Starting phenix.real_space_refine on Tue Mar 19 14:31:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/03_2024/7wv4_32845_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/03_2024/7wv4_32845.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/03_2024/7wv4_32845_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/03_2024/7wv4_32845_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/03_2024/7wv4_32845_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/03_2024/7wv4_32845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/03_2024/7wv4_32845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/03_2024/7wv4_32845_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv4_32845/03_2024/7wv4_32845_updated.pdb" } resolution = 3.35 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= -0.006 sd= 1.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 158 5.49 5 S 68 5.16 5 C 15040 2.51 5 N 4144 2.21 5 O 5080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 81": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 639": "OE1" <-> "OE2" Residue "B PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 442": "OE1" <-> "OE2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "C PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 639": "OE1" <-> "OE2" Residue "C PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D GLU 442": "OE1" <-> "OE2" Residue "D GLU 456": "OE1" <-> "OE2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 639": "OE1" <-> "OE2" Residue "D PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24490 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1597 Classifications: {'RNA': 80} Modifications used: {'5*END': 1, 'rna3p_pyr': 80} Link IDs: {'rna3p': 79} Chain: "F" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1757 Classifications: {'RNA': 80} Modifications used: {'5*END': 1, 'rna3p': 80} Link IDs: {'rna3p': 79} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Time building chain proxies: 13.00, per 1000 atoms: 0.53 Number of scatterers: 24490 At special positions: 0 Unit cell: (98.5545, 113.215, 257.382, 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 68 16.00 P 158 15.00 O 5080 8.00 N 4144 7.00 C 15040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 677 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 677 " distance=2.03 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 649 " - pdb=" SG CYS D 677 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.34 Conformation dependent library (CDL) restraints added in 3.7 seconds 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 16 sheets defined 9.1% alpha, 7.9% beta 0 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 11.32 Creating SS restraints... Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.611A pdb=" N ASP A 192 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE A 193 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 195 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN A 196 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 400 through 404 removed outlier: 4.378A pdb=" N SER A 403 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 627 through 630 No H-bonds generated for 'chain 'A' and resid 627 through 630' Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'B' and resid 68 through 71 Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.610A pdb=" N ASP B 192 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE B 193 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN B 196 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 400 through 404 removed outlier: 4.378A pdb=" N SER B 403 " --> pdb=" O THR B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 627 through 630 No H-bonds generated for 'chain 'B' and resid 627 through 630' Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 681 through 683 No H-bonds generated for 'chain 'B' and resid 681 through 683' Processing helix chain 'C' and resid 68 through 71 Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.611A pdb=" N ASP C 192 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE C 193 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA C 195 " --> pdb=" O ASP C 192 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASN C 196 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 400 through 404 removed outlier: 4.378A pdb=" N SER C 403 " --> pdb=" O THR C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 452 No H-bonds generated for 'chain 'C' and resid 450 through 452' Processing helix chain 'C' and resid 523 through 525 No H-bonds generated for 'chain 'C' and resid 523 through 525' Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 627 through 630 No H-bonds generated for 'chain 'C' and resid 627 through 630' Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 655 through 662 Processing helix chain 'C' and resid 681 through 683 No H-bonds generated for 'chain 'C' and resid 681 through 683' Processing helix chain 'D' and resid 68 through 71 Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.611A pdb=" N ASP D 192 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE D 193 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 195 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASN D 196 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 244 Processing helix chain 'D' and resid 269 through 271 No H-bonds generated for 'chain 'D' and resid 269 through 271' Processing helix chain 'D' and resid 400 through 404 removed outlier: 4.378A pdb=" N SER D 403 " --> pdb=" O THR D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 523 through 525 No H-bonds generated for 'chain 'D' and resid 523 through 525' Processing helix chain 'D' and resid 544 through 546 No H-bonds generated for 'chain 'D' and resid 544 through 546' Processing helix chain 'D' and resid 627 through 630 No H-bonds generated for 'chain 'D' and resid 627 through 630' Processing helix chain 'D' and resid 632 through 634 No H-bonds generated for 'chain 'D' and resid 632 through 634' Processing helix chain 'D' and resid 655 through 662 Processing helix chain 'D' and resid 681 through 683 No H-bonds generated for 'chain 'D' and resid 681 through 683' Processing sheet with id= A, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.618A pdb=" N VAL A 55 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER A 79 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 103 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU A 127 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR A 151 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU A 175 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS A 201 " --> pdb=" O LEU A 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 225 through 227 removed outlier: 6.322A pdb=" N ASN A 252 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N MET A 278 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR A 302 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR A 326 " --> pdb=" O PHE A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 383 through 385 removed outlier: 6.104A pdb=" N ILE A 411 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 435 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU A 460 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG A 484 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 510 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 534 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE A 566 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 590 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER A 614 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU A 639 " --> pdb=" O LEU A 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 444 through 446 removed outlier: 6.140A pdb=" N TYR A 468 " --> pdb=" O GLN A 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 34 through 36 removed outlier: 6.619A pdb=" N VAL B 55 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER B 79 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 103 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU B 127 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 151 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU B 175 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS B 201 " --> pdb=" O LEU B 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 225 through 227 removed outlier: 6.322A pdb=" N ASN B 252 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N MET B 278 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR B 302 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR B 326 " --> pdb=" O PHE B 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 383 through 385 removed outlier: 6.104A pdb=" N ILE B 411 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL B 435 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU B 460 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 484 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 510 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE B 534 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE B 566 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 590 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N SER B 614 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU B 639 " --> pdb=" O LEU B 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 444 through 446 removed outlier: 6.140A pdb=" N TYR B 468 " --> pdb=" O GLN B 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 34 through 36 removed outlier: 6.618A pdb=" N VAL C 55 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER C 79 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 103 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU C 127 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR C 151 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU C 175 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS C 201 " --> pdb=" O LEU C 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 225 through 227 removed outlier: 6.322A pdb=" N ASN C 252 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N MET C 278 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR C 302 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR C 326 " --> pdb=" O PHE C 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 383 through 385 removed outlier: 6.103A pdb=" N ILE C 411 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL C 435 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C 460 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG C 484 " --> pdb=" O ILE C 461 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 510 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 534 " --> pdb=" O LEU C 511 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE C 566 " --> pdb=" O LEU C 535 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE C 590 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER C 614 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU C 639 " --> pdb=" O LEU C 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 444 through 446 removed outlier: 6.140A pdb=" N TYR C 468 " --> pdb=" O GLN C 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 34 through 36 removed outlier: 6.618A pdb=" N VAL D 55 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER D 79 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL D 103 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU D 127 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR D 151 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU D 175 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS D 201 " --> pdb=" O LEU D 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 225 through 227 removed outlier: 6.322A pdb=" N ASN D 252 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N MET D 278 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR D 302 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR D 326 " --> pdb=" O PHE D 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 383 through 385 removed outlier: 6.103A pdb=" N ILE D 411 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL D 435 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU D 460 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG D 484 " --> pdb=" O ILE D 461 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE D 510 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE D 534 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE D 566 " --> pdb=" O LEU D 535 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 590 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER D 614 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU D 639 " --> pdb=" O LEU D 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 444 through 446 removed outlier: 6.140A pdb=" N TYR D 468 " --> pdb=" O GLN D 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= P 52 hydrogen bonds defined for protein. 120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 8.39 Time building geometry restraints manager: 11.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7019 1.34 - 1.45: 4710 1.45 - 1.57: 13191 1.57 - 1.69: 316 1.69 - 1.81: 100 Bond restraints: 25336 Sorted by residual: bond pdb=" C2 I F 63 " pdb=" N3 I F 63 " ideal model delta sigma weight residual 1.462 1.314 0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" C2 I F 66 " pdb=" N3 I F 66 " ideal model delta sigma weight residual 1.462 1.314 0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" C2 I F 68 " pdb=" N3 I F 68 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C2 I F 48 " pdb=" N3 I F 48 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C2 I F 65 " pdb=" N3 I F 65 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.42e+01 ... (remaining 25331 not shown) Histogram of bond angle deviations from ideal: 99.85 - 106.68: 1373 106.68 - 113.51: 14538 113.51 - 120.34: 8823 120.34 - 127.17: 9835 127.17 - 134.00: 559 Bond angle restraints: 35128 Sorted by residual: angle pdb=" C1' I F 64 " pdb=" N9 I F 64 " pdb=" C4 I F 64 " ideal model delta sigma weight residual 106.08 125.48 -19.40 3.00e+00 1.11e-01 4.18e+01 angle pdb=" C1' I F 63 " pdb=" N9 I F 63 " pdb=" C4 I F 63 " ideal model delta sigma weight residual 106.08 125.26 -19.18 3.00e+00 1.11e-01 4.09e+01 angle pdb=" C1' I F 79 " pdb=" N9 I F 79 " pdb=" C4 I F 79 " ideal model delta sigma weight residual 106.08 125.00 -18.92 3.00e+00 1.11e-01 3.98e+01 angle pdb=" C1' I F 5 " pdb=" N9 I F 5 " pdb=" C4 I F 5 " ideal model delta sigma weight residual 106.08 124.92 -18.84 3.00e+00 1.11e-01 3.94e+01 angle pdb=" C1' I F 74 " pdb=" N9 I F 74 " pdb=" C4 I F 74 " ideal model delta sigma weight residual 106.08 124.85 -18.77 3.00e+00 1.11e-01 3.91e+01 ... (remaining 35123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13289 17.99 - 35.98: 1098 35.98 - 53.97: 457 53.97 - 71.96: 174 71.96 - 89.95: 254 Dihedral angle restraints: 15272 sinusoidal: 7520 harmonic: 7752 Sorted by residual: dihedral pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " pdb=" SG CYS C 677 " pdb=" CB CYS C 677 " ideal model delta sinusoidal sigma weight residual 93.00 163.12 -70.12 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS A 649 " pdb=" SG CYS A 649 " pdb=" SG CYS A 677 " pdb=" CB CYS A 677 " ideal model delta sinusoidal sigma weight residual 93.00 163.12 -70.12 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS D 649 " pdb=" SG CYS D 649 " pdb=" SG CYS D 677 " pdb=" CB CYS D 677 " ideal model delta sinusoidal sigma weight residual 93.00 163.08 -70.08 1 1.00e+01 1.00e-02 6.33e+01 ... (remaining 15269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2478 0.036 - 0.071: 999 0.071 - 0.107: 231 0.107 - 0.142: 83 0.142 - 0.178: 12 Chirality restraints: 3803 Sorted by residual: chirality pdb=" CB VAL B 82 " pdb=" CA VAL B 82 " pdb=" CG1 VAL B 82 " pdb=" CG2 VAL B 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CB VAL D 82 " pdb=" CA VAL D 82 " pdb=" CG1 VAL D 82 " pdb=" CG2 VAL D 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CB VAL C 82 " pdb=" CA VAL C 82 " pdb=" CG1 VAL C 82 " pdb=" CG2 VAL C 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 3800 not shown) Planarity restraints: 3996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' I F 39 " 0.219 2.00e-02 2.50e+03 6.12e-01 8.42e+03 pdb=" C2' I F 39 " -0.165 2.00e-02 2.50e+03 pdb=" C3' I F 39 " -0.604 2.00e-02 2.50e+03 pdb=" C4' I F 39 " 0.431 2.00e-02 2.50e+03 pdb=" C5' I F 39 " 0.075 2.00e-02 2.50e+03 pdb=" N9 I F 39 " -0.943 2.00e-02 2.50e+03 pdb=" O2' I F 39 " 1.003 2.00e-02 2.50e+03 pdb=" O3' I F 39 " -0.656 2.00e-02 2.50e+03 pdb=" O4' I F 39 " 0.641 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 73 " 0.200 2.00e-02 2.50e+03 6.01e-01 8.13e+03 pdb=" C2' I F 73 " -0.223 2.00e-02 2.50e+03 pdb=" C3' I F 73 " -0.586 2.00e-02 2.50e+03 pdb=" C4' I F 73 " 0.458 2.00e-02 2.50e+03 pdb=" C5' I F 73 " 0.034 2.00e-02 2.50e+03 pdb=" N9 I F 73 " -0.944 2.00e-02 2.50e+03 pdb=" O2' I F 73 " 0.904 2.00e-02 2.50e+03 pdb=" O3' I F 73 " -0.588 2.00e-02 2.50e+03 pdb=" O4' I F 73 " 0.745 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 4 " -0.201 2.00e-02 2.50e+03 5.99e-01 8.07e+03 pdb=" C2' I F 4 " 0.224 2.00e-02 2.50e+03 pdb=" C3' I F 4 " 0.589 2.00e-02 2.50e+03 pdb=" C4' I F 4 " -0.453 2.00e-02 2.50e+03 pdb=" C5' I F 4 " -0.034 2.00e-02 2.50e+03 pdb=" N9 I F 4 " 0.937 2.00e-02 2.50e+03 pdb=" O2' I F 4 " -0.903 2.00e-02 2.50e+03 pdb=" O3' I F 4 " 0.583 2.00e-02 2.50e+03 pdb=" O4' I F 4 " -0.743 2.00e-02 2.50e+03 ... (remaining 3993 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3566 2.76 - 3.30: 23180 3.30 - 3.83: 44173 3.83 - 4.37: 52701 4.37 - 4.90: 83771 Nonbonded interactions: 207391 Sorted by model distance: nonbonded pdb=" OG SER A 571 " pdb=" OP1 C E 57 " model vdw 2.227 2.440 nonbonded pdb=" O PHE C 84 " pdb=" O2' I F 39 " model vdw 2.228 3.040 nonbonded pdb=" ND1 HIS A 39 " pdb=" OP1 I F 7 " model vdw 2.249 2.520 nonbonded pdb=" ND1 HIS B 39 " pdb=" OP2 C E 42 " model vdw 2.265 2.520 nonbonded pdb=" N4 C E 11 " pdb=" O6 I F 70 " model vdw 2.344 2.520 ... (remaining 207386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 28.580 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 71.540 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.014 0.148 25336 Z= 0.780 Angle : 1.482 19.403 35128 Z= 0.547 Chirality : 0.042 0.178 3803 Planarity : 0.082 0.612 3996 Dihedral : 20.414 89.949 10176 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.40 (0.17), residues: 2628 helix: -1.64 (0.44), residues: 124 sheet: -1.69 (0.27), residues: 460 loop : -0.71 (0.15), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 273 HIS 0.002 0.000 HIS D 39 PHE 0.020 0.001 PHE C 143 TYR 0.008 0.001 TYR C 468 ARG 0.006 0.001 ARG B 643 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 2.503 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: A 308 ASN cc_start: 0.7405 (t0) cc_final: 0.6904 (m-40) REVERT: A 364 ASP cc_start: 0.7979 (m-30) cc_final: 0.7312 (m-30) REVERT: A 374 MET cc_start: 0.7451 (ttm) cc_final: 0.7197 (ptp) REVERT: B 111 LEU cc_start: 0.8720 (mp) cc_final: 0.8443 (mp) REVERT: B 237 LEU cc_start: 0.8494 (tp) cc_final: 0.8109 (tp) REVERT: B 353 TRP cc_start: 0.6663 (m100) cc_final: 0.6209 (m100) REVERT: B 354 LEU cc_start: 0.8091 (mm) cc_final: 0.7405 (pp) REVERT: B 378 LEU cc_start: 0.7942 (mm) cc_final: 0.7363 (mt) REVERT: C 473 ARG cc_start: 0.7041 (ttp80) cc_final: 0.6719 (ttt-90) REVERT: D 494 ASN cc_start: 0.7864 (t0) cc_final: 0.7521 (t0) REVERT: D 626 GLU cc_start: 0.7937 (pm20) cc_final: 0.7657 (pm20) REVERT: D 683 TYR cc_start: 0.7737 (m-80) cc_final: 0.7446 (m-80) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.3472 time to fit residues: 273.1764 Evaluate side-chains 223 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.0770 chunk 203 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 156 optimal weight: 0.5980 chunk 243 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN B 597 ASN B 645 ASN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 ASN D 597 ASN ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25336 Z= 0.185 Angle : 1.862 17.171 35128 Z= 1.155 Chirality : 0.041 0.228 3803 Planarity : 0.016 0.118 3996 Dihedral : 23.659 112.096 4976 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.14 % Allowed : 10.32 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.25 (0.17), residues: 2628 helix: -1.46 (0.44), residues: 124 sheet: -1.91 (0.26), residues: 472 loop : -0.50 (0.15), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 296 HIS 0.005 0.000 HIS A 39 PHE 0.026 0.001 PHE D 574 TYR 0.012 0.001 TYR D 683 ARG 0.003 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 235 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ASN cc_start: 0.7445 (t0) cc_final: 0.6726 (m110) REVERT: A 525 MET cc_start: 0.7837 (tpp) cc_final: 0.7622 (tpp) REVERT: B 237 LEU cc_start: 0.8393 (tp) cc_final: 0.7928 (tp) REVERT: B 353 TRP cc_start: 0.6771 (m100) cc_final: 0.6342 (m100) REVERT: B 505 LEU cc_start: 0.8075 (mt) cc_final: 0.7858 (mp) REVERT: D 153 ASP cc_start: 0.7198 (t0) cc_final: 0.6947 (t0) REVERT: D 683 TYR cc_start: 0.7788 (m-80) cc_final: 0.7564 (m-80) outliers start: 28 outliers final: 14 residues processed: 258 average time/residue: 0.3179 time to fit residues: 133.9952 Evaluate side-chains 195 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 679 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 202 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN A 410 HIS ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS A 678 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS B 597 ASN B 599 ASN ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS C 470 GLN ** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS D 316 HIS D 359 HIS ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 ASN D 494 ASN D 597 ASN D 599 ASN D 616 ASN ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 25336 Z= 0.503 Angle : 1.871 16.078 35128 Z= 1.136 Chirality : 0.049 0.190 3803 Planarity : 0.017 0.128 3996 Dihedral : 23.901 105.979 4976 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.26 % Allowed : 12.11 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.57 (0.17), residues: 2628 helix: -1.93 (0.40), residues: 132 sheet: -1.66 (0.28), residues: 396 loop : -0.90 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 273 HIS 0.009 0.002 HIS B 108 PHE 0.032 0.003 PHE B 333 TYR 0.018 0.002 TYR C 74 ARG 0.009 0.001 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 192 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8419 (mtmm) REVERT: A 278 MET cc_start: 0.8511 (tmm) cc_final: 0.8042 (tmm) REVERT: A 308 ASN cc_start: 0.7903 (t0) cc_final: 0.7257 (m-40) REVERT: A 331 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7527 (mmm-85) REVERT: A 364 ASP cc_start: 0.8375 (t70) cc_final: 0.7833 (t70) REVERT: A 570 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7415 (mm-30) REVERT: B 175 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: B 237 LEU cc_start: 0.8540 (tp) cc_final: 0.8319 (tp) REVERT: B 592 ASP cc_start: 0.7262 (t0) cc_final: 0.6909 (t0) REVERT: B 626 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: C 90 LEU cc_start: 0.7803 (tp) cc_final: 0.7600 (tp) REVERT: C 100 MET cc_start: 0.6381 (tpp) cc_final: 0.5930 (tpp) REVERT: C 327 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8329 (mp) REVERT: C 331 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7869 (mmm-85) REVERT: C 576 GLU cc_start: 0.6784 (tt0) cc_final: 0.6427 (tm-30) REVERT: D 126 THR cc_start: 0.8896 (p) cc_final: 0.8439 (p) REVERT: D 361 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7678 (t0) REVERT: D 651 CYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7519 (p) REVERT: D 683 TYR cc_start: 0.8120 (m-80) cc_final: 0.7895 (m-80) outliers start: 80 outliers final: 32 residues processed: 261 average time/residue: 0.3228 time to fit residues: 138.2978 Evaluate side-chains 185 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 145 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 599 ASN Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 651 CYS Chi-restraints excluded: chain D residue 679 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 231 optimal weight: 0.0170 chunk 69 optimal weight: 9.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 599 ASN B 645 ASN C 172 ASN C 229 ASN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 678 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 ASN ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25336 Z= 0.179 Angle : 1.759 15.435 35128 Z= 1.099 Chirality : 0.041 0.222 3803 Planarity : 0.016 0.119 3996 Dihedral : 23.826 95.871 4976 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.31 % Allowed : 15.13 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.17), residues: 2628 helix: -1.64 (0.43), residues: 132 sheet: -1.90 (0.26), residues: 432 loop : -0.76 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.004 0.001 HIS C 684 PHE 0.020 0.001 PHE A 143 TYR 0.007 0.001 TYR D 683 ARG 0.003 0.000 ARG D 643 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7217 (pmm) cc_final: 0.6595 (pmm) REVERT: A 278 MET cc_start: 0.8575 (tmm) cc_final: 0.8178 (tmm) REVERT: A 296 TRP cc_start: 0.7741 (m100) cc_final: 0.7459 (m-90) REVERT: A 308 ASN cc_start: 0.7838 (t0) cc_final: 0.6811 (m110) REVERT: A 364 ASP cc_start: 0.8245 (t70) cc_final: 0.7711 (t0) REVERT: A 648 ASP cc_start: 0.8371 (t70) cc_final: 0.7378 (p0) REVERT: B 175 GLU cc_start: 0.7964 (tp30) cc_final: 0.7701 (tt0) REVERT: B 237 LEU cc_start: 0.8414 (tp) cc_final: 0.8136 (tp) REVERT: B 353 TRP cc_start: 0.6915 (m100) cc_final: 0.6666 (m100) REVERT: B 626 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: D 102 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8080 (tppt) REVERT: D 200 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7557 (tptt) REVERT: D 302 TYR cc_start: 0.7345 (m-80) cc_final: 0.7059 (m-80) REVERT: D 361 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7538 (t0) REVERT: D 461 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8370 (mp) REVERT: D 679 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8102 (t) REVERT: D 683 TYR cc_start: 0.8009 (m-80) cc_final: 0.7765 (m-80) outliers start: 32 outliers final: 20 residues processed: 212 average time/residue: 0.3241 time to fit residues: 112.8776 Evaluate side-chains 172 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 679 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 192 optimal weight: 0.0070 chunk 106 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 232 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 172 ASN B 285 ASN C 133 ASN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN D 365 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25336 Z= 0.270 Angle : 1.731 15.820 35128 Z= 1.086 Chirality : 0.043 0.190 3803 Planarity : 0.017 0.121 3996 Dihedral : 23.937 97.080 4976 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.57 % Allowed : 15.05 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.59 (0.17), residues: 2628 helix: -2.10 (0.39), residues: 156 sheet: -1.94 (0.27), residues: 428 loop : -0.78 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 546 HIS 0.004 0.001 HIS B 108 PHE 0.016 0.002 PHE C 217 TYR 0.010 0.001 TYR B 683 ARG 0.004 0.001 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 164 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8127 (pt) REVERT: A 233 LEU cc_start: 0.8381 (mm) cc_final: 0.8113 (tp) REVERT: A 308 ASN cc_start: 0.7835 (t0) cc_final: 0.6833 (m110) REVERT: A 331 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7617 (mmm-85) REVERT: A 364 ASP cc_start: 0.8363 (t70) cc_final: 0.7687 (t70) REVERT: B 175 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: B 626 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: C 524 ASP cc_start: 0.7159 (p0) cc_final: 0.6710 (t0) REVERT: D 102 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8061 (tppt) REVERT: D 200 LYS cc_start: 0.8295 (mtmt) cc_final: 0.7702 (tptt) REVERT: D 212 PHE cc_start: 0.6213 (m-80) cc_final: 0.5662 (m-80) REVERT: D 302 TYR cc_start: 0.7493 (m-80) cc_final: 0.7204 (m-80) REVERT: D 361 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7637 (t0) REVERT: D 461 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8389 (mp) REVERT: D 683 TYR cc_start: 0.8031 (m-80) cc_final: 0.7750 (m-80) outliers start: 63 outliers final: 34 residues processed: 215 average time/residue: 0.3295 time to fit residues: 116.1469 Evaluate side-chains 187 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 679 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 5.9990 chunk 233 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 259 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN C 311 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25336 Z= 0.296 Angle : 1.725 15.767 35128 Z= 1.085 Chirality : 0.043 0.144 3803 Planarity : 0.017 0.121 3996 Dihedral : 23.998 97.426 4976 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.65 % Allowed : 16.31 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.72 (0.17), residues: 2628 helix: -2.32 (0.38), residues: 156 sheet: -2.10 (0.27), residues: 412 loop : -0.87 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 273 HIS 0.005 0.001 HIS D 108 PHE 0.022 0.002 PHE D 212 TYR 0.010 0.001 TYR C 74 ARG 0.004 0.001 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 159 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8140 (pt) REVERT: A 331 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7551 (mmm-85) REVERT: A 364 ASP cc_start: 0.8370 (t70) cc_final: 0.7683 (t70) REVERT: B 626 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: C 331 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.7914 (mmm-85) REVERT: C 524 ASP cc_start: 0.7164 (p0) cc_final: 0.6655 (t0) REVERT: D 102 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8066 (tppt) REVERT: D 200 LYS cc_start: 0.8385 (mtmt) cc_final: 0.7849 (tptt) REVERT: D 461 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8396 (mp) REVERT: D 556 TYR cc_start: 0.8174 (m-80) cc_final: 0.7872 (m-80) REVERT: D 683 TYR cc_start: 0.8027 (m-80) cc_final: 0.7732 (m-80) outliers start: 65 outliers final: 41 residues processed: 215 average time/residue: 0.3166 time to fit residues: 111.9427 Evaluate side-chains 181 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 135 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 599 ASN Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 679 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 258 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN C 39 HIS ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25336 Z= 0.241 Angle : 1.703 15.733 35128 Z= 1.079 Chirality : 0.042 0.182 3803 Planarity : 0.016 0.119 3996 Dihedral : 24.014 94.377 4976 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.41 % Allowed : 17.41 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.75 (0.17), residues: 2628 helix: -2.39 (0.37), residues: 156 sheet: -2.12 (0.27), residues: 412 loop : -0.88 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 546 HIS 0.004 0.001 HIS D 108 PHE 0.025 0.001 PHE D 212 TYR 0.009 0.001 TYR B 683 ARG 0.004 0.000 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 151 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8195 (pt) REVERT: A 233 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8098 (tp) REVERT: A 331 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7543 (mmm-85) REVERT: A 364 ASP cc_start: 0.8372 (t70) cc_final: 0.7670 (t70) REVERT: A 576 GLU cc_start: 0.6748 (tm-30) cc_final: 0.6358 (tm-30) REVERT: A 648 ASP cc_start: 0.8485 (t70) cc_final: 0.7525 (p0) REVERT: A 667 ASN cc_start: 0.8259 (t0) cc_final: 0.7945 (t0) REVERT: B 626 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: C 524 ASP cc_start: 0.7073 (p0) cc_final: 0.6602 (t0) REVERT: D 102 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8045 (tppt) REVERT: D 200 LYS cc_start: 0.8388 (mtmt) cc_final: 0.7872 (tptt) REVERT: D 373 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8433 (t0) REVERT: D 461 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8421 (mp) REVERT: D 556 TYR cc_start: 0.8140 (m-80) cc_final: 0.7932 (m-80) REVERT: D 679 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8227 (t) REVERT: D 683 TYR cc_start: 0.7989 (m-80) cc_final: 0.7700 (m-80) outliers start: 59 outliers final: 34 residues processed: 203 average time/residue: 0.3089 time to fit residues: 105.0492 Evaluate side-chains 178 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 373 ASN Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 679 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 164 optimal weight: 0.1980 chunk 175 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25336 Z= 0.279 Angle : 1.703 15.699 35128 Z= 1.078 Chirality : 0.043 0.252 3803 Planarity : 0.017 0.120 3996 Dihedral : 24.051 96.867 4976 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.65 % Allowed : 17.82 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.94 (0.17), residues: 2628 helix: -2.51 (0.34), residues: 180 sheet: -2.19 (0.27), residues: 412 loop : -1.01 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 546 HIS 0.005 0.001 HIS D 108 PHE 0.021 0.002 PHE D 212 TYR 0.010 0.001 TYR C 74 ARG 0.004 0.001 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 142 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8190 (pt) REVERT: A 331 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8009 (mmm-85) REVERT: A 482 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8094 (mp) REVERT: A 576 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6493 (tm-30) REVERT: A 648 ASP cc_start: 0.8515 (t70) cc_final: 0.7560 (p0) REVERT: A 667 ASN cc_start: 0.8266 (t0) cc_final: 0.7976 (t0) REVERT: B 90 LEU cc_start: 0.8570 (tp) cc_final: 0.8292 (tt) REVERT: B 626 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: C 331 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7876 (mmm-85) REVERT: C 446 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: C 524 ASP cc_start: 0.7304 (p0) cc_final: 0.6552 (t0) REVERT: D 155 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8411 (m) REVERT: D 200 LYS cc_start: 0.8428 (mtmt) cc_final: 0.7943 (tptt) REVERT: D 361 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7692 (t0) REVERT: D 461 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8379 (mp) REVERT: D 525 MET cc_start: 0.7954 (ptt) cc_final: 0.7576 (ptt) REVERT: D 683 TYR cc_start: 0.7966 (m-80) cc_final: 0.7685 (m-80) outliers start: 65 outliers final: 44 residues processed: 198 average time/residue: 0.3165 time to fit residues: 104.7733 Evaluate side-chains 188 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 135 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain D residue 679 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 0.2980 chunk 225 optimal weight: 5.9990 chunk 240 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 217 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 ASN D 124 ASN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25336 Z= 0.211 Angle : 1.683 15.635 35128 Z= 1.073 Chirality : 0.042 0.206 3803 Planarity : 0.016 0.118 3996 Dihedral : 24.033 98.452 4976 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.00 % Allowed : 18.72 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.86 (0.17), residues: 2628 helix: -2.44 (0.35), residues: 180 sheet: -2.19 (0.27), residues: 412 loop : -0.94 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 656 HIS 0.004 0.001 HIS B 312 PHE 0.023 0.001 PHE A 303 TYR 0.009 0.001 TYR C 74 ARG 0.002 0.000 ARG D 544 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 148 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8165 (pt) REVERT: A 331 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8094 (mmm-85) REVERT: A 648 ASP cc_start: 0.8391 (t70) cc_final: 0.7577 (p0) REVERT: A 667 ASN cc_start: 0.8208 (t0) cc_final: 0.7958 (t0) REVERT: B 90 LEU cc_start: 0.8517 (tp) cc_final: 0.8237 (tt) REVERT: B 525 MET cc_start: 0.8019 (tpp) cc_final: 0.7435 (tmm) REVERT: B 626 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: C 139 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7050 (mttp) REVERT: C 331 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7877 (mmm-85) REVERT: C 446 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: C 524 ASP cc_start: 0.7258 (p0) cc_final: 0.6577 (t0) REVERT: D 155 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8491 (m) REVERT: D 200 LYS cc_start: 0.8405 (mtmt) cc_final: 0.7941 (tptt) REVERT: D 361 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7663 (t0) REVERT: D 461 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8400 (mp) REVERT: D 525 MET cc_start: 0.7832 (ptt) cc_final: 0.7470 (ptt) REVERT: D 556 TYR cc_start: 0.8153 (m-80) cc_final: 0.7855 (m-80) REVERT: D 683 TYR cc_start: 0.7961 (m-80) cc_final: 0.7665 (m-80) outliers start: 49 outliers final: 35 residues processed: 188 average time/residue: 0.3442 time to fit residues: 105.0124 Evaluate side-chains 179 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 136 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 374 MET Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 667 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 120 optimal weight: 0.0670 chunk 176 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 overall best weight: 3.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 597 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS B 285 ASN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 ASN C 597 ASN C 609 GLN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 25336 Z= 0.382 Angle : 1.728 15.678 35128 Z= 1.085 Chirality : 0.046 0.243 3803 Planarity : 0.017 0.123 3996 Dihedral : 24.140 97.258 4976 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.45 % Allowed : 18.52 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.16), residues: 2628 helix: -2.60 (0.34), residues: 180 sheet: -2.37 (0.26), residues: 404 loop : -1.20 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 296 HIS 0.008 0.001 HIS D 108 PHE 0.021 0.002 PHE B 333 TYR 0.011 0.002 TYR D 326 ARG 0.007 0.001 ARG C 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 135 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8172 (tp) REVERT: A 308 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7413 (t0) REVERT: A 331 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8060 (mmm-85) REVERT: A 576 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6643 (tm-30) REVERT: A 667 ASN cc_start: 0.8228 (t0) cc_final: 0.7974 (t0) REVERT: B 626 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: C 331 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7913 (mmm-85) REVERT: C 446 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: C 524 ASP cc_start: 0.7202 (p0) cc_final: 0.6610 (t0) REVERT: D 100 MET cc_start: 0.7346 (pmm) cc_final: 0.6939 (ppp) REVERT: D 155 SER cc_start: 0.8888 (OUTLIER) cc_final: 0.8538 (m) REVERT: D 200 LYS cc_start: 0.8442 (mtmt) cc_final: 0.7991 (tptt) REVERT: D 361 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7694 (t0) REVERT: D 373 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8449 (t0) REVERT: D 461 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8336 (mp) REVERT: D 525 MET cc_start: 0.7940 (ptt) cc_final: 0.7546 (ptt) REVERT: D 556 TYR cc_start: 0.8165 (m-80) cc_final: 0.7954 (m-80) REVERT: D 683 TYR cc_start: 0.8017 (m-80) cc_final: 0.7743 (m-80) outliers start: 60 outliers final: 44 residues processed: 186 average time/residue: 0.3173 time to fit residues: 98.8159 Evaluate side-chains 184 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 130 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 373 ASN Chi-restraints excluded: chain D residue 374 MET Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 599 ASN Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 667 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.0870 chunk 65 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 218 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN A 597 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 ASN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.082704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.071246 restraints weight = 101111.196| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.12 r_work: 0.3489 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25336 Z= 0.231 Angle : 1.694 15.985 35128 Z= 1.076 Chirality : 0.043 0.214 3803 Planarity : 0.016 0.120 3996 Dihedral : 24.049 99.645 4976 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.12 % Allowed : 18.56 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.17), residues: 2628 helix: -2.36 (0.35), residues: 180 sheet: -2.37 (0.26), residues: 412 loop : -1.09 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 656 HIS 0.005 0.001 HIS D 108 PHE 0.018 0.001 PHE A 303 TYR 0.008 0.001 TYR C 74 ARG 0.007 0.000 ARG A 473 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4819.81 seconds wall clock time: 89 minutes 2.30 seconds (5342.30 seconds total)