Starting phenix.real_space_refine on Thu Feb 15 13:49:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lw1_30002/02_2024/6lw1_30002_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lw1_30002/02_2024/6lw1_30002.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lw1_30002/02_2024/6lw1_30002_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lw1_30002/02_2024/6lw1_30002_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lw1_30002/02_2024/6lw1_30002_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lw1_30002/02_2024/6lw1_30002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lw1_30002/02_2024/6lw1_30002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lw1_30002/02_2024/6lw1_30002_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lw1_30002/02_2024/6lw1_30002_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 7956 2.51 5 N 2116 2.21 5 O 2278 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ARG 566": "NH1" <-> "NH2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A GLU 625": "OE1" <-> "OE2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 671": "OD1" <-> "OD2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A ASP 790": "OD1" <-> "OD2" Residue "A ASP 811": "OD1" <-> "OD2" Residue "A ASP 829": "OD1" <-> "OD2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 95": "OD1" <-> "OD2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 135": "OD1" <-> "OD2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 213": "OD1" <-> "OD2" Residue "B ASP 243": "OD1" <-> "OD2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B ASP 255": "OD1" <-> "OD2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ARG 473": "NH1" <-> "NH2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B ARG 566": "NH1" <-> "NH2" Residue "B PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 614": "NH1" <-> "NH2" Residue "B GLU 625": "OE1" <-> "OE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 671": "OD1" <-> "OD2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B ARG 696": "NH1" <-> "NH2" Residue "B GLU 716": "OE1" <-> "OE2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 769": "OE1" <-> "OE2" Residue "B ASP 790": "OD1" <-> "OD2" Residue "B ASP 811": "OD1" <-> "OD2" Residue "B ASP 829": "OD1" <-> "OD2" Residue "B TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 6170 Classifications: {'peptide': 763} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 33, 'TRANS': 727} Chain breaks: 2 Chain: "B" Number of atoms: 6170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 6170 Classifications: {'peptide': 763} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 33, 'TRANS': 727} Chain breaks: 2 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'EX3': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'EX3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.70, per 1000 atoms: 0.54 Number of scatterers: 12412 At special positions: 0 Unit cell: (100.596, 128.484, 105.576, 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 60 16.00 F 2 9.00 O 2278 8.00 N 2116 7.00 C 7956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 51 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 475 " distance=2.02 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 263 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 521 " distance=2.02 Simple disulfide: pdb=" SG CYS A 787 " - pdb=" SG CYS A 814 " distance=2.04 Simple disulfide: pdb=" SG CYS A 789 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 475 " distance=2.02 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 263 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 521 " distance=2.02 Simple disulfide: pdb=" SG CYS B 787 " - pdb=" SG CYS B 814 " distance=2.04 Simple disulfide: pdb=" SG CYS B 789 " - pdb=" SG CYS B 833 " 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: 4.65 Conformation dependent library (CDL) restraints added in 2.2 seconds 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 10 sheets defined 10.6% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 165 through 171 removed outlier: 4.804A pdb=" N GLU A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 334 through 338 removed outlier: 3.531A pdb=" N PHE A 338 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.555A pdb=" N SER A 368 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 395 removed outlier: 3.593A pdb=" N SER A 391 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Proline residue: A 392 - end of helix removed outlier: 4.138A pdb=" N ASN A 395 " --> pdb=" O PRO A 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 388 through 395' Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 492 through 494 No H-bonds generated for 'chain 'A' and resid 492 through 494' Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 631 through 634 No H-bonds generated for 'chain 'A' and resid 631 through 634' Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 695 through 697 No H-bonds generated for 'chain 'A' and resid 695 through 697' Processing helix chain 'A' and resid 718 through 721 No H-bonds generated for 'chain 'A' and resid 718 through 721' Processing helix chain 'A' and resid 769 through 774 removed outlier: 5.380A pdb=" N ASN A 774 " --> pdb=" O ASN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 removed outlier: 3.878A pdb=" N VAL A 792 " --> pdb=" O CYS A 789 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N TRP A 793 " --> pdb=" O ASP A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'B' and resid 165 through 171 removed outlier: 4.804A pdb=" N GLU B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 329 through 332 No H-bonds generated for 'chain 'B' and resid 329 through 332' Processing helix chain 'B' and resid 334 through 338 removed outlier: 3.532A pdb=" N PHE B 338 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.554A pdb=" N SER B 368 " --> pdb=" O ALA B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 395 removed outlier: 3.593A pdb=" N SER B 391 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 392 - end of helix removed outlier: 4.138A pdb=" N ASN B 395 " --> pdb=" O PRO B 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 388 through 395' Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 492 through 494 No H-bonds generated for 'chain 'B' and resid 492 through 494' Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'B' and resid 631 through 634 No H-bonds generated for 'chain 'B' and resid 631 through 634' Processing helix chain 'B' and resid 670 through 672 No H-bonds generated for 'chain 'B' and resid 670 through 672' Processing helix chain 'B' and resid 695 through 697 No H-bonds generated for 'chain 'B' and resid 695 through 697' Processing helix chain 'B' and resid 718 through 721 No H-bonds generated for 'chain 'B' and resid 718 through 721' Processing helix chain 'B' and resid 769 through 774 removed outlier: 5.379A pdb=" N ASN B 774 " --> pdb=" O ASN B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 798 removed outlier: 3.878A pdb=" N VAL B 792 " --> pdb=" O CYS B 789 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TRP B 793 " --> pdb=" O ASP B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 820 No H-bonds generated for 'chain 'B' and resid 818 through 820' Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing sheet with id= A, first strand: chain 'A' and resid 37 through 41 removed outlier: 3.597A pdb=" N ASP A 37 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASN A 69 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A 93 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER A 131 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 152 through 154 removed outlier: 6.343A pdb=" N ILE A 176 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 208 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU A 229 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 253 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A 294 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU A 318 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN A 344 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 374 " --> pdb=" O LEU A 345 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 401 through 403 removed outlier: 6.838A pdb=" N VAL A 425 " --> pdb=" O LEU A 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 497 through 499 removed outlier: 6.732A pdb=" N CYS A 521 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR A 546 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 570 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS A 600 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR A 623 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU A 654 " --> pdb=" O LEU A 624 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 530 through 532 removed outlier: 6.851A pdb=" N ARG A 553 " --> pdb=" O GLN A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.597A pdb=" N ASP B 37 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN B 69 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU B 93 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER B 131 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 152 through 154 removed outlier: 6.343A pdb=" N ILE B 176 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B 208 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU B 229 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 253 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 294 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU B 318 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN B 344 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE B 374 " --> pdb=" O LEU B 345 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 401 through 403 removed outlier: 6.839A pdb=" N VAL B 425 " --> pdb=" O LEU B 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 497 through 499 removed outlier: 6.731A pdb=" N CYS B 521 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYR B 546 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 570 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS B 600 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR B 623 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU B 654 " --> pdb=" O LEU B 624 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 530 through 532 removed outlier: 6.851A pdb=" N ARG B 553 " --> pdb=" O GLN B 531 " (cutoff:3.500A) No H-bonds generated for sheet with id= J 34 hydrogen bonds defined for protein. 42 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.63 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3741 1.33 - 1.46: 2544 1.46 - 1.58: 6311 1.58 - 1.70: 0 1.70 - 1.83: 82 Bond restraints: 12678 Sorted by residual: bond pdb=" C21 EX3 B1001 " pdb=" C23 EX3 B1001 " ideal model delta sigma weight residual 1.344 1.541 -0.197 2.00e-02 2.50e+03 9.68e+01 bond pdb=" C21 EX3 A1001 " pdb=" C23 EX3 A1001 " ideal model delta sigma weight residual 1.344 1.541 -0.197 2.00e-02 2.50e+03 9.66e+01 bond pdb=" C22 EX3 A1001 " pdb=" C25 EX3 A1001 " ideal model delta sigma weight residual 1.642 1.446 0.196 2.00e-02 2.50e+03 9.57e+01 bond pdb=" C22 EX3 B1001 " pdb=" C25 EX3 B1001 " ideal model delta sigma weight residual 1.642 1.446 0.196 2.00e-02 2.50e+03 9.57e+01 bond pdb=" C21 EX3 A1001 " pdb=" C25 EX3 A1001 " ideal model delta sigma weight residual 1.648 1.512 0.136 2.00e-02 2.50e+03 4.65e+01 ... (remaining 12673 not shown) Histogram of bond angle deviations from ideal: 75.22 - 87.26: 4 87.26 - 99.30: 6 99.30 - 111.34: 5589 111.34 - 123.39: 11132 123.39 - 135.43: 457 Bond angle restraints: 17188 Sorted by residual: angle pdb=" C22 EX3 A1001 " pdb=" C20 EX3 A1001 " pdb=" N5 EX3 A1001 " ideal model delta sigma weight residual 110.42 85.93 24.49 3.00e+00 1.11e-01 6.67e+01 angle pdb=" C22 EX3 B1001 " pdb=" C20 EX3 B1001 " pdb=" N5 EX3 B1001 " ideal model delta sigma weight residual 110.42 85.95 24.47 3.00e+00 1.11e-01 6.66e+01 angle pdb=" C22 EX3 A1001 " pdb=" N6 EX3 A1001 " pdb=" C23 EX3 A1001 " ideal model delta sigma weight residual 110.44 87.40 23.04 3.00e+00 1.11e-01 5.90e+01 angle pdb=" C22 EX3 B1001 " pdb=" N6 EX3 B1001 " pdb=" C23 EX3 B1001 " ideal model delta sigma weight residual 110.44 87.45 22.99 3.00e+00 1.11e-01 5.87e+01 angle pdb=" C25 EX3 A1001 " pdb=" C22 EX3 A1001 " pdb=" N6 EX3 A1001 " ideal model delta sigma weight residual 93.74 115.23 -21.49 3.00e+00 1.11e-01 5.13e+01 ... (remaining 17183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6618 17.91 - 35.81: 858 35.81 - 53.72: 204 53.72 - 71.62: 70 71.62 - 89.53: 12 Dihedral angle restraints: 7762 sinusoidal: 3234 harmonic: 4528 Sorted by residual: dihedral pdb=" CB CYS B 263 " pdb=" SG CYS B 263 " pdb=" SG CYS B 270 " pdb=" CB CYS B 270 " ideal model delta sinusoidal sigma weight residual 93.00 -177.47 -89.53 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CB CYS A 263 " pdb=" SG CYS A 263 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual 93.00 -177.48 -89.52 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CA SER B 429 " pdb=" C SER B 429 " pdb=" N VAL B 430 " pdb=" CA VAL B 430 " ideal model delta harmonic sigma weight residual -180.00 -140.70 -39.30 0 5.00e+00 4.00e-02 6.18e+01 ... (remaining 7759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.342: 1968 0.342 - 0.684: 0 0.684 - 1.026: 0 1.026 - 1.367: 0 1.367 - 1.709: 2 Chirality restraints: 1970 Sorted by residual: chirality pdb=" C22 EX3 A1001 " pdb=" C20 EX3 A1001 " pdb=" C25 EX3 A1001 " pdb=" N6 EX3 A1001 " both_signs ideal model delta sigma weight residual False 2.78 1.07 1.71 2.00e-01 2.50e+01 7.30e+01 chirality pdb=" C22 EX3 B1001 " pdb=" C20 EX3 B1001 " pdb=" C25 EX3 B1001 " pdb=" N6 EX3 B1001 " both_signs ideal model delta sigma weight residual False 2.78 1.07 1.70 2.00e-01 2.50e+01 7.27e+01 chirality pdb=" C21 EX3 A1001 " pdb=" C23 EX3 A1001 " pdb=" C25 EX3 A1001 " pdb=" N5 EX3 A1001 " both_signs ideal model delta sigma weight residual False 2.78 3.09 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1967 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N EX3 B1001 " -0.001 2.00e-02 2.50e+03 1.28e-02 5.30e+00 pdb=" C EX3 B1001 " 0.001 2.00e-02 2.50e+03 pdb=" O EX3 B1001 " -0.001 2.00e-02 2.50e+03 pdb=" C1 EX3 B1001 " 0.007 2.00e-02 2.50e+03 pdb=" C14 EX3 B1001 " -0.030 2.00e-02 2.50e+03 pdb=" C2 EX3 B1001 " -0.002 2.00e-02 2.50e+03 pdb=" C26 EX3 B1001 " -0.000 2.00e-02 2.50e+03 pdb=" C3 EX3 B1001 " -0.005 2.00e-02 2.50e+03 pdb=" C4 EX3 B1001 " 0.033 2.00e-02 2.50e+03 pdb=" C7 EX3 B1001 " -0.003 2.00e-02 2.50e+03 pdb=" N1 EX3 B1001 " -0.006 2.00e-02 2.50e+03 pdb=" N2 EX3 B1001 " 0.004 2.00e-02 2.50e+03 pdb=" N3 EX3 B1001 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N EX3 A1001 " 0.001 2.00e-02 2.50e+03 1.27e-02 5.21e+00 pdb=" C EX3 A1001 " -0.001 2.00e-02 2.50e+03 pdb=" O EX3 A1001 " 0.001 2.00e-02 2.50e+03 pdb=" C1 EX3 A1001 " -0.006 2.00e-02 2.50e+03 pdb=" C14 EX3 A1001 " 0.030 2.00e-02 2.50e+03 pdb=" C2 EX3 A1001 " 0.002 2.00e-02 2.50e+03 pdb=" C26 EX3 A1001 " 0.000 2.00e-02 2.50e+03 pdb=" C3 EX3 A1001 " 0.005 2.00e-02 2.50e+03 pdb=" C4 EX3 A1001 " -0.032 2.00e-02 2.50e+03 pdb=" C7 EX3 A1001 " 0.003 2.00e-02 2.50e+03 pdb=" N1 EX3 A1001 " 0.006 2.00e-02 2.50e+03 pdb=" N2 EX3 A1001 " -0.004 2.00e-02 2.50e+03 pdb=" N3 EX3 A1001 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 434 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 435 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 435 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 435 " 0.025 5.00e-02 4.00e+02 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 327 2.67 - 3.23: 11970 3.23 - 3.79: 18872 3.79 - 4.34: 28702 4.34 - 4.90: 45429 Nonbonded interactions: 105300 Sorted by model distance: nonbonded pdb=" O SER A 429 " pdb=" N ASN A 431 " model vdw 2.119 2.520 nonbonded pdb=" O SER B 429 " pdb=" N ASN B 431 " model vdw 2.119 2.520 nonbonded pdb=" O SER A 429 " pdb=" ND2 ASN A 431 " model vdw 2.161 2.520 nonbonded pdb=" O SER B 429 " pdb=" ND2 ASN B 431 " model vdw 2.161 2.520 nonbonded pdb=" O SER A 504 " pdb=" OG SER A 504 " model vdw 2.163 2.440 ... (remaining 105295 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' } 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.090 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 34.920 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.010 0.197 12678 Z= 0.634 Angle : 1.055 24.494 17188 Z= 0.485 Chirality : 0.075 1.709 1970 Planarity : 0.004 0.045 2180 Dihedral : 17.546 86.664 4754 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.30 % Favored : 89.17 % Rotamer: Outliers : 7.10 % Allowed : 24.30 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.85 (0.19), residues: 1514 helix: -4.31 (0.27), residues: 116 sheet: -3.65 (0.28), residues: 268 loop : -2.22 (0.16), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 793 HIS 0.006 0.001 HIS B 298 PHE 0.016 0.002 PHE A 96 TYR 0.020 0.002 TYR B 233 ARG 0.007 0.001 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 143 time to evaluate : 1.595 Fit side-chains REVERT: A 95 ASP cc_start: 0.7113 (t0) cc_final: 0.6855 (t0) REVERT: A 135 ASP cc_start: 0.7711 (m-30) cc_final: 0.7409 (m-30) REVERT: A 167 GLN cc_start: 0.7474 (pt0) cc_final: 0.7105 (pt0) REVERT: A 360 MET cc_start: 0.8385 (ttp) cc_final: 0.8173 (ttp) REVERT: A 514 GLN cc_start: 0.7736 (tt0) cc_final: 0.7469 (mt0) REVERT: A 723 ARG cc_start: 0.7154 (tpt90) cc_final: 0.6818 (mmm160) REVERT: A 759 ILE cc_start: 0.5021 (OUTLIER) cc_final: 0.4430 (tp) REVERT: A 829 ASP cc_start: 0.3973 (OUTLIER) cc_final: 0.3378 (t70) REVERT: B 130 LYS cc_start: 0.7276 (mttt) cc_final: 0.7034 (mmtp) REVERT: B 135 ASP cc_start: 0.7676 (m-30) cc_final: 0.7409 (m-30) REVERT: B 207 LYS cc_start: 0.8223 (mttm) cc_final: 0.7556 (mtmt) REVERT: B 360 MET cc_start: 0.8385 (ttp) cc_final: 0.8170 (ttp) REVERT: B 514 GLN cc_start: 0.7713 (tt0) cc_final: 0.7426 (mt0) REVERT: B 673 MET cc_start: 0.8356 (mmt) cc_final: 0.7706 (mtp) REVERT: B 697 TYR cc_start: 0.7550 (m-10) cc_final: 0.7244 (m-10) REVERT: B 710 GLN cc_start: 0.7603 (mp10) cc_final: 0.7358 (mp10) REVERT: B 759 ILE cc_start: 0.5006 (OUTLIER) cc_final: 0.4389 (tp) REVERT: B 829 ASP cc_start: 0.3755 (OUTLIER) cc_final: 0.3204 (t70) outliers start: 102 outliers final: 47 residues processed: 233 average time/residue: 0.8845 time to fit residues: 233.1036 Evaluate side-chains 174 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 123 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 THR Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 110 ASN A 159 ASN A 167 GLN A 181 GLN A 252 GLN A 276 ASN A 280 GLN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN A 389 GLN A 407 ASN A 503 ASN A 720 ASN A 727 ASN A 732 ASN A 744 GLN A 781 HIS B 66 ASN B 99 ASN B 110 ASN B 159 ASN B 167 GLN B 181 GLN B 252 GLN B 275 ASN B 276 ASN B 280 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 389 GLN B 407 ASN B 503 ASN B 720 ASN B 727 ASN B 732 ASN B 744 GLN B 781 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12678 Z= 0.165 Angle : 0.573 7.855 17188 Z= 0.291 Chirality : 0.045 0.139 1970 Planarity : 0.003 0.033 2180 Dihedral : 8.215 58.817 1722 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.74 % Favored : 93.00 % Rotamer: Outliers : 5.22 % Allowed : 23.96 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.94 (0.21), residues: 1514 helix: -4.36 (0.21), residues: 126 sheet: -3.17 (0.31), residues: 266 loop : -1.40 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 796 HIS 0.003 0.001 HIS A 46 PHE 0.015 0.001 PHE B 664 TYR 0.010 0.001 TYR A 233 ARG 0.006 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 128 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8024 (mttm) cc_final: 0.7411 (mtmt) REVERT: A 509 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7673 (tttm) REVERT: A 636 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.5641 (ttp-170) REVERT: A 697 TYR cc_start: 0.7539 (m-10) cc_final: 0.7160 (m-80) REVERT: A 710 GLN cc_start: 0.7541 (mp10) cc_final: 0.7135 (mp10) REVERT: A 723 ARG cc_start: 0.7057 (tpt90) cc_final: 0.6770 (mmm160) REVERT: A 734 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7038 (mp10) REVERT: A 759 ILE cc_start: 0.4972 (OUTLIER) cc_final: 0.4405 (tp) REVERT: A 782 HIS cc_start: 0.6144 (OUTLIER) cc_final: 0.5671 (m170) REVERT: A 829 ASP cc_start: 0.3845 (OUTLIER) cc_final: 0.3315 (t70) REVERT: B 50 ASP cc_start: 0.6876 (p0) cc_final: 0.5850 (m-30) REVERT: B 87 ARG cc_start: 0.4485 (OUTLIER) cc_final: 0.4190 (pmt170) REVERT: B 95 ASP cc_start: 0.7256 (t0) cc_final: 0.6836 (t70) REVERT: B 135 ASP cc_start: 0.7639 (m-30) cc_final: 0.7429 (m-30) REVERT: B 207 LYS cc_start: 0.8113 (mttm) cc_final: 0.7444 (mtmt) REVERT: B 246 ASN cc_start: 0.8110 (t0) cc_final: 0.7814 (t0) REVERT: B 509 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7663 (tttm) REVERT: B 514 GLN cc_start: 0.7617 (tt0) cc_final: 0.7365 (mt0) REVERT: B 697 TYR cc_start: 0.7630 (m-10) cc_final: 0.7318 (m-10) REVERT: B 710 GLN cc_start: 0.7520 (mp10) cc_final: 0.7306 (mp10) REVERT: B 734 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.7095 (mp10) REVERT: B 759 ILE cc_start: 0.4949 (OUTLIER) cc_final: 0.4375 (tp) REVERT: B 782 HIS cc_start: 0.6172 (OUTLIER) cc_final: 0.5707 (m170) REVERT: B 829 ASP cc_start: 0.3982 (OUTLIER) cc_final: 0.3457 (t70) outliers start: 75 outliers final: 33 residues processed: 194 average time/residue: 0.8227 time to fit residues: 181.2507 Evaluate side-chains 159 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 114 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 734 GLN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 782 HIS Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 40.0000 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 276 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 ASN B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12678 Z= 0.397 Angle : 0.647 8.488 17188 Z= 0.326 Chirality : 0.048 0.146 1970 Planarity : 0.004 0.032 2180 Dihedral : 7.954 58.343 1688 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.86 % Favored : 91.74 % Rotamer: Outliers : 6.13 % Allowed : 25.35 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.74 (0.21), residues: 1514 helix: -4.25 (0.23), residues: 126 sheet: -3.09 (0.31), residues: 272 loop : -1.22 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 796 HIS 0.005 0.001 HIS B 298 PHE 0.015 0.002 PHE B 325 TYR 0.017 0.002 TYR B 233 ARG 0.004 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 121 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.6485 (mtp-110) cc_final: 0.6238 (mtp-110) REVERT: A 509 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7682 (mtmm) REVERT: A 636 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.5705 (ttp-170) REVERT: A 710 GLN cc_start: 0.7699 (mp10) cc_final: 0.7343 (mp10) REVERT: A 723 ARG cc_start: 0.7145 (tpt90) cc_final: 0.6789 (mmm160) REVERT: A 759 ILE cc_start: 0.5159 (OUTLIER) cc_final: 0.4947 (tp) REVERT: A 829 ASP cc_start: 0.4023 (OUTLIER) cc_final: 0.3545 (t70) REVERT: B 135 ASP cc_start: 0.7734 (m-30) cc_final: 0.7519 (m-30) REVERT: B 207 LYS cc_start: 0.8209 (mttm) cc_final: 0.7561 (mtmt) REVERT: B 246 ASN cc_start: 0.8245 (t0) cc_final: 0.7937 (t0) REVERT: B 509 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7651 (tttm) REVERT: B 514 GLN cc_start: 0.7711 (tt0) cc_final: 0.7492 (mt0) REVERT: B 673 MET cc_start: 0.8435 (mmt) cc_final: 0.7665 (mtp) REVERT: B 697 TYR cc_start: 0.7670 (m-10) cc_final: 0.7309 (m-10) REVERT: B 829 ASP cc_start: 0.4096 (OUTLIER) cc_final: 0.3571 (t70) outliers start: 88 outliers final: 52 residues processed: 194 average time/residue: 0.7827 time to fit residues: 173.4589 Evaluate side-chains 170 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 112 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 167 GLN A 276 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 ASN B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN B 732 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12678 Z= 0.201 Angle : 0.565 9.355 17188 Z= 0.284 Chirality : 0.045 0.204 1970 Planarity : 0.003 0.032 2180 Dihedral : 7.094 59.580 1684 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.61 % Favored : 94.12 % Rotamer: Outliers : 4.87 % Allowed : 27.23 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.46 (0.22), residues: 1514 helix: -4.01 (0.27), residues: 126 sheet: -2.91 (0.32), residues: 272 loop : -1.02 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 796 HIS 0.003 0.001 HIS B 298 PHE 0.012 0.001 PHE B 507 TYR 0.015 0.001 TYR B 233 ARG 0.003 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 118 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8096 (mttm) cc_final: 0.7491 (mtmt) REVERT: A 509 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7698 (tttm) REVERT: A 636 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.5634 (ttp-170) REVERT: A 710 GLN cc_start: 0.7717 (mp10) cc_final: 0.7373 (mp10) REVERT: A 759 ILE cc_start: 0.4949 (OUTLIER) cc_final: 0.4740 (tp) REVERT: A 829 ASP cc_start: 0.3770 (OUTLIER) cc_final: 0.3311 (t70) REVERT: B 135 ASP cc_start: 0.7741 (m-30) cc_final: 0.7540 (m-30) REVERT: B 207 LYS cc_start: 0.8129 (mttm) cc_final: 0.7508 (mtmt) REVERT: B 246 ASN cc_start: 0.8147 (t0) cc_final: 0.7886 (t0) REVERT: B 509 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7699 (tttm) REVERT: B 697 TYR cc_start: 0.7670 (m-10) cc_final: 0.7312 (m-10) REVERT: B 738 LEU cc_start: 0.7085 (mp) cc_final: 0.6782 (tp) REVERT: B 829 ASP cc_start: 0.3802 (OUTLIER) cc_final: 0.3299 (t70) outliers start: 70 outliers final: 38 residues processed: 177 average time/residue: 0.8279 time to fit residues: 167.3205 Evaluate side-chains 153 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 109 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 75 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 276 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A 732 ASN B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN B 732 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12678 Z= 0.358 Angle : 0.633 9.319 17188 Z= 0.314 Chirality : 0.048 0.161 1970 Planarity : 0.004 0.032 2180 Dihedral : 7.240 58.959 1682 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.33 % Favored : 92.27 % Rotamer: Outliers : 5.71 % Allowed : 26.53 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.35 (0.22), residues: 1514 helix: -3.93 (0.29), residues: 126 sheet: -2.46 (0.36), residues: 236 loop : -1.12 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 796 HIS 0.005 0.001 HIS B 298 PHE 0.015 0.002 PHE A 325 TYR 0.018 0.002 TYR A 233 ARG 0.003 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 108 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7733 (mtmm) REVERT: A 636 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.5735 (ttp-170) REVERT: A 673 MET cc_start: 0.8407 (mmt) cc_final: 0.7683 (mtp) REVERT: A 678 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7028 (mttp) REVERT: A 697 TYR cc_start: 0.7922 (m-80) cc_final: 0.7478 (m-80) REVERT: A 710 GLN cc_start: 0.7750 (mp10) cc_final: 0.7294 (mm-40) REVERT: A 759 ILE cc_start: 0.5235 (OUTLIER) cc_final: 0.4894 (tp) REVERT: A 829 ASP cc_start: 0.4002 (OUTLIER) cc_final: 0.3589 (t70) REVERT: B 246 ASN cc_start: 0.8234 (t0) cc_final: 0.7960 (t0) REVERT: B 509 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7679 (tttm) REVERT: B 673 MET cc_start: 0.8412 (mmt) cc_final: 0.7737 (mtp) REVERT: B 678 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7083 (mttp) REVERT: B 697 TYR cc_start: 0.7644 (m-10) cc_final: 0.7295 (m-10) REVERT: B 738 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7033 (tp) REVERT: B 829 ASP cc_start: 0.4042 (OUTLIER) cc_final: 0.3589 (t70) outliers start: 82 outliers final: 52 residues processed: 182 average time/residue: 0.7452 time to fit residues: 157.8265 Evaluate side-chains 165 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 104 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 246 ASN A 276 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 ASN B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12678 Z= 0.191 Angle : 0.551 8.960 17188 Z= 0.277 Chirality : 0.044 0.141 1970 Planarity : 0.003 0.031 2180 Dihedral : 6.835 59.959 1682 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.94 % Favored : 93.79 % Rotamer: Outliers : 4.81 % Allowed : 27.86 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.24 (0.22), residues: 1514 helix: -3.72 (0.32), residues: 126 sheet: -2.72 (0.33), residues: 272 loop : -0.89 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 796 HIS 0.003 0.000 HIS B 298 PHE 0.013 0.001 PHE B 507 TYR 0.014 0.001 TYR B 233 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 115 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8101 (mttm) cc_final: 0.7501 (mtmt) REVERT: A 509 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7699 (tttm) REVERT: A 636 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.5720 (ttp-170) REVERT: A 710 GLN cc_start: 0.7763 (mp10) cc_final: 0.7295 (mm-40) REVERT: A 734 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: A 738 LEU cc_start: 0.7356 (mp) cc_final: 0.6987 (tp) REVERT: A 759 ILE cc_start: 0.5433 (OUTLIER) cc_final: 0.5086 (tp) REVERT: A 778 LEU cc_start: 0.6643 (tt) cc_final: 0.6081 (mp) REVERT: A 829 ASP cc_start: 0.4254 (OUTLIER) cc_final: 0.3796 (t70) REVERT: B 196 GLU cc_start: 0.7659 (pt0) cc_final: 0.7407 (pt0) REVERT: B 207 LYS cc_start: 0.8095 (mttm) cc_final: 0.7484 (mtmt) REVERT: B 246 ASN cc_start: 0.8158 (t0) cc_final: 0.7902 (t0) REVERT: B 509 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7658 (tttp) REVERT: B 673 MET cc_start: 0.8400 (mmt) cc_final: 0.7693 (mtp) REVERT: B 697 TYR cc_start: 0.7806 (m-10) cc_final: 0.7442 (m-10) REVERT: B 738 LEU cc_start: 0.7289 (mp) cc_final: 0.7078 (tp) REVERT: B 743 LEU cc_start: 0.7122 (mt) cc_final: 0.6909 (mt) REVERT: B 829 ASP cc_start: 0.4205 (OUTLIER) cc_final: 0.3730 (t70) outliers start: 69 outliers final: 37 residues processed: 175 average time/residue: 0.8237 time to fit residues: 164.2247 Evaluate side-chains 152 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 108 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 276 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN A 732 ASN B 66 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.066 12678 Z= 0.673 Angle : 0.796 9.199 17188 Z= 0.392 Chirality : 0.055 0.175 1970 Planarity : 0.005 0.043 2180 Dihedral : 7.540 59.467 1675 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.71 % Favored : 89.76 % Rotamer: Outliers : 6.48 % Allowed : 27.23 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.54 (0.22), residues: 1514 helix: -3.88 (0.30), residues: 126 sheet: -2.84 (0.33), residues: 272 loop : -1.14 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 796 HIS 0.008 0.001 HIS B 298 PHE 0.019 0.003 PHE A 382 TYR 0.022 0.003 TYR A 233 ARG 0.004 0.001 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 114 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.7750 (pt0) cc_final: 0.7528 (pt0) REVERT: A 673 MET cc_start: 0.8464 (mmt) cc_final: 0.7910 (mtp) REVERT: A 678 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7122 (mttp) REVERT: A 710 GLN cc_start: 0.7841 (mp10) cc_final: 0.7362 (mm-40) REVERT: A 734 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7373 (mp10) REVERT: A 759 ILE cc_start: 0.5393 (OUTLIER) cc_final: 0.4816 (tp) REVERT: A 829 ASP cc_start: 0.4178 (OUTLIER) cc_final: 0.3716 (t70) REVERT: B 196 GLU cc_start: 0.7701 (pt0) cc_final: 0.7397 (pt0) REVERT: B 509 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7647 (tttm) REVERT: B 673 MET cc_start: 0.8381 (mmt) cc_final: 0.7813 (mtp) REVERT: B 678 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.6981 (mttp) REVERT: B 697 TYR cc_start: 0.7651 (m-10) cc_final: 0.7352 (m-10) REVERT: B 734 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: B 829 ASP cc_start: 0.4210 (OUTLIER) cc_final: 0.3768 (t70) outliers start: 93 outliers final: 52 residues processed: 195 average time/residue: 0.7323 time to fit residues: 164.1884 Evaluate side-chains 168 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 108 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 734 GLN Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 72 optimal weight: 30.0000 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 140 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 246 ASN A 276 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12678 Z= 0.261 Angle : 0.591 9.851 17188 Z= 0.298 Chirality : 0.046 0.143 1970 Planarity : 0.003 0.032 2180 Dihedral : 6.855 58.704 1675 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.47 % Favored : 93.26 % Rotamer: Outliers : 5.15 % Allowed : 28.97 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.22 (0.22), residues: 1514 helix: -3.71 (0.32), residues: 126 sheet: -2.32 (0.38), residues: 236 loop : -1.06 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 796 HIS 0.005 0.001 HIS B 298 PHE 0.015 0.002 PHE B 507 TYR 0.014 0.001 TYR B 233 ARG 0.002 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 107 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.7714 (pt0) cc_final: 0.7502 (pt0) REVERT: A 509 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7732 (tttm) REVERT: A 636 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.5916 (ttp-170) REVERT: A 673 MET cc_start: 0.8394 (mmt) cc_final: 0.7810 (mtp) REVERT: A 678 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7021 (mttp) REVERT: A 710 GLN cc_start: 0.7720 (mp10) cc_final: 0.7215 (mm-40) REVERT: A 734 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: A 759 ILE cc_start: 0.5339 (OUTLIER) cc_final: 0.4823 (tp) REVERT: A 829 ASP cc_start: 0.4253 (OUTLIER) cc_final: 0.3848 (t70) REVERT: B 196 GLU cc_start: 0.7671 (pt0) cc_final: 0.7367 (pt0) REVERT: B 509 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7653 (tttm) REVERT: B 673 MET cc_start: 0.8416 (mmt) cc_final: 0.7822 (mtp) REVERT: B 678 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7011 (mttp) REVERT: B 697 TYR cc_start: 0.7779 (m-10) cc_final: 0.7424 (m-10) REVERT: B 734 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6965 (mp10) REVERT: B 829 ASP cc_start: 0.4195 (OUTLIER) cc_final: 0.3743 (t70) outliers start: 74 outliers final: 41 residues processed: 171 average time/residue: 0.8477 time to fit residues: 164.5336 Evaluate side-chains 156 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 105 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 734 GLN Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 246 ASN A 276 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A 732 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12678 Z= 0.221 Angle : 0.577 10.237 17188 Z= 0.287 Chirality : 0.045 0.147 1970 Planarity : 0.003 0.031 2180 Dihedral : 6.625 59.805 1675 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.27 % Favored : 92.47 % Rotamer: Outliers : 4.74 % Allowed : 29.18 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % 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: -2.02 (0.23), residues: 1514 helix: -3.57 (0.34), residues: 126 sheet: -2.21 (0.38), residues: 236 loop : -0.90 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 796 HIS 0.004 0.001 HIS B 298 PHE 0.014 0.001 PHE A 507 TYR 0.014 0.001 TYR B 233 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 109 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7805 (tttm) REVERT: A 673 MET cc_start: 0.8352 (mmt) cc_final: 0.7707 (mtp) REVERT: A 678 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.6964 (mttp) REVERT: A 710 GLN cc_start: 0.7716 (mp10) cc_final: 0.7239 (mm-40) REVERT: A 759 ILE cc_start: 0.5497 (OUTLIER) cc_final: 0.4904 (tp) REVERT: A 829 ASP cc_start: 0.4240 (OUTLIER) cc_final: 0.3815 (t70) REVERT: B 196 GLU cc_start: 0.7631 (pt0) cc_final: 0.7327 (pt0) REVERT: B 509 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7702 (tttm) REVERT: B 636 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.5920 (ttp-170) REVERT: B 673 MET cc_start: 0.8422 (mmt) cc_final: 0.7751 (mtp) REVERT: B 678 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.6902 (mttp) REVERT: B 697 TYR cc_start: 0.7858 (m-10) cc_final: 0.7490 (m-10) REVERT: B 829 ASP cc_start: 0.4368 (OUTLIER) cc_final: 0.3947 (t70) outliers start: 68 outliers final: 43 residues processed: 167 average time/residue: 0.7948 time to fit residues: 151.1681 Evaluate side-chains 155 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 104 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 chunk 95 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 246 ASN A 276 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A 732 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN B 732 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12678 Z= 0.230 Angle : 0.577 9.506 17188 Z= 0.288 Chirality : 0.045 0.140 1970 Planarity : 0.003 0.033 2180 Dihedral : 6.590 58.518 1675 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.61 % Favored : 93.13 % Rotamer: Outliers : 3.97 % Allowed : 30.01 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.11 (0.22), residues: 1514 helix: -3.62 (0.32), residues: 138 sheet: -2.62 (0.34), residues: 272 loop : -0.76 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 796 HIS 0.004 0.001 HIS B 298 PHE 0.013 0.001 PHE A 507 TYR 0.015 0.001 TYR B 233 ARG 0.002 0.000 ARG B 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 105 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7792 (tttm) REVERT: A 673 MET cc_start: 0.8347 (mmt) cc_final: 0.7695 (mtp) REVERT: A 678 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.6959 (mttp) REVERT: A 710 GLN cc_start: 0.7766 (mp10) cc_final: 0.7268 (mm-40) REVERT: A 759 ILE cc_start: 0.5631 (OUTLIER) cc_final: 0.5082 (tp) REVERT: A 829 ASP cc_start: 0.4338 (OUTLIER) cc_final: 0.3945 (t70) REVERT: B 196 GLU cc_start: 0.7508 (pt0) cc_final: 0.7174 (pt0) REVERT: B 509 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7724 (tttp) REVERT: B 636 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.5873 (ttp-170) REVERT: B 673 MET cc_start: 0.8416 (mmt) cc_final: 0.7734 (mtp) REVERT: B 678 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.6880 (mttp) REVERT: B 697 TYR cc_start: 0.7871 (m-10) cc_final: 0.7486 (m-10) REVERT: B 829 ASP cc_start: 0.4475 (OUTLIER) cc_final: 0.4074 (t70) outliers start: 57 outliers final: 42 residues processed: 155 average time/residue: 0.8830 time to fit residues: 155.9984 Evaluate side-chains 155 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 105 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 0.3980 chunk 17 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 246 ASN A 276 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A 732 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN B 732 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.208627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.134325 restraints weight = 12154.123| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.79 r_work: 0.3471 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12678 Z= 0.268 Angle : 0.597 9.317 17188 Z= 0.296 Chirality : 0.046 0.142 1970 Planarity : 0.003 0.033 2180 Dihedral : 6.667 58.571 1675 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.87 % Favored : 92.87 % Rotamer: Outliers : 4.04 % Allowed : 29.94 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.11 (0.22), residues: 1514 helix: -3.63 (0.31), residues: 138 sheet: -2.60 (0.34), residues: 272 loop : -0.76 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 796 HIS 0.004 0.001 HIS A 298 PHE 0.013 0.001 PHE A 507 TYR 0.016 0.001 TYR A 233 ARG 0.002 0.000 ARG B 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.48 seconds wall clock time: 73 minutes 4.75 seconds (4384.75 seconds total)