb=" N ILE B 52 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.845A pdb=" N ILE C 52 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.829A pdb=" N ILE D 52 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.816A pdb=" N ILE E 52 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.840A pdb=" N ILE F 52 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.833A pdb=" N ILE G 52 " --> pdb=" O PHE G 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.815A pdb=" N ILE H 52 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.843A pdb=" N ILE I 52 " --> pdb=" O PHE I 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.816A pdb=" N ILE J 52 " --> pdb=" O PHE J 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.814A pdb=" N ILE K 52 " --> pdb=" O PHE K 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.838A pdb=" N ILE L 52 " --> pdb=" O PHE L 180 " (cutoff:3.500A) 1381 hydrogen bonds defined for protein. 4107 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: 2.91 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5495 1.34 - 1.46: 4673 1.46 - 1.58: 8552 1.58 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 18960 Sorted by residual: bond pdb=" CB VAL L 43 " pdb=" CG2 VAL L 43 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.57e-01 bond pdb=" CB VAL J 43 " pdb=" CG2 VAL J 43 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.13e-01 bond pdb=" CB VAL I 43 " pdb=" CG2 VAL I 43 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.04e-01 bond pdb=" CB VAL E 43 " pdb=" CG2 VAL E 43 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.02e-01 bond pdb=" CB VAL F 43 " pdb=" CG2 VAL F 43 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.98e-01 ... (remaining 18955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 24697 0.97 - 1.94: 958 1.94 - 2.91: 112 2.91 - 3.88: 72 3.88 - 4.85: 33 Bond angle restraints: 25872 Sorted by residual: angle pdb=" N PRO G 172 " pdb=" CA PRO G 172 " pdb=" C PRO G 172 " ideal model delta sigma weight residual 112.10 115.88 -3.78 2.60e+00 1.48e-01 2.12e+00 angle pdb=" N PRO A 172 " pdb=" CA PRO A 172 " pdb=" C PRO A 172 " ideal model delta sigma weight residual 112.10 115.85 -3.75 2.60e+00 1.48e-01 2.08e+00 angle pdb=" N PRO F 172 " pdb=" CA PRO F 172 " pdb=" C PRO F 172 " ideal model delta sigma weight residual 112.10 115.85 -3.75 2.60e+00 1.48e-01 2.08e+00 angle pdb=" N PRO D 172 " pdb=" CA PRO D 172 " pdb=" C PRO D 172 " ideal model delta sigma weight residual 112.10 115.84 -3.74 2.60e+00 1.48e-01 2.07e+00 angle pdb=" N PRO I 172 " pdb=" CA PRO I 172 " pdb=" C PRO I 172 " ideal model delta sigma weight residual 112.10 115.83 -3.73 2.60e+00 1.48e-01 2.05e+00 ... (remaining 25867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.90: 9444 8.90 - 17.79: 1020 17.79 - 26.69: 365 26.69 - 35.59: 110 35.59 - 44.48: 137 Dihedral angle restraints: 11076 sinusoidal: 4236 harmonic: 6840 Sorted by residual: dihedral pdb=" N GLU C 208 " pdb=" CA GLU C 208 " pdb=" CB GLU C 208 " pdb=" CG GLU C 208 " ideal model delta sinusoidal sigma weight residual -60.00 -104.36 44.36 3 1.50e+01 4.44e-03 7.98e+00 dihedral pdb=" N GLU G 208 " pdb=" CA GLU G 208 " pdb=" CB GLU G 208 " pdb=" CG GLU G 208 " ideal model delta sinusoidal sigma weight residual -60.00 -104.32 44.32 3 1.50e+01 4.44e-03 7.97e+00 dihedral pdb=" N GLU D 208 " pdb=" CA GLU D 208 " pdb=" CB GLU D 208 " pdb=" CG GLU D 208 " ideal model delta sinusoidal sigma weight residual -60.00 -104.26 44.26 3 1.50e+01 4.44e-03 7.96e+00 ... (remaining 11073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1530 0.024 - 0.048: 862 0.048 - 0.071: 488 0.071 - 0.095: 134 0.095 - 0.119: 94 Chirality restraints: 3108 Sorted by residual: chirality pdb=" CA THR B 86 " pdb=" N THR B 86 " pdb=" C THR B 86 " pdb=" CB THR B 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.54e-01 chirality pdb=" CA THR C 86 " pdb=" N THR C 86 " pdb=" C THR C 86 " pdb=" CB THR C 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA THR I 86 " pdb=" N THR I 86 " pdb=" C THR I 86 " pdb=" CB THR I 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 3105 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 57 " -0.016 5.00e-02 4.00e+02 2.36e-02 8.92e-01 pdb=" N PRO A 58 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 57 " 0.016 5.00e-02 4.00e+02 2.36e-02 8.89e-01 pdb=" N PRO D 58 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO D 58 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 58 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN J 57 " 0.015 5.00e-02 4.00e+02 2.34e-02 8.78e-01 pdb=" N PRO J 58 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO J 58 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO J 58 " 0.013 5.00e-02 4.00e+02 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 2.66 - 3.10: 13319 3.10 - 3.55: 21009 3.55 - 4.00: 27160 4.00 - 4.45: 35134 4.45 - 4.90: 51426 Nonbonded interactions: 148048 Sorted by model distance: nonbonded pdb=" N ASN A 14 " pdb=" O ASN A 14 " model vdw 2.656 2.496 nonbonded pdb=" N ASN B 14 " pdb=" O ASN B 14 " model vdw 2.658 2.496 nonbonded pdb=" N ASN K 14 " pdb=" O ASN K 14 " model vdw 2.661 2.496 nonbonded pdb=" N ASN I 14 " pdb=" O ASN I 14 " model vdw 2.661 2.496 nonbonded pdb=" N ASN L 14 " pdb=" O ASN L 14 " model vdw 2.662 2.496 ... (remaining 148043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.730 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.830 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18996 Z= 0.129 Angle : 0.484 4.855 25944 Z= 0.260 Chirality : 0.040 0.119 3108 Planarity : 0.003 0.024 3084 Dihedral : 10.481 44.485 6528 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.58 (0.17), residues: 2268 helix: 3.29 (0.11), residues: 1656 sheet: 1.63 (0.47), residues: 132 loop : -1.01 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 164 TYR 0.011 0.001 TYR E 65 PHE 0.009 0.002 PHE L 51 TRP 0.007 0.001 TRP B 77 HIS 0.002 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00280 (18960) covalent geometry : angle 0.48096 (25872) SS BOND : bond 0.00348 ( 36) SS BOND : angle 1.09669 ( 72) hydrogen bonds : bond 0.11399 ( 1381) hydrogen bonds : angle 4.07841 ( 4107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.662 Fit side-chains REVERT: A 22 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.7957 (ttm-80) REVERT: B 16 HIS cc_start: 0.8602 (m170) cc_final: 0.8354 (m-70) REVERT: B 22 ARG cc_start: 0.8413 (ttm-80) cc_final: 0.7929 (ttm-80) REVERT: C 16 HIS cc_start: 0.8375 (m170) cc_final: 0.8167 (m-70) REVERT: C 22 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.7970 (ttm-80) REVERT: C 211 TYR cc_start: 0.7680 (t80) cc_final: 0.7475 (t80) REVERT: D 22 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.8074 (ttm-80) REVERT: E 16 HIS cc_start: 0.8477 (m170) cc_final: 0.8226 (m-70) REVERT: E 22 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.8123 (ttm-80) REVERT: F 22 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.8028 (ttm-80) REVERT: H 22 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.8120 (ttm-80) REVERT: I 16 HIS cc_start: 0.8429 (m170) cc_final: 0.8201 (m-70) REVERT: I 22 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.7986 (ttm-80) REVERT: J 22 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.8069 (ttm-80) REVERT: K 22 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.8029 (ttm-80) REVERT: L 22 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8000 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.4961 time to fit residues: 235.1943 Evaluate side-chains 248 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.0370 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 100 HIS A 175 ASN B 16 HIS B 67 GLN B 175 ASN C 16 HIS C 67 GLN C 100 HIS C 175 ASN D 67 GLN D 175 ASN E 67 GLN E 175 ASN F 67 GLN F 175 ASN G 67 GLN G 175 ASN H 67 GLN H 175 ASN I 16 HIS I 67 GLN I 100 HIS I 175 ASN J 67 GLN J 175 ASN K 67 GLN K 175 ASN L 67 GLN L 100 HIS L 175 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.084278 restraints weight = 20641.403| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.60 r_work: 0.2829 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18996 Z= 0.129 Angle : 0.492 4.736 25944 Z= 0.262 Chirality : 0.040 0.154 3108 Planarity : 0.003 0.026 3084 Dihedral : 3.203 18.483 2496 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.22 % Allowed : 11.18 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.80 (0.17), residues: 2268 helix: 3.50 (0.11), residues: 1656 sheet: 1.63 (0.46), residues: 132 loop : -1.09 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 22 TYR 0.013 0.001 TYR E 65 PHE 0.010 0.002 PHE C 51 TRP 0.005 0.001 TRP D 132 HIS 0.006 0.001 HIS J 16 Details of bonding type rmsd covalent geometry : bond 0.00283 (18960) covalent geometry : angle 0.49140 (25872) SS BOND : bond 0.00200 ( 36) SS BOND : angle 0.62561 ( 72) hydrogen bonds : bond 0.05633 ( 1381) hydrogen bonds : angle 3.29680 ( 4107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 247 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 HIS cc_start: 0.8621 (m-70) cc_final: 0.8292 (m-70) REVERT: B 22 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7902 (ttp-110) REVERT: B 105 MET cc_start: 0.4324 (mpp) cc_final: 0.3360 (pmt) REVERT: C 16 HIS cc_start: 0.8415 (m-70) cc_final: 0.8126 (m-70) REVERT: C 22 ARG cc_start: 0.8262 (ttm-80) cc_final: 0.7956 (ttm-80) REVERT: C 105 MET cc_start: 0.4210 (OUTLIER) cc_final: 0.3527 (pmt) REVERT: C 144 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8530 (mp) REVERT: D 22 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.8067 (ttm-80) REVERT: D 105 MET cc_start: 0.4528 (mmm) cc_final: 0.3372 (pmt) REVERT: E 16 HIS cc_start: 0.8428 (m170) cc_final: 0.8208 (m-70) REVERT: F 22 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7930 (ttm-80) REVERT: F 144 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8533 (mp) REVERT: G 22 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8037 (ttp80) REVERT: H 22 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.8071 (ttm-80) REVERT: H 105 MET cc_start: 0.4500 (mmm) cc_final: 0.3570 (pmt) REVERT: I 16 HIS cc_start: 0.8486 (m-70) cc_final: 0.8197 (m-70) REVERT: I 22 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.8005 (ttm-80) REVERT: I 105 MET cc_start: 0.4028 (mpm) cc_final: 0.3316 (pmt) REVERT: I 144 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8533 (mp) REVERT: J 22 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.8077 (ttm-80) REVERT: J 41 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: K 41 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: L 16 HIS cc_start: 0.8320 (m-70) cc_final: 0.8063 (m90) REVERT: L 22 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7874 (ttm-80) REVERT: L 144 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8535 (mp) outliers start: 46 outliers final: 22 residues processed: 262 average time/residue: 0.6198 time to fit residues: 181.4823 Evaluate side-chains 268 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain J residue 41 GLU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 209 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 15 optimal weight: 0.0060 chunk 199 optimal weight: 8.9990 chunk 61 optimal weight: 0.0170 chunk 112 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS D 16 HIS E 16 HIS G 16 HIS K 16 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.135268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.087372 restraints weight = 20819.418| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.60 r_work: 0.2882 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 18996 Z= 0.102 Angle : 0.432 4.671 25944 Z= 0.226 Chirality : 0.038 0.140 3108 Planarity : 0.003 0.021 3084 Dihedral : 2.968 14.317 2496 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.99 % Allowed : 10.07 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.17 (0.17), residues: 2268 helix: 3.82 (0.11), residues: 1656 sheet: 1.73 (0.47), residues: 132 loop : -1.18 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 22 TYR 0.009 0.001 TYR D 160 PHE 0.007 0.001 PHE G 51 TRP 0.005 0.001 TRP D 132 HIS 0.003 0.001 HIS L 16 Details of bonding type rmsd covalent geometry : bond 0.00192 (18960) covalent geometry : angle 0.43148 (25872) SS BOND : bond 0.00068 ( 36) SS BOND : angle 0.51283 ( 72) hydrogen bonds : bond 0.04558 ( 1381) hydrogen bonds : angle 3.06374 ( 4107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 278 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.8047 (ttp80) REVERT: A 105 MET cc_start: 0.3906 (OUTLIER) cc_final: 0.3594 (pmt) REVERT: B 16 HIS cc_start: 0.8591 (m-70) cc_final: 0.8285 (m-70) REVERT: B 22 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7901 (ttp-110) REVERT: B 105 MET cc_start: 0.4282 (mpp) cc_final: 0.3311 (pmt) REVERT: C 16 HIS cc_start: 0.8453 (m-70) cc_final: 0.8156 (m-70) REVERT: C 22 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7969 (ttm-80) REVERT: C 105 MET cc_start: 0.3995 (OUTLIER) cc_final: 0.3514 (pmt) REVERT: D 16 HIS cc_start: 0.8438 (m-70) cc_final: 0.8225 (m90) REVERT: D 22 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.8035 (ttm-80) REVERT: E 16 HIS cc_start: 0.8485 (m-70) cc_final: 0.8185 (m-70) REVERT: E 105 MET cc_start: 0.4314 (mmm) cc_final: 0.3419 (pmt) REVERT: F 22 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7936 (ttm-80) REVERT: F 144 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8528 (mp) REVERT: G 22 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.7983 (ttp80) REVERT: H 22 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.8104 (ttm-80) REVERT: H 105 MET cc_start: 0.4454 (mmm) cc_final: 0.3590 (pmt) REVERT: I 16 HIS cc_start: 0.8506 (m-70) cc_final: 0.8202 (m-70) REVERT: I 22 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7986 (ttm-80) REVERT: I 105 MET cc_start: 0.4118 (OUTLIER) cc_final: 0.3517 (pmt) REVERT: J 22 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.8053 (ttm-80) REVERT: K 41 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: K 105 MET cc_start: 0.4770 (mmm) cc_final: 0.3668 (pmt) REVERT: L 22 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7970 (ttm-80) REVERT: L 105 MET cc_start: 0.3909 (OUTLIER) cc_final: 0.3460 (pmt) outliers start: 62 outliers final: 23 residues processed: 314 average time/residue: 0.5109 time to fit residues: 181.7821 Evaluate side-chains 289 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 260 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 209 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 219 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 210 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 190 optimal weight: 20.0000 chunk 153 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 HIS H 16 HIS ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.082368 restraints weight = 20841.229| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.62 r_work: 0.2795 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18996 Z= 0.160 Angle : 0.521 6.089 25944 Z= 0.275 Chirality : 0.042 0.162 3108 Planarity : 0.003 0.026 3084 Dihedral : 3.160 11.334 2496 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.50 % Allowed : 12.19 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.87 (0.17), residues: 2268 helix: 3.59 (0.11), residues: 1656 sheet: 1.54 (0.46), residues: 132 loop : -1.21 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 22 TYR 0.016 0.001 TYR E 65 PHE 0.013 0.002 PHE H 180 TRP 0.005 0.001 TRP A 24 HIS 0.003 0.001 HIS J 94 Details of bonding type rmsd covalent geometry : bond 0.00384 (18960) covalent geometry : angle 0.51985 (25872) SS BOND : bond 0.00324 ( 36) SS BOND : angle 0.75027 ( 72) hydrogen bonds : bond 0.05991 ( 1381) hydrogen bonds : angle 3.14924 ( 4107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 250 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8018 (ttp80) REVERT: A 105 MET cc_start: 0.3988 (OUTLIER) cc_final: 0.3606 (pmt) REVERT: B 16 HIS cc_start: 0.8595 (m-70) cc_final: 0.8281 (m-70) REVERT: B 22 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7857 (ttp-110) REVERT: C 105 MET cc_start: 0.4055 (OUTLIER) cc_final: 0.3534 (pmt) REVERT: D 22 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7993 (ttm-80) REVERT: D 105 MET cc_start: 0.4422 (mmm) cc_final: 0.3422 (pmt) REVERT: E 16 HIS cc_start: 0.8515 (m-70) cc_final: 0.8183 (m-70) REVERT: E 105 MET cc_start: 0.4306 (mmm) cc_final: 0.3448 (pmt) REVERT: F 144 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8526 (mp) REVERT: G 16 HIS cc_start: 0.8440 (m-70) cc_final: 0.8185 (m90) REVERT: H 16 HIS cc_start: 0.8463 (m-70) cc_final: 0.8199 (m-70) REVERT: H 22 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.8109 (ttm-80) REVERT: H 105 MET cc_start: 0.4459 (mmm) cc_final: 0.3592 (pmt) REVERT: I 144 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8512 (mp) REVERT: J 22 ARG cc_start: 0.8265 (ttm-80) cc_final: 0.8028 (ttm-80) REVERT: K 41 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: K 105 MET cc_start: 0.4784 (mmm) cc_final: 0.3748 (pmt) REVERT: L 22 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7959 (ttm-80) outliers start: 52 outliers final: 27 residues processed: 272 average time/residue: 0.6563 time to fit residues: 198.1105 Evaluate side-chains 274 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 209 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 217 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS K 16 HIS ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.082500 restraints weight = 20650.032| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.61 r_work: 0.2796 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18996 Z= 0.146 Angle : 0.501 5.549 25944 Z= 0.267 Chirality : 0.041 0.157 3108 Planarity : 0.003 0.027 3084 Dihedral : 3.152 10.691 2496 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.70 % Allowed : 11.85 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.86 (0.17), residues: 2268 helix: 3.60 (0.11), residues: 1656 sheet: 1.48 (0.46), residues: 132 loop : -1.28 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 22 TYR 0.015 0.001 TYR C 65 PHE 0.013 0.002 PHE E 180 TRP 0.005 0.001 TRP K 24 HIS 0.003 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00344 (18960) covalent geometry : angle 0.49982 (25872) SS BOND : bond 0.00283 ( 36) SS BOND : angle 0.75304 ( 72) hydrogen bonds : bond 0.05844 ( 1381) hydrogen bonds : angle 3.11041 ( 4107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8477 (mp) REVERT: B 16 HIS cc_start: 0.8604 (m-70) cc_final: 0.8248 (m-70) REVERT: B 22 ARG cc_start: 0.8110 (ttm-80) cc_final: 0.7794 (ttm-80) REVERT: C 105 MET cc_start: 0.4063 (OUTLIER) cc_final: 0.3555 (pmt) REVERT: D 16 HIS cc_start: 0.8436 (m-70) cc_final: 0.8176 (m90) REVERT: D 22 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.8022 (ttm-80) REVERT: D 105 MET cc_start: 0.4468 (mmm) cc_final: 0.3507 (pmt) REVERT: E 16 HIS cc_start: 0.8499 (m-70) cc_final: 0.8273 (m-70) REVERT: E 22 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.8082 (ttp80) REVERT: F 144 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8525 (mp) REVERT: G 16 HIS cc_start: 0.8385 (m-70) cc_final: 0.8155 (m90) REVERT: G 105 MET cc_start: 0.4411 (mmm) cc_final: 0.3381 (pmt) REVERT: H 16 HIS cc_start: 0.8455 (m-70) cc_final: 0.8172 (m-70) REVERT: H 22 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8054 (ttm-80) REVERT: I 105 MET cc_start: 0.4195 (OUTLIER) cc_final: 0.3530 (pmt) REVERT: J 22 ARG cc_start: 0.8292 (ttm-80) cc_final: 0.8053 (ttm-80) REVERT: K 22 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.8329 (ttm-80) REVERT: K 41 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: K 105 MET cc_start: 0.4829 (mmm) cc_final: 0.3770 (pmt) outliers start: 56 outliers final: 31 residues processed: 273 average time/residue: 0.6731 time to fit residues: 204.7941 Evaluate side-chains 272 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 209 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 178 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 147 optimal weight: 0.0020 chunk 47 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 152 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 15 optimal weight: 0.4980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS K 16 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.087204 restraints weight = 20765.836| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.60 r_work: 0.2880 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 18996 Z= 0.102 Angle : 0.433 5.293 25944 Z= 0.226 Chirality : 0.038 0.140 3108 Planarity : 0.002 0.019 3084 Dihedral : 2.889 10.377 2496 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.93 % Allowed : 13.20 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.26 (0.17), residues: 2268 helix: 3.92 (0.11), residues: 1656 sheet: 1.79 (0.48), residues: 132 loop : -1.32 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 22 TYR 0.010 0.001 TYR G 160 PHE 0.007 0.001 PHE G 51 TRP 0.009 0.001 TRP B 44 HIS 0.002 0.001 HIS H 73 Details of bonding type rmsd covalent geometry : bond 0.00203 (18960) covalent geometry : angle 0.43274 (25872) SS BOND : bond 0.00072 ( 36) SS BOND : angle 0.53808 ( 72) hydrogen bonds : bond 0.04386 ( 1381) hydrogen bonds : angle 2.92995 ( 4107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7558 (ppt170) REVERT: A 16 HIS cc_start: 0.8568 (m-70) cc_final: 0.8268 (m90) REVERT: B 16 HIS cc_start: 0.8586 (m-70) cc_final: 0.8249 (m-70) REVERT: B 22 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7852 (ttp-110) REVERT: C 105 MET cc_start: 0.4046 (OUTLIER) cc_final: 0.3555 (pmt) REVERT: E 16 HIS cc_start: 0.8482 (m-70) cc_final: 0.8244 (m-70) REVERT: E 22 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.8102 (ttp80) REVERT: H 16 HIS cc_start: 0.8447 (m-70) cc_final: 0.8157 (m-70) REVERT: H 22 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.8031 (ttm-80) REVERT: H 105 MET cc_start: 0.4362 (mmm) cc_final: 0.3529 (pmt) REVERT: I 105 MET cc_start: 0.4167 (OUTLIER) cc_final: 0.3591 (pmt) REVERT: J 22 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.8042 (ttm-80) REVERT: K 22 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.8321 (ttm-80) REVERT: K 41 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: K 105 MET cc_start: 0.4765 (mmm) cc_final: 0.3774 (pmt) outliers start: 40 outliers final: 22 residues processed: 281 average time/residue: 0.6032 time to fit residues: 190.7113 Evaluate side-chains 273 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 209 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 73 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 211 optimal weight: 7.9990 chunk 214 optimal weight: 0.3980 chunk 94 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 16 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.084699 restraints weight = 20891.490| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.62 r_work: 0.2834 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18996 Z= 0.117 Angle : 0.461 5.198 25944 Z= 0.244 Chirality : 0.039 0.146 3108 Planarity : 0.003 0.021 3084 Dihedral : 2.960 10.398 2496 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.64 % Allowed : 13.34 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.17 (0.17), residues: 2268 helix: 3.85 (0.11), residues: 1656 sheet: 1.69 (0.47), residues: 132 loop : -1.29 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 22 TYR 0.013 0.001 TYR I 65 PHE 0.011 0.002 PHE H 180 TRP 0.004 0.001 TRP I 132 HIS 0.003 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00257 (18960) covalent geometry : angle 0.46095 (25872) SS BOND : bond 0.00173 ( 36) SS BOND : angle 0.58211 ( 72) hydrogen bonds : bond 0.04989 ( 1381) hydrogen bonds : angle 2.95520 ( 4107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7483 (ppt170) REVERT: A 16 HIS cc_start: 0.8570 (m-70) cc_final: 0.8166 (m90) REVERT: B 16 HIS cc_start: 0.8580 (m-70) cc_final: 0.8230 (m-70) REVERT: B 22 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7786 (ttm-80) REVERT: C 105 MET cc_start: 0.4054 (OUTLIER) cc_final: 0.3550 (pmt) REVERT: D 16 HIS cc_start: 0.8374 (m-70) cc_final: 0.8119 (m90) REVERT: D 105 MET cc_start: 0.4261 (mmm) cc_final: 0.3383 (pmt) REVERT: E 16 HIS cc_start: 0.8482 (m-70) cc_final: 0.8222 (m-70) REVERT: H 16 HIS cc_start: 0.8455 (m-70) cc_final: 0.8158 (m-70) REVERT: H 22 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.8010 (ttm-80) REVERT: J 22 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.8028 (ttm-80) REVERT: K 41 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: K 105 MET cc_start: 0.4691 (mmm) cc_final: 0.3753 (pmt) outliers start: 34 outliers final: 25 residues processed: 267 average time/residue: 0.6498 time to fit residues: 194.0476 Evaluate side-chains 269 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 209 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 96 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 189 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 16 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.084959 restraints weight = 20678.980| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.61 r_work: 0.2841 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18996 Z= 0.112 Angle : 0.449 4.900 25944 Z= 0.237 Chirality : 0.039 0.145 3108 Planarity : 0.003 0.020 3084 Dihedral : 2.941 10.440 2496 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.69 % Allowed : 13.39 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.19 (0.17), residues: 2268 helix: 3.86 (0.11), residues: 1656 sheet: 1.73 (0.47), residues: 132 loop : -1.29 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 22 TYR 0.012 0.001 TYR D 160 PHE 0.010 0.002 PHE E 180 TRP 0.004 0.001 TRP I 132 HIS 0.003 0.001 HIS K 73 Details of bonding type rmsd covalent geometry : bond 0.00240 (18960) covalent geometry : angle 0.44875 (25872) SS BOND : bond 0.00156 ( 36) SS BOND : angle 0.56260 ( 72) hydrogen bonds : bond 0.04852 ( 1381) hydrogen bonds : angle 2.94270 ( 4107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 HIS cc_start: 0.8549 (m-70) cc_final: 0.8223 (m90) REVERT: A 105 MET cc_start: 0.3840 (OUTLIER) cc_final: 0.3604 (pmt) REVERT: B 22 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7778 (ttm-80) REVERT: C 105 MET cc_start: 0.4081 (OUTLIER) cc_final: 0.3573 (pmt) REVERT: D 16 HIS cc_start: 0.8352 (m-70) cc_final: 0.8128 (m90) REVERT: D 105 MET cc_start: 0.4290 (mmm) cc_final: 0.3425 (pmt) REVERT: E 16 HIS cc_start: 0.8478 (m-70) cc_final: 0.8195 (m-70) REVERT: G 105 MET cc_start: 0.4400 (mmm) cc_final: 0.3449 (pmt) REVERT: H 16 HIS cc_start: 0.8437 (m-70) cc_final: 0.8143 (m-70) REVERT: H 22 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.7974 (ttp-110) REVERT: H 105 MET cc_start: 0.4462 (mmm) cc_final: 0.3710 (pmt) REVERT: J 22 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.8015 (ttm-80) REVERT: K 22 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.8329 (ttm-80) REVERT: K 105 MET cc_start: 0.4714 (mmm) cc_final: 0.3773 (pmt) outliers start: 35 outliers final: 24 residues processed: 269 average time/residue: 0.6715 time to fit residues: 201.7556 Evaluate side-chains 267 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 209 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 66 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 226 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 16 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.133918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.085685 restraints weight = 20818.205| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.61 r_work: 0.2853 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18996 Z= 0.105 Angle : 0.441 4.846 25944 Z= 0.232 Chirality : 0.039 0.141 3108 Planarity : 0.003 0.019 3084 Dihedral : 2.905 10.447 2496 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.45 % Allowed : 13.78 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.25 (0.17), residues: 2268 helix: 3.91 (0.11), residues: 1656 sheet: 1.75 (0.47), residues: 132 loop : -1.31 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 22 TYR 0.013 0.001 TYR J 160 PHE 0.009 0.002 PHE K 180 TRP 0.004 0.001 TRP I 132 HIS 0.003 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00218 (18960) covalent geometry : angle 0.44041 (25872) SS BOND : bond 0.00115 ( 36) SS BOND : angle 0.52903 ( 72) hydrogen bonds : bond 0.04628 ( 1381) hydrogen bonds : angle 2.91687 ( 4107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.3816 (OUTLIER) cc_final: 0.3591 (pmt) REVERT: B 22 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7755 (ttm-80) REVERT: C 105 MET cc_start: 0.4106 (OUTLIER) cc_final: 0.3601 (pmt) REVERT: D 16 HIS cc_start: 0.8332 (m-70) cc_final: 0.8085 (m90) REVERT: E 16 HIS cc_start: 0.8479 (m-70) cc_final: 0.8198 (m-70) REVERT: F 16 HIS cc_start: 0.8408 (m-70) cc_final: 0.8181 (m90) REVERT: G 16 HIS cc_start: 0.8321 (m-70) cc_final: 0.8102 (m90) REVERT: H 16 HIS cc_start: 0.8407 (m-70) cc_final: 0.8107 (m-70) REVERT: H 22 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.7966 (ttp-110) REVERT: H 105 MET cc_start: 0.4470 (mmm) cc_final: 0.3730 (pmt) REVERT: J 22 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.8019 (ttm-80) REVERT: K 105 MET cc_start: 0.4670 (mmm) cc_final: 0.3738 (pmt) outliers start: 30 outliers final: 23 residues processed: 262 average time/residue: 0.6295 time to fit residues: 184.8271 Evaluate side-chains 267 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 HIS K 16 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.084684 restraints weight = 20758.793| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.61 r_work: 0.2834 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18996 Z= 0.115 Angle : 0.457 4.848 25944 Z= 0.241 Chirality : 0.039 0.147 3108 Planarity : 0.003 0.021 3084 Dihedral : 2.961 14.393 2496 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.20 % Allowed : 14.07 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.19 (0.17), residues: 2268 helix: 3.86 (0.11), residues: 1656 sheet: 1.70 (0.47), residues: 132 loop : -1.28 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 22 TYR 0.018 0.001 TYR C 160 PHE 0.011 0.002 PHE E 180 TRP 0.004 0.001 TRP B 132 HIS 0.003 0.001 HIS H 73 Details of bonding type rmsd covalent geometry : bond 0.00253 (18960) covalent geometry : angle 0.45643 (25872) SS BOND : bond 0.00169 ( 36) SS BOND : angle 0.57640 ( 72) hydrogen bonds : bond 0.04917 ( 1381) hydrogen bonds : angle 2.94215 ( 4107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.3834 (OUTLIER) cc_final: 0.3608 (pmt) REVERT: B 22 ARG cc_start: 0.8057 (ttm-80) cc_final: 0.7752 (ttm-80) REVERT: D 16 HIS cc_start: 0.8324 (m-70) cc_final: 0.8060 (m90) REVERT: E 16 HIS cc_start: 0.8469 (m-70) cc_final: 0.8174 (m-70) REVERT: F 16 HIS cc_start: 0.8429 (m-70) cc_final: 0.8193 (m90) REVERT: G 16 HIS cc_start: 0.8328 (m-70) cc_final: 0.8097 (m90) REVERT: H 16 HIS cc_start: 0.8404 (m-70) cc_final: 0.8093 (m-70) REVERT: H 22 ARG cc_start: 0.8262 (ttm-80) cc_final: 0.7948 (ttp-110) REVERT: H 105 MET cc_start: 0.4422 (mmm) cc_final: 0.3714 (pmt) REVERT: J 22 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.8006 (ttm-80) REVERT: K 105 MET cc_start: 0.4733 (mmm) cc_final: 0.3808 (pmt) outliers start: 25 outliers final: 24 residues processed: 260 average time/residue: 0.6414 time to fit residues: 186.8533 Evaluate side-chains 267 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 16 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.084078 restraints weight = 20839.352| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.62 r_work: 0.2826 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18996 Z= 0.120 Angle : 0.463 4.784 25944 Z= 0.245 Chirality : 0.039 0.148 3108 Planarity : 0.003 0.021 3084 Dihedral : 2.989 10.849 2496 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.35 % Allowed : 13.97 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.16 (0.17), residues: 2268 helix: 3.83 (0.11), residues: 1656 sheet: 1.69 (0.47), residues: 132 loop : -1.25 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 22 TYR 0.013 0.001 TYR I 65 PHE 0.011 0.002 PHE K 180 TRP 0.006 0.001 TRP G 24 HIS 0.003 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00264 (18960) covalent geometry : angle 0.46273 (25872) SS BOND : bond 0.00190 ( 36) SS BOND : angle 0.60093 ( 72) hydrogen bonds : bond 0.05101 ( 1381) hydrogen bonds : angle 2.97216 ( 4107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7284.70 seconds wall clock time: 124 minutes 38.19 seconds (7478.19 seconds total)