Starting phenix.real_space_refine on Thu Jul 25 11:13:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppq_17808/07_2024/8ppq_17808_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppq_17808/07_2024/8ppq_17808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppq_17808/07_2024/8ppq_17808.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppq_17808/07_2024/8ppq_17808.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppq_17808/07_2024/8ppq_17808_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppq_17808/07_2024/8ppq_17808_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.172 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 102 5.16 5 C 9271 2.51 5 N 2578 2.21 5 O 2745 1.98 5 H 14659 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 2": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 99": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 316": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 339": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 343": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 401": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 472": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 99": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 316": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 339": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 343": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 401": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 472": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 2": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 99": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 316": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 339": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 343": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 401": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 472": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 119": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 119": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 119": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 29355 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 7502 Classifications: {'peptide': 496} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 476} Chain: "B" Number of atoms: 7501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 7501 Classifications: {'peptide': 496} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 476} Chain: "C" Number of atoms: 7501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 7501 Classifications: {'peptide': 496} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 476} Chain: "a" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2296 Classifications: {'peptide': 147} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 2 Chain: "b" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2251 Classifications: {'peptide': 144} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain breaks: 2 Chain: "c" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2262 Classifications: {'peptide': 144} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain breaks: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.85, per 1000 atoms: 0.44 Number of scatterers: 29355 At special positions: 0 Unit cell: (172, 160.175, 139.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 102 16.00 O 2745 8.00 N 2578 7.00 C 9271 6.00 H 14659 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=1.99 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=1.96 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.00 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 290 " distance=2.04 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 338 " distance=2.02 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.01 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 121 " distance=1.98 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.05 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 290 " distance=2.00 Simple disulfide: pdb=" SG CYS B 307 " - pdb=" SG CYS B 338 " distance=2.02 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.01 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.00 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.04 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.04 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 290 " distance=2.01 Simple disulfide: pdb=" SG CYS C 307 " - pdb=" SG CYS C 338 " distance=2.02 Simple disulfide: pdb=" SG CYS a 30 " - pdb=" SG CYS a 65 " distance=1.98 Simple disulfide: pdb=" SG CYS a 49 " - pdb=" SG CYS a 63 " distance=1.99 Simple disulfide: pdb=" SG CYS b 30 " - pdb=" SG CYS b 65 " distance=2.01 Simple disulfide: pdb=" SG CYS b 49 " - pdb=" SG CYS b 63 " distance=2.01 Simple disulfide: pdb=" SG CYS c 30 " - pdb=" SG CYS c 65 " distance=2.02 Simple disulfide: pdb=" SG CYS c 49 " - pdb=" SG CYS c 63 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 154 " " NAG B 501 " - " ASN B 154 " " NAG C 501 " - " ASN C 154 " Time building additional restraints: 20.77 Conformation dependent library (CDL) restraints added in 3.3 seconds 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3460 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 34 sheets defined 25.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.556A pdb=" N LEU A 6 " --> pdb=" O CYS A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.809A pdb=" N HIS A 86 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.660A pdb=" N ASP A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 240 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 397 through 416 Processing helix chain 'A' and resid 417 through 421 removed outlier: 4.185A pdb=" N TRP A 421 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 443 removed outlier: 4.536A pdb=" N GLY A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 469 removed outlier: 3.833A pdb=" N LEU A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 Processing helix chain 'A' and resid 477 through 490 removed outlier: 4.231A pdb=" N LEU A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 6 removed outlier: 4.077A pdb=" N HIS B 5 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 6 " --> pdb=" O CYS B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 260 through 268 Processing helix chain 'B' and resid 397 through 417 removed outlier: 3.903A pdb=" N GLY B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 421 removed outlier: 4.055A pdb=" N TRP B 421 " --> pdb=" O GLU B 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 421' Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 443 through 447 removed outlier: 3.693A pdb=" N ASN B 446 " --> pdb=" O GLY B 443 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 447 " --> pdb=" O ALA B 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 443 through 447' Processing helix chain 'B' and resid 454 through 469 removed outlier: 3.683A pdb=" N LEU B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 476 Processing helix chain 'B' and resid 477 through 490 removed outlier: 4.119A pdb=" N LEU B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 removed outlier: 3.723A pdb=" N HIS C 5 " --> pdb=" O ARG C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.866A pdb=" N HIS C 86 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 260 through 268 Processing helix chain 'C' and resid 397 through 417 removed outlier: 4.102A pdb=" N GLY C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 421 removed outlier: 4.189A pdb=" N TRP C 421 " --> pdb=" O GLU C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 418 through 421' Processing helix chain 'C' and resid 425 through 442 Processing helix chain 'C' and resid 443 through 447 removed outlier: 3.737A pdb=" N ASN C 446 " --> pdb=" O GLY C 443 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 447 " --> pdb=" O ALA C 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 443 through 447' Processing helix chain 'C' and resid 454 through 469 removed outlier: 3.859A pdb=" N LEU C 458 " --> pdb=" O PHE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 Processing helix chain 'C' and resid 477 through 490 removed outlier: 4.383A pdb=" N LEU C 481 " --> pdb=" O SER C 477 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 127 Processing helix chain 'a' and resid 127 through 142 Processing helix chain 'a' and resid 144 through 159 Processing helix chain 'a' and resid 160 through 162 No H-bonds generated for 'chain 'a' and resid 160 through 162' Processing helix chain 'b' and resid 113 through 127 Processing helix chain 'b' and resid 127 through 142 Processing helix chain 'b' and resid 144 through 158 Processing helix chain 'c' and resid 113 through 127 Processing helix chain 'c' and resid 127 through 142 Processing helix chain 'c' and resid 144 through 159 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.475A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 removed outlier: 3.507A pdb=" N VAL A 21 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 165 removed outlier: 3.560A pdb=" N LYS A 161 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216 removed outlier: 6.025A pdb=" N ALA A 127 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU A 58 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY A 129 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 54 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 228 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 97 removed outlier: 6.736A pdb=" N SER A 112 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA A 72 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 114 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL A 70 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS A 116 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR A 68 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 120 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 15.404A pdb=" N LYS A 64 " --> pdb=" O TRP a 40 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ASP a 42 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER A 66 " --> pdb=" O ASP a 42 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER a 44 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU a 48 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ALA A 72 " --> pdb=" O GLU a 48 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP a 43 " --> pdb=" O ARG a 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 244 removed outlier: 3.612A pdb=" N GLU A 243 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 320 removed outlier: 6.550A pdb=" N GLU A 329 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA A 317 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 327 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA9, first strand: chain 'A' and resid 342 through 346 removed outlier: 3.733A pdb=" N GLY A 379 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 394 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 381 " --> pdb=" O TRP A 392 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 392 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'B' and resid 21 through 26 removed outlier: 3.814A pdb=" N HIS B 287 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA B 189 " --> pdb=" O HIS B 287 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 161 through 165 removed outlier: 3.588A pdb=" N GLU B 277 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.768A pdb=" N ALA B 54 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.544A pdb=" N LYS B 228 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 63 through 73 removed outlier: 3.750A pdb=" N ALA B 120 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 68 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N CYS B 116 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 114 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA B 72 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER B 112 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 242 through 244 Processing sheet with id=AB8, first strand: chain 'B' and resid 312 through 314 removed outlier: 3.515A pdb=" N THR B 313 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 319 through 320 removed outlier: 3.625A pdb=" N THR B 319 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 338 through 339 Processing sheet with id=AC2, first strand: chain 'B' and resid 342 through 345 Processing sheet with id=AC3, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.907A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 21 through 25 removed outlier: 3.566A pdb=" N VAL C 21 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS C 287 " --> pdb=" O ALA C 189 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 161 through 165 Processing sheet with id=AC6, first strand: chain 'C' and resid 213 through 216 removed outlier: 3.922A pdb=" N ARG C 57 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL C 131 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS C 55 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 90 through 97 removed outlier: 5.203A pdb=" N LYS C 118 " --> pdb=" O ASP C 67 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASP C 67 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA C 120 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU C 65 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 16.069A pdb=" N LYS C 64 " --> pdb=" O TRP c 40 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N ASP c 42 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER C 66 " --> pdb=" O ASP c 42 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER c 44 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU c 48 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA C 72 " --> pdb=" O GLU c 48 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP c 43 " --> pdb=" O ARG c 77 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG c 77 " --> pdb=" O ASP c 43 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL c 71 " --> pdb=" O CYS c 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 242 through 244 removed outlier: 3.707A pdb=" N GLU C 243 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR C 255 " --> pdb=" O GLU C 243 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 312 through 314 Processing sheet with id=AD1, first strand: chain 'C' and resid 319 through 320 Processing sheet with id=AD2, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AD3, first strand: chain 'C' and resid 342 through 346 Processing sheet with id=AD4, first strand: chain 'a' and resid 21 through 24 removed outlier: 3.993A pdb=" N THR a 21 " --> pdb=" O ILE a 32 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE a 32 " --> pdb=" O THR a 21 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'b' and resid 2 through 4 removed outlier: 7.459A pdb=" N ASP b 43 " --> pdb=" O ARG b 77 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'b' and resid 22 through 25 removed outlier: 3.534A pdb=" N PHE b 64 " --> pdb=" O VAL b 31 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'c' and resid 21 through 25 removed outlier: 3.735A pdb=" N THR c 21 " --> pdb=" O ILE c 32 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1503 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: 10.25 Time building geometry restraints manager: 22.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 14650 1.12 - 1.30: 2556 1.30 - 1.47: 5675 1.47 - 1.65: 6620 1.65 - 1.82: 147 Bond restraints: 29648 Sorted by residual: bond pdb=" CD2 HIS B 104 " pdb=" HD2 HIS B 104 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LYS C 64 " pdb=" H LYS C 64 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE1 PHE C 165 " pdb=" HE1 PHE C 165 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD2 TYR B 255 " pdb=" HD2 TYR B 255 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NH1 ARG B 401 " pdb="HH11 ARG B 401 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 29643 not shown) Histogram of bond angle deviations from ideal: 95.58 - 103.60: 148 103.60 - 111.62: 32563 111.62 - 119.64: 11335 119.64 - 127.66: 9423 127.66 - 135.69: 184 Bond angle restraints: 53653 Sorted by residual: angle pdb=" CB ASN C 154 " pdb=" CG ASN C 154 " pdb=" ND2 ASN C 154 " ideal model delta sigma weight residual 116.40 100.94 15.46 1.50e+00 4.44e-01 1.06e+02 angle pdb=" CB ASN A 154 " pdb=" CG ASN A 154 " pdb=" ND2 ASN A 154 " ideal model delta sigma weight residual 116.40 101.04 15.36 1.50e+00 4.44e-01 1.05e+02 angle pdb=" N ASN A 154 " pdb=" CA ASN A 154 " pdb=" CB ASN A 154 " ideal model delta sigma weight residual 110.32 97.69 12.63 1.82e+00 3.02e-01 4.81e+01 angle pdb=" CA ASN A 154 " pdb=" CB ASN A 154 " pdb=" CG ASN A 154 " ideal model delta sigma weight residual 112.60 119.50 -6.90 1.00e+00 1.00e+00 4.76e+01 angle pdb=" C ALA A 153 " pdb=" N ASN A 154 " pdb=" CA ASN A 154 " ideal model delta sigma weight residual 120.99 133.64 -12.65 1.86e+00 2.89e-01 4.63e+01 ... (remaining 53648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 12435 17.62 - 35.23: 921 35.23 - 52.85: 325 52.85 - 70.46: 232 70.46 - 88.08: 17 Dihedral angle restraints: 13930 sinusoidal: 7648 harmonic: 6282 Sorted by residual: dihedral pdb=" CB CYS c 49 " pdb=" SG CYS c 49 " pdb=" SG CYS c 63 " pdb=" CB CYS c 63 " ideal model delta sinusoidal sigma weight residual 93.00 166.50 -73.50 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS a 49 " pdb=" SG CYS a 49 " pdb=" SG CYS a 63 " pdb=" CB CYS a 63 " ideal model delta sinusoidal sigma weight residual 93.00 147.87 -54.87 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" N ASN A 154 " pdb=" C ASN A 154 " pdb=" CA ASN A 154 " pdb=" CB ASN A 154 " ideal model delta harmonic sigma weight residual 122.80 109.04 13.76 0 2.50e+00 1.60e-01 3.03e+01 ... (remaining 13927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1378 0.079 - 0.159: 706 0.159 - 0.238: 222 0.238 - 0.318: 43 0.318 - 0.397: 8 Chirality restraints: 2357 Sorted by residual: chirality pdb=" CA ARG A 2 " pdb=" N ARG A 2 " pdb=" C ARG A 2 " pdb=" CB ARG A 2 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CA THR a 35 " pdb=" N THR a 35 " pdb=" C THR a 35 " pdb=" CB THR a 35 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA TRP A 44 " pdb=" N TRP A 44 " pdb=" C TRP A 44 " pdb=" CB TRP A 44 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 2354 not shown) Planarity restraints: 4422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 44 " 0.424 2.00e-02 2.50e+03 1.62e-01 1.04e+03 pdb=" CG TRP C 44 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP C 44 " -0.088 2.00e-02 2.50e+03 pdb=" CD2 TRP C 44 " -0.055 2.00e-02 2.50e+03 pdb=" NE1 TRP C 44 " -0.132 2.00e-02 2.50e+03 pdb=" CE2 TRP C 44 " -0.052 2.00e-02 2.50e+03 pdb=" CE3 TRP C 44 " -0.108 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 44 " 0.069 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 44 " -0.094 2.00e-02 2.50e+03 pdb=" CH2 TRP C 44 " 0.035 2.00e-02 2.50e+03 pdb=" HD1 TRP C 44 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 TRP C 44 " -0.204 2.00e-02 2.50e+03 pdb=" HE3 TRP C 44 " -0.141 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 44 " 0.263 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 44 " -0.118 2.00e-02 2.50e+03 pdb=" HH2 TRP C 44 " 0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 44 " -0.278 2.00e-02 2.50e+03 1.61e-01 1.04e+03 pdb=" CG TRP A 44 " -0.166 2.00e-02 2.50e+03 pdb=" CD1 TRP A 44 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TRP A 44 " -0.055 2.00e-02 2.50e+03 pdb=" NE1 TRP A 44 " 0.096 2.00e-02 2.50e+03 pdb=" CE2 TRP A 44 " -0.055 2.00e-02 2.50e+03 pdb=" CE3 TRP A 44 " 0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 44 " -0.144 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 44 " 0.113 2.00e-02 2.50e+03 pdb=" CH2 TRP A 44 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 TRP A 44 " 0.119 2.00e-02 2.50e+03 pdb=" HE1 TRP A 44 " 0.327 2.00e-02 2.50e+03 pdb=" HE3 TRP A 44 " 0.099 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 44 " -0.278 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 44 " 0.205 2.00e-02 2.50e+03 pdb=" HH2 TRP A 44 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 154 " -0.307 2.00e-02 2.50e+03 2.24e-01 7.53e+02 pdb=" CG ASN C 154 " 0.094 2.00e-02 2.50e+03 pdb=" OD1 ASN C 154 " 0.136 2.00e-02 2.50e+03 pdb=" ND2 ASN C 154 " 0.022 2.00e-02 2.50e+03 pdb="HD21 ASN C 154 " 0.325 2.00e-02 2.50e+03 pdb=" C1 NAG C 501 " -0.270 2.00e-02 2.50e+03 ... (remaining 4419 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1470 2.17 - 2.77: 49462 2.77 - 3.38: 74980 3.38 - 3.99: 94428 3.99 - 4.60: 137998 Nonbonded interactions: 358338 Sorted by model distance: nonbonded pdb=" OD1 ASP c 7 " pdb=" HG SER c 9 " model vdw 1.558 1.850 nonbonded pdb=" O ALA A 47 " pdb=" HG1 THR A 140 " model vdw 1.582 1.850 nonbonded pdb=" HG SER C 321 " pdb=" OG1 THR C 325 " model vdw 1.587 1.850 nonbonded pdb=" O ILE B 358 " pdb=" HG1 THR B 359 " model vdw 1.589 1.850 nonbonded pdb=" HG1 THR A 325 " pdb=" OE2 GLU A 373 " model vdw 1.602 1.850 ... (remaining 358333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 o \ r name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2) \ ) or resid 6 through 496 or resid 501)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'a' and (resid 1 through 95 or resid 112 through 161)) selection = (chain 'b' and (resid 1 through 95 or resid 112 through 161)) selection = (chain 'c' and resid 1 through 161) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.510 Extract box with map and model: 1.210 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 85.950 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 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 : 0.013 0.078 14989 Z= 0.839 Angle : 1.919 15.463 20335 Z= 1.279 Chirality : 0.102 0.397 2357 Planarity : 0.019 0.196 2574 Dihedral : 13.259 88.077 5415 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.19), residues: 1899 helix: 2.07 (0.26), residues: 412 sheet: -0.41 (0.22), residues: 537 loop : -1.43 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.247 0.031 TRP C 44 HIS 0.043 0.005 HIS B 146 PHE 0.067 0.017 PHE C 220 TYR 0.191 0.035 TYR b 47 ARG 0.027 0.002 ARG c 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 SER cc_start: 0.8552 (t) cc_final: 0.7876 (p) REVERT: A 34 THR cc_start: 0.8444 (p) cc_final: 0.8193 (m) REVERT: A 48 ILE cc_start: 0.8514 (mt) cc_final: 0.8242 (mt) REVERT: A 58 GLU cc_start: 0.6767 (tt0) cc_final: 0.6394 (tt0) REVERT: A 82 LEU cc_start: 0.8308 (mt) cc_final: 0.8091 (mt) REVERT: A 96 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8017 (mm-40) REVERT: A 116 CYS cc_start: 0.5317 (m) cc_final: 0.4902 (m) REVERT: A 187 ARG cc_start: 0.7916 (ttt-90) cc_final: 0.7421 (ttm110) REVERT: A 227 TRP cc_start: 0.8129 (p-90) cc_final: 0.7914 (p-90) REVERT: A 285 SER cc_start: 0.6911 (t) cc_final: 0.6648 (p) REVERT: A 294 LEU cc_start: 0.8303 (tp) cc_final: 0.7997 (tp) REVERT: A 306 MET cc_start: 0.5747 (ttt) cc_final: 0.5392 (ttt) REVERT: A 471 MET cc_start: 0.2646 (mpp) cc_final: 0.2362 (mpp) REVERT: B 23 LEU cc_start: 0.7521 (mt) cc_final: 0.7309 (mt) REVERT: B 24 VAL cc_start: 0.8286 (m) cc_final: 0.7956 (p) REVERT: B 117 VAL cc_start: 0.8441 (t) cc_final: 0.8198 (m) REVERT: B 209 LEU cc_start: 0.7636 (mt) cc_final: 0.7410 (mt) REVERT: B 356 MET cc_start: 0.5792 (ttm) cc_final: 0.4941 (tpt) REVERT: C 33 ILE cc_start: 0.8055 (mt) cc_final: 0.7811 (mt) REVERT: C 65 LEU cc_start: 0.7899 (mt) cc_final: 0.7598 (mt) REVERT: C 174 LEU cc_start: 0.7189 (mp) cc_final: 0.6938 (mp) REVERT: C 211 THR cc_start: 0.6975 (p) cc_final: 0.5244 (m) REVERT: C 380 ASP cc_start: 0.7891 (m-30) cc_final: 0.7461 (p0) REVERT: a 13 ARG cc_start: 0.7174 (ptm160) cc_final: 0.6833 (ttm170) REVERT: a 23 VAL cc_start: 0.7855 (t) cc_final: 0.7653 (p) REVERT: b 13 ARG cc_start: 0.6575 (ptm160) cc_final: 0.5068 (ptp-170) REVERT: c 24 ARG cc_start: 0.5498 (mmt180) cc_final: 0.5196 (ptt-90) REVERT: c 59 VAL cc_start: 0.8887 (t) cc_final: 0.8646 (p) REVERT: c 61 VAL cc_start: 0.8526 (m) cc_final: 0.8267 (p) REVERT: c 119 ARG cc_start: 0.7346 (ttt180) cc_final: 0.6919 (ttm110) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.5125 time to fit residues: 325.5205 Evaluate side-chains 363 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS A 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14989 Z= 0.240 Angle : 0.661 7.107 20335 Z= 0.362 Chirality : 0.045 0.241 2357 Planarity : 0.006 0.063 2574 Dihedral : 5.848 65.449 2105 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.64 % Allowed : 8.22 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 1899 helix: 2.01 (0.26), residues: 415 sheet: -0.53 (0.20), residues: 600 loop : -1.65 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 44 HIS 0.016 0.002 HIS A 282 PHE 0.027 0.002 PHE c 64 TYR 0.019 0.002 TYR b 47 ARG 0.004 0.000 ARG C 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 357 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 SER cc_start: 0.8334 (t) cc_final: 0.7701 (p) REVERT: A 82 LEU cc_start: 0.8213 (mt) cc_final: 0.7935 (mt) REVERT: A 98 ASP cc_start: 0.7903 (t0) cc_final: 0.7593 (p0) REVERT: A 116 CYS cc_start: 0.4868 (m) cc_final: 0.4530 (m) REVERT: A 161 LYS cc_start: 0.8493 (mptt) cc_final: 0.8246 (mptt) REVERT: A 187 ARG cc_start: 0.7544 (ttt-90) cc_final: 0.7079 (ttm110) REVERT: A 230 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7917 (mm-30) REVERT: A 285 SER cc_start: 0.6843 (t) cc_final: 0.6526 (p) REVERT: A 294 LEU cc_start: 0.8243 (tp) cc_final: 0.7932 (tp) REVERT: A 471 MET cc_start: 0.2969 (mpp) cc_final: 0.2559 (mpp) REVERT: A 478 MET cc_start: 0.3650 (mmp) cc_final: 0.2948 (mmp) REVERT: B 27 LEU cc_start: 0.8322 (mt) cc_final: 0.8029 (mt) REVERT: B 57 ARG cc_start: 0.7899 (mtp180) cc_final: 0.7527 (mmm-85) REVERT: B 285 SER cc_start: 0.7648 (t) cc_final: 0.7353 (m) REVERT: B 356 MET cc_start: 0.5289 (ttm) cc_final: 0.4982 (tpt) REVERT: C 24 VAL cc_start: 0.7586 (OUTLIER) cc_final: 0.7328 (p) REVERT: C 211 THR cc_start: 0.6808 (p) cc_final: 0.5038 (m) REVERT: C 380 ASP cc_start: 0.7656 (m-30) cc_final: 0.7322 (p0) REVERT: C 392 TRP cc_start: 0.7829 (t-100) cc_final: 0.7620 (t-100) REVERT: b 13 ARG cc_start: 0.6232 (ptm160) cc_final: 0.4988 (ptp-170) REVERT: c 43 ASP cc_start: 0.7910 (t0) cc_final: 0.7668 (t0) REVERT: c 59 VAL cc_start: 0.8894 (t) cc_final: 0.8677 (p) REVERT: c 74 GLU cc_start: 0.5425 (pt0) cc_final: 0.5172 (pt0) REVERT: c 119 ARG cc_start: 0.7285 (ttt180) cc_final: 0.6941 (ttm110) outliers start: 26 outliers final: 21 residues processed: 368 average time/residue: 0.5163 time to fit residues: 284.6844 Evaluate side-chains 353 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 331 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain b residue 130 LEU Chi-restraints excluded: chain c residue 1 THR Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 52 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14989 Z= 0.326 Angle : 0.640 5.580 20335 Z= 0.351 Chirality : 0.045 0.170 2357 Planarity : 0.004 0.053 2574 Dihedral : 5.968 59.181 2105 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.34 % Allowed : 11.70 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.19), residues: 1899 helix: 1.94 (0.26), residues: 415 sheet: -0.66 (0.21), residues: 581 loop : -1.98 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 44 HIS 0.014 0.002 HIS B 323 PHE 0.021 0.002 PHE c 64 TYR 0.033 0.003 TYR b 47 ARG 0.007 0.001 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 336 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 SER cc_start: 0.8658 (t) cc_final: 0.8203 (p) REVERT: A 82 LEU cc_start: 0.8258 (mt) cc_final: 0.8042 (mt) REVERT: A 98 ASP cc_start: 0.7938 (t0) cc_final: 0.7627 (p0) REVERT: A 116 CYS cc_start: 0.4826 (m) cc_final: 0.4476 (m) REVERT: A 161 LYS cc_start: 0.8511 (mptt) cc_final: 0.8260 (mptt) REVERT: A 187 ARG cc_start: 0.7601 (ttt-90) cc_final: 0.7212 (ttm110) REVERT: A 230 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7813 (mm-30) REVERT: A 285 SER cc_start: 0.6985 (t) cc_final: 0.6587 (p) REVERT: A 294 LEU cc_start: 0.8409 (tp) cc_final: 0.8073 (tp) REVERT: A 471 MET cc_start: 0.2952 (mpp) cc_final: 0.2695 (mpp) REVERT: B 20 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7479 (mtp180) REVERT: B 256 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8189 (t0) REVERT: B 285 SER cc_start: 0.7732 (t) cc_final: 0.7421 (m) REVERT: C 24 VAL cc_start: 0.7708 (OUTLIER) cc_final: 0.7436 (p) REVERT: C 211 THR cc_start: 0.6684 (p) cc_final: 0.4925 (m) REVERT: C 333 SER cc_start: 0.7889 (t) cc_final: 0.7369 (p) REVERT: C 356 MET cc_start: 0.2403 (ttp) cc_final: 0.2118 (ttm) REVERT: C 380 ASP cc_start: 0.7713 (m-30) cc_final: 0.7435 (p0) REVERT: C 392 TRP cc_start: 0.7955 (t-100) cc_final: 0.7507 (t-100) REVERT: b 13 ARG cc_start: 0.6732 (ptm160) cc_final: 0.5502 (ptp-170) REVERT: c 43 ASP cc_start: 0.7901 (t0) cc_final: 0.7696 (t0) REVERT: c 74 GLU cc_start: 0.5573 (pt0) cc_final: 0.5308 (pt0) REVERT: c 119 ARG cc_start: 0.7251 (ttt180) cc_final: 0.6930 (ttm110) outliers start: 37 outliers final: 32 residues processed: 354 average time/residue: 0.5522 time to fit residues: 298.6810 Evaluate side-chains 363 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 329 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain c residue 1 THR Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 163 optimal weight: 0.0570 chunk 49 optimal weight: 4.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14989 Z= 0.236 Angle : 0.580 7.388 20335 Z= 0.316 Chirality : 0.044 0.232 2357 Planarity : 0.004 0.043 2574 Dihedral : 5.762 59.254 2105 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.47 % Allowed : 13.28 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.19), residues: 1899 helix: 2.08 (0.27), residues: 416 sheet: -0.63 (0.21), residues: 578 loop : -1.93 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 44 HIS 0.008 0.002 HIS A 248 PHE 0.018 0.001 PHE c 64 TYR 0.022 0.002 TYR b 47 ARG 0.003 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 328 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 SER cc_start: 0.8613 (t) cc_final: 0.7911 (p) REVERT: A 98 ASP cc_start: 0.7996 (t0) cc_final: 0.7668 (p0) REVERT: A 116 CYS cc_start: 0.4785 (m) cc_final: 0.4388 (m) REVERT: A 146 HIS cc_start: 0.6700 (OUTLIER) cc_final: 0.5735 (t-90) REVERT: A 161 LYS cc_start: 0.8568 (mptt) cc_final: 0.8358 (mptt) REVERT: A 164 SER cc_start: 0.8588 (p) cc_final: 0.8336 (p) REVERT: A 187 ARG cc_start: 0.7455 (ttt-90) cc_final: 0.7188 (ttm110) REVERT: A 230 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7853 (mm-30) REVERT: A 285 SER cc_start: 0.6926 (t) cc_final: 0.6522 (p) REVERT: A 294 LEU cc_start: 0.8407 (tp) cc_final: 0.8065 (tp) REVERT: A 471 MET cc_start: 0.2996 (mpp) cc_final: 0.2760 (mpp) REVERT: B 20 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7371 (mtp180) REVERT: B 27 LEU cc_start: 0.8336 (mt) cc_final: 0.8007 (mt) REVERT: B 285 SER cc_start: 0.7747 (t) cc_final: 0.7438 (m) REVERT: C 24 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7426 (p) REVERT: C 92 CYS cc_start: 0.5535 (m) cc_final: 0.5160 (m) REVERT: C 211 THR cc_start: 0.6620 (p) cc_final: 0.4877 (m) REVERT: C 333 SER cc_start: 0.7888 (t) cc_final: 0.7429 (p) REVERT: C 356 MET cc_start: 0.2309 (ttp) cc_final: 0.2055 (ttm) REVERT: C 380 ASP cc_start: 0.7668 (m-30) cc_final: 0.7437 (p0) REVERT: b 13 ARG cc_start: 0.6642 (ptm160) cc_final: 0.5921 (ptp-170) REVERT: c 43 ASP cc_start: 0.7928 (t0) cc_final: 0.7714 (t0) REVERT: c 119 ARG cc_start: 0.7232 (ttt180) cc_final: 0.6921 (ttm110) outliers start: 39 outliers final: 29 residues processed: 348 average time/residue: 0.5233 time to fit residues: 277.5519 Evaluate side-chains 355 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 324 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain c residue 1 THR Chi-restraints excluded: chain c residue 68 VAL Chi-restraints excluded: chain c residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 14989 Z= 0.299 Angle : 0.602 8.700 20335 Z= 0.327 Chirality : 0.044 0.237 2357 Planarity : 0.004 0.046 2574 Dihedral : 5.667 55.366 2105 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.66 % Allowed : 14.29 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1899 helix: 2.04 (0.27), residues: 416 sheet: -0.76 (0.21), residues: 575 loop : -2.04 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 227 HIS 0.010 0.002 HIS B 282 PHE 0.029 0.002 PHE B 371 TYR 0.027 0.002 TYR b 47 ARG 0.005 0.001 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 324 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 SER cc_start: 0.8681 (t) cc_final: 0.8274 (p) REVERT: A 98 ASP cc_start: 0.7995 (t0) cc_final: 0.7771 (p0) REVERT: A 116 CYS cc_start: 0.4808 (m) cc_final: 0.4479 (m) REVERT: A 161 LYS cc_start: 0.8616 (mptt) cc_final: 0.8393 (mptt) REVERT: A 164 SER cc_start: 0.8574 (p) cc_final: 0.8321 (p) REVERT: A 187 ARG cc_start: 0.7569 (ttt-90) cc_final: 0.7212 (ttm110) REVERT: A 221 ASN cc_start: 0.6099 (t0) cc_final: 0.5843 (t0) REVERT: A 230 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 285 SER cc_start: 0.6995 (t) cc_final: 0.6595 (p) REVERT: A 294 LEU cc_start: 0.8415 (tp) cc_final: 0.8086 (tp) REVERT: A 471 MET cc_start: 0.3045 (mpp) cc_final: 0.2755 (mpp) REVERT: B 20 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7337 (mtp180) REVERT: B 57 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7829 (mtt180) REVERT: B 268 LEU cc_start: 0.8647 (tp) cc_final: 0.8238 (tp) REVERT: B 285 SER cc_start: 0.7817 (t) cc_final: 0.7483 (m) REVERT: C 24 VAL cc_start: 0.7645 (OUTLIER) cc_final: 0.7386 (p) REVERT: C 92 CYS cc_start: 0.5492 (m) cc_final: 0.5153 (m) REVERT: C 211 THR cc_start: 0.6677 (p) cc_final: 0.4979 (m) REVERT: C 328 MET cc_start: 0.2231 (tpt) cc_final: 0.1721 (mmm) REVERT: C 333 SER cc_start: 0.7852 (t) cc_final: 0.7444 (p) REVERT: C 356 MET cc_start: 0.2209 (ttp) cc_final: 0.1913 (ttm) REVERT: C 380 ASP cc_start: 0.7715 (m-30) cc_final: 0.7496 (p0) REVERT: b 13 ARG cc_start: 0.6828 (ptm160) cc_final: 0.6175 (ptp-170) REVERT: c 43 ASP cc_start: 0.7910 (t0) cc_final: 0.7700 (t0) REVERT: c 57 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7164 (mm-30) REVERT: c 119 ARG cc_start: 0.7245 (ttt180) cc_final: 0.6911 (ttm110) REVERT: c 121 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6613 (mp0) outliers start: 42 outliers final: 32 residues processed: 342 average time/residue: 0.5089 time to fit residues: 263.5484 Evaluate side-chains 355 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 321 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain b residue 114 ARG Chi-restraints excluded: chain c residue 1 THR Chi-restraints excluded: chain c residue 68 VAL Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 151 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 96 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14989 Z= 0.241 Angle : 0.574 9.106 20335 Z= 0.309 Chirality : 0.043 0.213 2357 Planarity : 0.004 0.042 2574 Dihedral : 5.451 51.375 2105 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.40 % Allowed : 15.05 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 1899 helix: 2.15 (0.27), residues: 416 sheet: -0.73 (0.21), residues: 584 loop : -1.96 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 227 HIS 0.006 0.001 HIS B 323 PHE 0.018 0.001 PHE c 64 TYR 0.022 0.002 TYR b 47 ARG 0.004 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 314 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 CYS cc_start: 0.4814 (m) cc_final: 0.4468 (m) REVERT: A 161 LYS cc_start: 0.8596 (mptt) cc_final: 0.8369 (mptt) REVERT: A 164 SER cc_start: 0.8535 (p) cc_final: 0.8280 (p) REVERT: A 187 ARG cc_start: 0.7526 (ttt-90) cc_final: 0.7178 (ttm110) REVERT: A 221 ASN cc_start: 0.6067 (t0) cc_final: 0.5836 (t0) REVERT: A 230 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7880 (mm-30) REVERT: A 294 LEU cc_start: 0.8425 (tp) cc_final: 0.8083 (tp) REVERT: A 471 MET cc_start: 0.3048 (mpp) cc_final: 0.2749 (mpp) REVERT: A 478 MET cc_start: 0.3288 (mmp) cc_final: 0.2973 (mmp) REVERT: B 20 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7304 (mtp180) REVERT: B 57 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7807 (mtt180) REVERT: B 256 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.7990 (t0) REVERT: B 268 LEU cc_start: 0.8678 (tp) cc_final: 0.8289 (tp) REVERT: B 285 SER cc_start: 0.7818 (t) cc_final: 0.7535 (m) REVERT: C 24 VAL cc_start: 0.7625 (OUTLIER) cc_final: 0.7372 (p) REVERT: C 92 CYS cc_start: 0.5495 (m) cc_final: 0.5193 (m) REVERT: C 211 THR cc_start: 0.6683 (p) cc_final: 0.4992 (m) REVERT: C 328 MET cc_start: 0.2243 (tpt) cc_final: 0.1396 (mmm) REVERT: C 333 SER cc_start: 0.8023 (t) cc_final: 0.7608 (p) REVERT: C 356 MET cc_start: 0.2065 (ttp) cc_final: 0.1773 (ttm) REVERT: C 380 ASP cc_start: 0.7708 (m-30) cc_final: 0.7506 (p0) REVERT: b 13 ARG cc_start: 0.6775 (ptm160) cc_final: 0.6041 (ptp-170) REVERT: c 43 ASP cc_start: 0.7944 (t0) cc_final: 0.7725 (t0) REVERT: c 57 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7222 (mm-30) REVERT: c 119 ARG cc_start: 0.7242 (ttt180) cc_final: 0.6903 (ttm110) REVERT: c 121 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6528 (mp0) outliers start: 38 outliers final: 30 residues processed: 334 average time/residue: 0.5072 time to fit residues: 257.1625 Evaluate side-chains 346 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 313 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain c residue 1 THR Chi-restraints excluded: chain c residue 68 VAL Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 5.9990 chunk 20 optimal weight: 0.0470 chunk 104 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14989 Z= 0.195 Angle : 0.550 10.011 20335 Z= 0.293 Chirality : 0.043 0.202 2357 Planarity : 0.003 0.038 2574 Dihedral : 5.188 49.027 2105 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.02 % Allowed : 16.13 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.19), residues: 1899 helix: 2.27 (0.27), residues: 416 sheet: -0.71 (0.20), residues: 584 loop : -1.87 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 227 HIS 0.006 0.001 HIS B 323 PHE 0.018 0.001 PHE A 332 TYR 0.019 0.002 TYR b 47 ARG 0.004 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 319 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 CYS cc_start: 0.4797 (m) cc_final: 0.4454 (m) REVERT: A 146 HIS cc_start: 0.6651 (OUTLIER) cc_final: 0.6446 (t-90) REVERT: A 161 LYS cc_start: 0.8569 (mptt) cc_final: 0.8330 (mptt) REVERT: A 164 SER cc_start: 0.8506 (p) cc_final: 0.8277 (p) REVERT: A 187 ARG cc_start: 0.7501 (ttt-90) cc_final: 0.7178 (ttm110) REVERT: A 221 ASN cc_start: 0.6064 (t0) cc_final: 0.5832 (t0) REVERT: A 230 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7880 (mm-30) REVERT: A 294 LEU cc_start: 0.8395 (tp) cc_final: 0.8055 (tp) REVERT: A 471 MET cc_start: 0.3059 (mpp) cc_final: 0.2775 (mpp) REVERT: B 20 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7258 (mtp180) REVERT: B 57 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7792 (mtt180) REVERT: B 268 LEU cc_start: 0.8671 (tp) cc_final: 0.8270 (tp) REVERT: B 285 SER cc_start: 0.7774 (t) cc_final: 0.7478 (m) REVERT: C 24 VAL cc_start: 0.7597 (OUTLIER) cc_final: 0.7354 (p) REVERT: C 92 CYS cc_start: 0.5455 (m) cc_final: 0.5111 (m) REVERT: C 211 THR cc_start: 0.6458 (p) cc_final: 0.4744 (m) REVERT: C 328 MET cc_start: 0.2273 (tpt) cc_final: 0.1395 (mmm) REVERT: C 333 SER cc_start: 0.8027 (t) cc_final: 0.7627 (p) REVERT: C 356 MET cc_start: 0.2042 (ttp) cc_final: 0.1731 (ttm) REVERT: b 13 ARG cc_start: 0.6709 (ptm160) cc_final: 0.5968 (ptp-170) REVERT: c 43 ASP cc_start: 0.7940 (t0) cc_final: 0.7721 (t0) REVERT: c 57 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7269 (mm-30) REVERT: c 119 ARG cc_start: 0.7224 (ttt180) cc_final: 0.6890 (ttm110) REVERT: c 121 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6682 (mp0) outliers start: 32 outliers final: 25 residues processed: 336 average time/residue: 0.5380 time to fit residues: 275.0974 Evaluate side-chains 345 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 317 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain c residue 68 VAL Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14989 Z= 0.234 Angle : 0.561 9.958 20335 Z= 0.299 Chirality : 0.043 0.201 2357 Planarity : 0.003 0.049 2574 Dihedral : 5.152 46.901 2105 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.28 % Allowed : 16.70 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1899 helix: 2.28 (0.27), residues: 416 sheet: -0.73 (0.20), residues: 584 loop : -1.91 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 227 HIS 0.006 0.001 HIS B 323 PHE 0.018 0.001 PHE A 332 TYR 0.022 0.002 TYR b 47 ARG 0.003 0.000 ARG c 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 315 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 CYS cc_start: 0.4795 (m) cc_final: 0.4445 (m) REVERT: A 161 LYS cc_start: 0.8568 (mptt) cc_final: 0.8321 (mptt) REVERT: A 164 SER cc_start: 0.8512 (p) cc_final: 0.8279 (p) REVERT: A 187 ARG cc_start: 0.7530 (ttt-90) cc_final: 0.7221 (ttm110) REVERT: A 221 ASN cc_start: 0.6094 (t0) cc_final: 0.5845 (t0) REVERT: A 230 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7875 (mm-30) REVERT: A 294 LEU cc_start: 0.8402 (tp) cc_final: 0.8059 (tp) REVERT: A 471 MET cc_start: 0.3096 (mpp) cc_final: 0.2806 (mpp) REVERT: B 20 ARG cc_start: 0.8041 (mtp85) cc_final: 0.7267 (mtp180) REVERT: B 57 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7812 (mtt180) REVERT: B 268 LEU cc_start: 0.8680 (tp) cc_final: 0.8277 (tp) REVERT: B 285 SER cc_start: 0.7812 (t) cc_final: 0.7511 (m) REVERT: C 24 VAL cc_start: 0.7611 (OUTLIER) cc_final: 0.7367 (p) REVERT: C 211 THR cc_start: 0.6626 (p) cc_final: 0.4919 (m) REVERT: C 328 MET cc_start: 0.2301 (tpt) cc_final: 0.1404 (mmm) REVERT: C 333 SER cc_start: 0.7971 (t) cc_final: 0.7624 (p) REVERT: C 356 MET cc_start: 0.2052 (ttp) cc_final: 0.1748 (ttm) REVERT: b 13 ARG cc_start: 0.6758 (ptm160) cc_final: 0.5997 (ptp-170) REVERT: c 57 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7289 (mm-30) REVERT: c 119 ARG cc_start: 0.7221 (ttt180) cc_final: 0.6895 (ttm110) outliers start: 36 outliers final: 29 residues processed: 332 average time/residue: 0.5020 time to fit residues: 253.4858 Evaluate side-chains 341 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 311 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain a residue 94 SER Chi-restraints excluded: chain b residue 37 MET Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain c residue 1 THR Chi-restraints excluded: chain c residue 68 VAL Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 3.9990 chunk 159 optimal weight: 0.0870 chunk 169 optimal weight: 0.0270 chunk 102 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 153 optimal weight: 0.5980 chunk 160 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 14989 Z= 0.151 Angle : 0.525 8.195 20335 Z= 0.278 Chirality : 0.043 0.189 2357 Planarity : 0.003 0.039 2574 Dihedral : 4.804 45.199 2105 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.39 % Allowed : 17.96 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1899 helix: 2.48 (0.27), residues: 416 sheet: -0.59 (0.21), residues: 557 loop : -1.62 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 227 HIS 0.005 0.001 HIS A 438 PHE 0.017 0.001 PHE c 64 TYR 0.012 0.001 TYR b 47 ARG 0.004 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 315 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 CYS cc_start: 0.4828 (m) cc_final: 0.4468 (m) REVERT: A 161 LYS cc_start: 0.8525 (mptt) cc_final: 0.8241 (mptt) REVERT: A 164 SER cc_start: 0.8426 (p) cc_final: 0.8189 (p) REVERT: A 187 ARG cc_start: 0.7445 (ttt-90) cc_final: 0.7190 (ttm110) REVERT: A 221 ASN cc_start: 0.6050 (t0) cc_final: 0.5834 (t0) REVERT: A 230 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7875 (mm-30) REVERT: A 294 LEU cc_start: 0.8359 (tp) cc_final: 0.8046 (tp) REVERT: A 471 MET cc_start: 0.2971 (mpp) cc_final: 0.2684 (mpp) REVERT: B 20 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7184 (mtp180) REVERT: B 209 LEU cc_start: 0.7630 (mt) cc_final: 0.7361 (mt) REVERT: B 285 SER cc_start: 0.7728 (t) cc_final: 0.7452 (m) REVERT: C 24 VAL cc_start: 0.7584 (m) cc_final: 0.7358 (p) REVERT: C 211 THR cc_start: 0.6538 (p) cc_final: 0.4773 (m) REVERT: C 299 MET cc_start: 0.5006 (mtt) cc_final: 0.4763 (mtt) REVERT: C 328 MET cc_start: 0.2216 (tpt) cc_final: 0.1855 (mmm) REVERT: C 333 SER cc_start: 0.7944 (t) cc_final: 0.7563 (p) REVERT: C 356 MET cc_start: 0.2099 (ttp) cc_final: 0.1788 (ttm) REVERT: b 13 ARG cc_start: 0.6621 (ptm160) cc_final: 0.5981 (ptp-170) REVERT: b 57 GLU cc_start: 0.7121 (pm20) cc_final: 0.6859 (pm20) REVERT: c 119 ARG cc_start: 0.7217 (ttt180) cc_final: 0.6899 (ttm110) outliers start: 22 outliers final: 19 residues processed: 326 average time/residue: 0.5086 time to fit residues: 253.6574 Evaluate side-chains 332 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 313 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain c residue 1 THR Chi-restraints excluded: chain c residue 68 VAL Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 4.9990 chunk 85 optimal weight: 0.0870 chunk 124 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 173 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 0.0370 chunk 115 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14989 Z= 0.177 Angle : 0.529 8.877 20335 Z= 0.280 Chirality : 0.043 0.193 2357 Planarity : 0.003 0.041 2574 Dihedral : 4.751 45.040 2105 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.20 % Allowed : 18.53 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1899 helix: 2.50 (0.27), residues: 416 sheet: -0.54 (0.21), residues: 557 loop : -1.62 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 227 HIS 0.006 0.001 HIS B 323 PHE 0.016 0.001 PHE c 64 TYR 0.018 0.001 TYR b 47 ARG 0.004 0.000 ARG c 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 320 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7466 (tt) REVERT: A 116 CYS cc_start: 0.4834 (m) cc_final: 0.4469 (m) REVERT: A 161 LYS cc_start: 0.8530 (mptt) cc_final: 0.8280 (mptt) REVERT: A 164 SER cc_start: 0.8435 (p) cc_final: 0.8206 (p) REVERT: A 187 ARG cc_start: 0.7462 (ttt-90) cc_final: 0.7207 (ttm110) REVERT: A 221 ASN cc_start: 0.6049 (t0) cc_final: 0.5829 (t0) REVERT: A 230 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7887 (mm-30) REVERT: A 294 LEU cc_start: 0.8398 (tp) cc_final: 0.8084 (tp) REVERT: A 471 MET cc_start: 0.3010 (mpp) cc_final: 0.2719 (mpp) REVERT: B 20 ARG cc_start: 0.7996 (mtp85) cc_final: 0.7206 (mtp180) REVERT: B 285 SER cc_start: 0.7905 (t) cc_final: 0.7564 (m) REVERT: C 24 VAL cc_start: 0.7609 (m) cc_final: 0.7379 (p) REVERT: C 211 THR cc_start: 0.6519 (p) cc_final: 0.4738 (m) REVERT: C 299 MET cc_start: 0.5109 (mtt) cc_final: 0.4858 (mtt) REVERT: C 328 MET cc_start: 0.2205 (tpt) cc_final: 0.1338 (mmm) REVERT: C 333 SER cc_start: 0.7963 (t) cc_final: 0.7582 (p) REVERT: b 13 ARG cc_start: 0.6752 (ptm160) cc_final: 0.6026 (ptp-170) REVERT: c 119 ARG cc_start: 0.7215 (ttt180) cc_final: 0.6903 (ttm110) outliers start: 19 outliers final: 16 residues processed: 329 average time/residue: 0.5137 time to fit residues: 254.6255 Evaluate side-chains 333 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 316 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain c residue 68 VAL Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.0020 chunk 131 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.186032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144792 restraints weight = 65867.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.151628 restraints weight = 27440.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155907 restraints weight = 14822.409| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14989 Z= 0.228 Angle : 0.549 8.735 20335 Z= 0.292 Chirality : 0.043 0.197 2357 Planarity : 0.003 0.042 2574 Dihedral : 4.819 44.054 2105 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.39 % Allowed : 18.72 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1899 helix: 2.46 (0.27), residues: 416 sheet: -0.59 (0.21), residues: 584 loop : -1.72 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 227 HIS 0.006 0.001 HIS B 323 PHE 0.041 0.001 PHE B 371 TYR 0.021 0.002 TYR b 47 ARG 0.004 0.000 ARG A 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6270.39 seconds wall clock time: 109 minutes 45.34 seconds (6585.34 seconds total)