Starting phenix.real_space_refine on Wed Dec 13 03:16:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/12_2023/6zp5_11336_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/12_2023/6zp5_11336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/12_2023/6zp5_11336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/12_2023/6zp5_11336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/12_2023/6zp5_11336_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/12_2023/6zp5_11336_updated.pdb" } resolution = 3.1 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 14927 2.51 5 N 3780 2.21 5 O 4807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 26": "OD1" <-> "OD2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A ASP 541": "OD1" <-> "OD2" Residue "A ASP 547": "OD1" <-> "OD2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 559": "OD1" <-> "OD2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ASP 636": "OD1" <-> "OD2" Residue "A ASP 710": "OD1" <-> "OD2" Residue "A ASP 718": "OD1" <-> "OD2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A ARG 788": "NH1" <-> "NH2" Residue "A GLU 841": "OE1" <-> "OE2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A ASP 967": "OD1" <-> "OD2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ASP 1091": "OD1" <-> "OD2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B ASP 260": "OD1" <-> "OD2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "B ASP 324": "OD1" <-> "OD2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B ASP 496": "OD1" <-> "OD2" Residue "B TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 566": "OD1" <-> "OD2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 782": "OD1" <-> "OD2" Residue "B GLU 785": "OE1" <-> "OE2" Residue "B GLU 889": "OE1" <-> "OE2" Residue "B ASP 924": "OD1" <-> "OD2" Residue "B GLU 941": "OE1" <-> "OE2" Residue "C PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 14": "OD1" <-> "OD2" Residue "C ASP 27": "OD1" <-> "OD2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 490": "OE1" <-> "OE2" Residue "C ASP 542": "OD1" <-> "OD2" Residue "C ASP 588": "OD1" <-> "OD2" Residue "C GLU 635": "OE1" <-> "OE2" Residue "C TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 782": "OD1" <-> "OD2" Residue "C ARG 789": "NH1" <-> "NH2" Residue "C PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 953": "OD1" <-> "OD2" Residue "C GLU 964": "OE1" <-> "OE2" Residue "C GLU 991": "OE1" <-> "OE2" Residue "C GLU 1066": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 23615 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7709 Classifications: {'peptide': 988} Link IDs: {'PTRANS': 48, 'TRANS': 939} Chain breaks: 8 Chain: "B" Number of atoms: 7367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 7367 Classifications: {'peptide': 943} Link IDs: {'PTRANS': 45, 'TRANS': 897} Chain breaks: 12 Chain: "C" Number of atoms: 7243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7243 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 44, 'TRANS': 885} Chain breaks: 10 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 114 Unusual residues: {'DMS': 3, 'MAN': 1, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 12.93, per 1000 atoms: 0.55 Number of scatterers: 23615 At special positions: 0 Unit cell: (127.734, 130.875, 195.789, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 101 16.00 O 4807 8.00 N 3780 7.00 C 14927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 274 " distance=2.00 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 334 " distance=2.05 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 405 " distance=2.06 Simple disulfide: pdb=" SG CYS A 453 " - pdb=" SG CYS A 461 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 563 " distance=2.04 Simple disulfide: pdb=" SG CYS A 590 " - pdb=" SG CYS A 622 " distance=1.97 Simple disulfide: pdb=" SG CYS A 635 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 733 " distance=2.02 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 722 " distance=2.05 Simple disulfide: pdb=" SG CYS A1005 " - pdb=" SG CYS A1016 " distance=2.01 Simple disulfide: pdb=" SG CYS A1055 " - pdb=" SG CYS A1099 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 98 " distance=1.77 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 197 " distance=2.05 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 376 " distance=2.01 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 441 " distance=2.08 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 482 " distance=2.01 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 504 " distance=2.02 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 581 " distance=2.02 Simple disulfide: pdb=" SG CYS B 564 " - pdb=" SG CYS B 570 " distance=2.05 Simple disulfide: pdb=" SG CYS B 829 " - pdb=" SG CYS B 840 " distance=2.02 Simple disulfide: pdb=" SG CYS B 879 " - pdb=" SG CYS B 923 " distance=2.03 Simple disulfide: pdb=" SG CYS C 265 " - pdb=" SG CYS C 275 " distance=2.07 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 353 " - pdb=" SG CYS C 406 " distance=2.02 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 499 " distance=2.03 Simple disulfide: pdb=" SG CYS C 512 " - pdb=" SG CYS C 564 " distance=2.00 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 623 " distance=2.02 Simple disulfide: pdb=" SG CYS C 636 " - pdb=" SG CYS C 645 " distance=2.01 Simple disulfide: pdb=" SG CYS C 712 " - pdb=" SG CYS C 734 " distance=2.03 Simple disulfide: pdb=" SG CYS C 717 " - pdb=" SG CYS C 723 " distance=2.04 Simple disulfide: pdb=" SG CYS C1006 " - pdb=" SG CYS C1017 " distance=2.05 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1100 " 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 Atom "HETATM23556 O5 NAG C1301 .*. O " rejected from bonding due to valence issues. Atom "HETATM23586 O5 NAG C1303 .*. O " rejected from bonding due to valence issues. Atom "HETATM22680 O5 NAG N 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 316 " " NAG A1302 " - " ASN A 576 " " NAG A1303 " - " ASN A 589 " " NAG A1304 " - " ASN A 95 " " NAG A1305 " - " ASN A 138 " " NAG A1306 " - " ASN A 207 " " NAG B1101 " - " ASN B 227 " " NAG B1102 " - " ASN B 467 " " NAG B1103 " - " ASN B 490 " " NAG B1104 " - " ASN B 239 " " NAG B1105 " - " ASN B 97 " " NAG B1106 " - " ASN B 35 " " NAG B1107 " - " ASN B 454 " " NAG B1108 " - " ASN B 81 " " NAG C1301 " - " ASN C 590 " " NAG C1302 " - " ASN C 577 " " NAG C1303 " - " ASN C 305 " " NAG C1305 " - " ASN C 139 " " NAG D 1 " - " ASN A 630 " " NAG E 1 " - " ASN A 690 " " NAG F 1 " - " ASN A 774 " " NAG G 1 " - " ASN A1047 " " NAG H 1 " - " ASN A1071 " " NAG I 1 " - " ASN A1107 " " NAG J 1 " - " ASN A 255 " " NAG K 1 " - " ASN A 304 " " NAG L 1 " - " ASN A 682 " " NAG M 1 " - " ASN B 530 " " NAG N 1 " - " ASN B 931 " " NAG O 1 " - " ASN B 871 " " NAG P 1 " - " ASN B 895 " " NAG Q 1 " - " ASN B 622 " " NAG R 1 " - " ASN B 538 " " NAG S 1 " - " ASN B 178 " " NAG T 1 " - " ASN B 151 " " NAG U 1 " - " ASN C1108 " " NAG V 1 " - " ASN C1072 " " NAG W 1 " - " ASN C1048 " " NAG X 1 " - " ASN C 775 " " NAG Y 1 " - " ASN C 691 " " NAG Z 1 " - " ASN C 683 " " NAG a 1 " - " ASN C 256 " " NAG b 1 " - " ASN C 317 " " NAG c 1 " - " ASN C 96 " " NAG d 1 " - " ASN C 631 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.79 Conformation dependent library (CDL) restraints added in 4.1 seconds 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 42 sheets defined 23.7% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.45 Creating SS restraints... Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 312 through 315 No H-bonds generated for 'chain 'A' and resid 312 through 315' Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 377 through 382 removed outlier: 4.383A pdb=" N ARG A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 382' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 720 through 729 removed outlier: 3.677A pdb=" N LEU A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 755 removed outlier: 3.719A pdb=" N ASP A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 840 through 856 Processing helix chain 'A' and resid 860 through 863 No H-bonds generated for 'chain 'A' and resid 860 through 863' Processing helix chain 'A' and resid 871 through 882 removed outlier: 3.751A pdb=" N ILE A 882 " --> pdb=" O ARG A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 893 through 912 Processing helix chain 'A' and resid 919 through 940 removed outlier: 4.130A pdb=" N LEU A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER A 940 " --> pdb=" O VAL A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 955 Processing helix chain 'A' and resid 959 through 1004 removed outlier: 4.136A pdb=" N VAL A 964 " --> pdb=" O PRO A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1119 removed outlier: 4.152A pdb=" N GLU A1117 " --> pdb=" O PRO A1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 313 through 316 No H-bonds generated for 'chain 'B' and resid 313 through 316' Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 568 through 577 removed outlier: 3.929A pdb=" N GLN B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 603 removed outlier: 3.503A pdb=" N ASP B 596 " --> pdb=" O ALA B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 684 through 687 No H-bonds generated for 'chain 'B' and resid 684 through 687' Processing helix chain 'B' and resid 695 through 706 Processing helix chain 'B' and resid 710 through 715 removed outlier: 3.880A pdb=" N GLU B 715 " --> pdb=" O VAL B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 737 Processing helix chain 'B' and resid 743 through 764 removed outlier: 4.206A pdb=" N LEU B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER B 764 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 779 Processing helix chain 'B' and resid 783 through 829 removed outlier: 3.951A pdb=" N VAL B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 793 " --> pdb=" O GLN B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 942 removed outlier: 3.700A pdb=" N GLU B 941 " --> pdb=" O PRO B 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 277 Processing helix chain 'C' and resid 313 through 316 No H-bonds generated for 'chain 'C' and resid 313 through 316' Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 358 through 362 removed outlier: 4.125A pdb=" N ASN C 362 " --> pdb=" O THR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 383 removed outlier: 4.370A pdb=" N ARG C 382 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 395 Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 712 through 717 Processing helix chain 'C' and resid 721 through 728 Processing helix chain 'C' and resid 733 through 756 removed outlier: 3.548A pdb=" N ASP C 749 " --> pdb=" O ALA C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 799 Processing helix chain 'C' and resid 841 through 858 Processing helix chain 'C' and resid 861 through 864 No H-bonds generated for 'chain 'C' and resid 861 through 864' Processing helix chain 'C' and resid 872 through 883 Processing helix chain 'C' and resid 887 through 892 removed outlier: 3.936A pdb=" N GLU C 892 " --> pdb=" O VAL C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 914 removed outlier: 3.600A pdb=" N GLN C 909 " --> pdb=" O ILE C 905 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 910 " --> pdb=" O GLY C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 941 removed outlier: 4.123A pdb=" N LEU C 940 " --> pdb=" O LEU C 936 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER C 941 " --> pdb=" O VAL C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 956 Processing helix chain 'C' and resid 960 through 1006 removed outlier: 4.238A pdb=" N VAL C 965 " --> pdb=" O PRO C 961 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1120 removed outlier: 4.175A pdb=" N GLU C1118 " --> pdb=" O PRO C1114 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 removed outlier: 3.763A pdb=" N SER A 33 " --> pdb=" O SER A 4 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 21 through 24 removed outlier: 3.765A pdb=" N ASP A 260 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 36 through 38 removed outlier: 3.537A pdb=" N ILE A 176 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 200 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER A 178 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 77 through 79 Processing sheet with id= E, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= F, first strand: chain 'A' and resid 299 through 301 Processing sheet with id= G, first strand: chain 'A' and resid 327 through 331 removed outlier: 4.064A pdb=" N VAL A 368 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 425 through 427 Processing sheet with id= I, first strand: chain 'A' and resid 524 through 527 removed outlier: 3.878A pdb=" N GLU A 556 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP A 547 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY A 539 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 615 through 618 removed outlier: 4.941A pdb=" N GLY A 567 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 570 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLN A 287 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR A 572 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE A 285 " --> pdb=" O THR A 572 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 644 through 648 Processing sheet with id= L, first strand: chain 'A' and resid 684 through 688 removed outlier: 3.746A pdb=" N ALA A1051 " --> pdb=" O PHE A1068 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE A1068 " --> pdb=" O ALA A1051 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 690 through 701 removed outlier: 6.029A pdb=" N TYR A1040 " --> pdb=" O HIS A1021 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HIS A1021 " --> pdb=" O TYR A1040 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 706 through 709 removed outlier: 4.434A pdb=" N LYS A 706 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1053 through 1056 Processing sheet with id= P, first strand: chain 'B' and resid 2 through 4 removed outlier: 6.962A pdb=" N ASN B 35 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR B 165 " --> pdb=" O ASN B 35 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.763A pdb=" N ASP B 183 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 62 through 65 Processing sheet with id= S, first strand: chain 'B' and resid 86 through 88 Processing sheet with id= T, first strand: chain 'B' and resid 222 through 224 removed outlier: 5.250A pdb=" N ASP B 425 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY B 417 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 250 through 254 Processing sheet with id= V, first strand: chain 'B' and resid 475 through 477 removed outlier: 4.267A pdb=" N GLY B 445 " --> pdb=" O GLN B 464 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 212 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 448 " --> pdb=" O GLN B 210 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLN B 210 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR B 450 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE B 208 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 513 through 517 removed outlier: 6.470A pdb=" N ALA B 505 " --> pdb=" O PRO B 498 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 532 through 536 Processing sheet with id= Y, first strand: chain 'B' and resid 538 through 549 removed outlier: 6.177A pdb=" N TYR B 864 " --> pdb=" O HIS B 845 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N HIS B 845 " --> pdb=" O TYR B 864 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 555 through 557 Processing sheet with id= AA, first strand: chain 'B' and resid 877 through 879 Processing sheet with id= AB, first strand: chain 'B' and resid 891 through 894 Processing sheet with id= AC, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= AD, first strand: chain 'C' and resid 22 through 25 removed outlier: 3.679A pdb=" N ASP C 261 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 28 through 30 Processing sheet with id= AF, first strand: chain 'C' and resid 238 through 243 removed outlier: 4.253A pdb=" N ALA C 238 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C 69 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER C 68 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 164 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 100 through 103 Processing sheet with id= AH, first strand: chain 'C' and resid 300 through 302 removed outlier: 3.823A pdb=" N ILE C 300 " --> pdb=" O ASN C 514 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 328 through 332 removed outlier: 4.762A pdb=" N ASN C 368 " --> pdb=" O GLU C 490 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU C 490 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 622 through 625 removed outlier: 4.778A pdb=" N GLY C 568 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL C 571 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLN C 288 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR C 573 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE C 286 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLY C 575 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LYS C 284 " --> pdb=" O GLY C 575 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 665 through 670 removed outlier: 6.441A pdb=" N ALA C 646 " --> pdb=" O PRO C 639 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 685 through 689 Processing sheet with id= AM, first strand: chain 'C' and resid 691 through 702 removed outlier: 6.061A pdb=" N TYR C1041 " --> pdb=" O HIS C1022 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N HIS C1022 " --> pdb=" O TYR C1041 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 707 through 710 removed outlier: 4.324A pdb=" N LYS C 707 " --> pdb=" O LEU C 835 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 1055 through 1057 Processing sheet with id= AP, first strand: chain 'C' and resid 1068 through 1071 818 hydrogen bonds defined for protein. 2256 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: 9.99 Time building geometry restraints manager: 10.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.54: 23772 1.54 - 1.86: 314 1.86 - 2.18: 1 2.18 - 2.51: 0 2.51 - 2.83: 1 Bond restraints: 24088 Sorted by residual: bond pdb=" C CYS A 498 " pdb=" N GLY A 499 " ideal model delta sigma weight residual 1.330 2.829 -1.498 1.49e-02 4.50e+03 1.01e+04 bond pdb=" C LEU A 308 " pdb=" N CYS A 309 " ideal model delta sigma weight residual 1.331 1.991 -0.660 2.07e-02 2.33e+03 1.02e+03 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sigma weight residual 1.410 1.475 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C4 BMA Q 3 " pdb=" C5 BMA Q 3 " ideal model delta sigma weight residual 1.528 1.589 -0.061 2.00e-02 2.50e+03 9.41e+00 ... (remaining 24083 not shown) Histogram of bond angle deviations from ideal: 88.10 - 98.50: 6 98.50 - 108.91: 1690 108.91 - 119.31: 18567 119.31 - 129.72: 12476 129.72 - 140.13: 79 Bond angle restraints: 32818 Sorted by residual: angle pdb=" O LEU A 308 " pdb=" C LEU A 308 " pdb=" N CYS A 309 " ideal model delta sigma weight residual 122.81 90.99 31.82 1.42e+00 4.96e-01 5.02e+02 angle pdb=" C CYS A 498 " pdb=" N GLY A 499 " pdb=" CA GLY A 499 " ideal model delta sigma weight residual 121.87 88.10 33.77 1.57e+00 4.06e-01 4.63e+02 angle pdb=" CA LEU A 308 " pdb=" C LEU A 308 " pdb=" N CYS A 309 " ideal model delta sigma weight residual 115.54 140.13 -24.59 1.52e+00 4.33e-01 2.62e+02 angle pdb=" O CYS A 498 " pdb=" C CYS A 498 " pdb=" N GLY A 499 " ideal model delta sigma weight residual 123.24 108.38 14.86 1.23e+00 6.61e-01 1.46e+02 angle pdb=" O1 NAG W 2 " pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 108.68 135.04 -26.36 3.00e+00 1.11e-01 7.72e+01 ... (remaining 32813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.06: 14386 23.06 - 46.13: 778 46.13 - 69.19: 150 69.19 - 92.25: 34 92.25 - 115.32: 6 Dihedral angle restraints: 15354 sinusoidal: 7024 harmonic: 8330 Sorted by residual: dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 563 " pdb=" CB CYS A 563 " ideal model delta sinusoidal sigma weight residual -86.00 -10.58 -75.42 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS C 636 " pdb=" SG CYS C 636 " pdb=" SG CYS C 645 " pdb=" CB CYS C 645 " ideal model delta sinusoidal sigma weight residual -86.00 -13.25 -72.75 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS C 512 " pdb=" SG CYS C 512 " pdb=" SG CYS C 564 " pdb=" CB CYS C 564 " ideal model delta sinusoidal sigma weight residual -86.00 -153.68 67.68 1 1.00e+01 1.00e-02 5.95e+01 ... (remaining 15351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.030: 4060 1.030 - 2.060: 8 2.060 - 3.091: 0 3.091 - 4.121: 1 4.121 - 5.151: 2 Chirality restraints: 4071 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O1 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 2.75 -5.15 2.00e-02 2.50e+03 6.63e+04 chirality pdb=" C1 NAG C1302 " pdb=" C2 NAG C1302 " pdb=" O1 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False 2.31 -2.43 4.74 2.00e-01 2.50e+01 5.62e+02 chirality pdb=" C1 NAG W 2 " pdb=" C2 NAG W 2 " pdb=" O1 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False 2.31 -1.09 3.40 2.00e-01 2.50e+01 2.90e+02 ... (remaining 4068 not shown) Planarity restraints: 4123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O DMS A1308 " -0.204 2.00e-02 2.50e+03 2.77e-01 7.69e+02 pdb=" C1 DMS A1308 " -0.137 2.00e-02 2.50e+03 pdb=" C2 DMS A1308 " -0.137 2.00e-02 2.50e+03 pdb=" S DMS A1308 " 0.478 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O DMS A1309 " 0.201 2.00e-02 2.50e+03 2.76e-01 7.59e+02 pdb=" C1 DMS A1309 " 0.137 2.00e-02 2.50e+03 pdb=" C2 DMS A1309 " 0.137 2.00e-02 2.50e+03 pdb=" S DMS A1309 " -0.475 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O DMS A1310 " 0.173 2.00e-02 2.50e+03 2.40e-01 5.77e+02 pdb=" C1 DMS A1310 " 0.122 2.00e-02 2.50e+03 pdb=" C2 DMS A1310 " 0.119 2.00e-02 2.50e+03 pdb=" S DMS A1310 " -0.415 2.00e-02 2.50e+03 ... (remaining 4120 not shown) Histogram of nonbonded interaction distances: 0.01 - 0.99: 41 0.99 - 1.97: 133 1.97 - 2.94: 11821 2.94 - 3.92: 61618 3.92 - 4.90: 114567 Warning: very small nonbonded interaction distances. Nonbonded interactions: 188180 Sorted by model distance: nonbonded pdb=" O4 NAG I 1 " pdb=" O1 NAG I 2 " model vdw 0.012 2.440 nonbonded pdb=" O4 NAG N 1 " pdb=" O1 NAG N 2 " model vdw 0.015 2.440 nonbonded pdb=" O4 NAG c 1 " pdb=" O1 NAG c 2 " model vdw 0.023 2.440 nonbonded pdb=" O4 NAG Z 1 " pdb=" O1 NAG Z 2 " model vdw 0.027 2.440 nonbonded pdb=" O4 NAG Y 1 " pdb=" O1 NAG Y 2 " model vdw 0.031 2.440 ... (remaining 188175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 39 or resid 55 through 104 or resid 138 through \ 145 or resid 162 through 214 or resid 238 through 415 or resid 433 through 443 o \ r resid 483 through 593 or resid 614 through 801 or resid 827 through 1119 or re \ sid 1306)) selection = (chain 'B' and (resid 2 through 90 or resid 97 through 104 or resid 106 through \ 158 or resid 161 through 338 or resid 345 through 355 or resid 361 through 471 o \ r resid 474 through 649 or resid 651 through 943 or resid 1104)) selection = (chain 'C' and (resid 2 through 105 or resid 139 through 146 or resid 163 throug \ h 215 or resid 239 through 416 or resid 434 through 1120 or resid 1301)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'R' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 17.590 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 66.420 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.498 24088 Z= 0.861 Angle : 0.920 33.774 32818 Z= 0.467 Chirality : 0.153 5.151 4071 Planarity : 0.009 0.277 4078 Dihedral : 14.266 115.315 9865 Min Nonbonded Distance : 0.012 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.52 % Allowed : 5.46 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 2793 helix: 0.57 (0.19), residues: 661 sheet: -0.18 (0.19), residues: 640 loop : -1.37 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 860 HIS 0.005 0.001 HIS B 488 PHE 0.037 0.002 PHE B 410 TYR 0.025 0.002 TYR C1041 ARG 0.013 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 331 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 342 average time/residue: 0.3814 time to fit residues: 198.3178 Evaluate side-chains 170 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 165 time to evaluate : 2.626 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2122 time to fit residues: 5.3899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.3980 chunk 216 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 258 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 529 ASN A 536 GLN A 537 GLN A 617 GLN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 GLN A 724 ASN A 735 GLN A 777 GLN A 874 GLN A 887 ASN A1009 GLN A1061 HIS A1079 GLN A1108 ASN B 128 ASN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN B 415 GLN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 GLN B 868 GLN B 898 HIS B 916 ASN C 396 ASN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 758 GLN C 761 GLN C 887 GLN ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN C 927 ASN C 929 ASN C 976 GLN C 985 GLN C1032 HIS C1045 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 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 : 0.003 0.054 24088 Z= 0.220 Angle : 0.925 28.635 32818 Z= 0.387 Chirality : 0.115 4.919 4071 Planarity : 0.004 0.043 4078 Dihedral : 12.095 126.113 4767 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.31 % Allowed : 11.99 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 2795 helix: 1.50 (0.20), residues: 655 sheet: -0.04 (0.19), residues: 632 loop : -1.16 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 38 HIS 0.008 0.001 HIS C1075 PHE 0.020 0.002 PHE B 29 TYR 0.023 0.001 TYR C1041 ARG 0.009 0.001 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 12 residues processed: 211 average time/residue: 0.3310 time to fit residues: 112.8686 Evaluate side-chains 163 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 2.534 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.2091 time to fit residues: 8.0990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 176 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 208 optimal weight: 0.9980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 307 ASN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 927 ASN C 976 GLN C1075 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24088 Z= 0.230 Angle : 0.814 22.249 32818 Z= 0.346 Chirality : 0.112 4.825 4071 Planarity : 0.004 0.047 4078 Dihedral : 9.647 131.356 4767 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.83 % Allowed : 13.86 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2795 helix: 1.92 (0.20), residues: 653 sheet: 0.10 (0.19), residues: 617 loop : -1.02 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 409 HIS 0.005 0.001 HIS A 39 PHE 0.018 0.001 PHE B 155 TYR 0.019 0.001 TYR C1041 ARG 0.008 0.001 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 158 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 197 average time/residue: 0.3188 time to fit residues: 104.9007 Evaluate side-chains 156 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 2.801 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 2 residues processed: 19 average time/residue: 0.2206 time to fit residues: 11.7031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 GLN C 923 GLN C 976 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24088 Z= 0.311 Angle : 0.815 22.366 32818 Z= 0.350 Chirality : 0.111 4.824 4071 Planarity : 0.004 0.048 4078 Dihedral : 9.151 131.398 4767 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.31 % Allowed : 14.86 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 2795 helix: 1.98 (0.20), residues: 656 sheet: 0.06 (0.19), residues: 643 loop : -1.00 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 409 HIS 0.005 0.001 HIS C1062 PHE 0.022 0.001 PHE B 155 TYR 0.018 0.001 TYR C1041 ARG 0.006 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 151 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 28 residues processed: 200 average time/residue: 0.3166 time to fit residues: 108.0417 Evaluate side-chains 164 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 2.591 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 2 residues processed: 28 average time/residue: 0.2280 time to fit residues: 15.8409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 9.9990 chunk 156 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 235 optimal weight: 0.2980 chunk 190 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 247 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 GLN ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24088 Z= 0.229 Angle : 0.770 22.103 32818 Z= 0.328 Chirality : 0.111 4.829 4071 Planarity : 0.003 0.053 4078 Dihedral : 8.689 135.542 4767 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.43 % Allowed : 16.25 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 2795 helix: 2.04 (0.20), residues: 658 sheet: 0.22 (0.19), residues: 627 loop : -0.96 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 409 HIS 0.003 0.001 HIS C1062 PHE 0.012 0.001 PHE B 155 TYR 0.017 0.001 TYR B 864 ARG 0.004 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 14 residues processed: 187 average time/residue: 0.3156 time to fit residues: 100.7437 Evaluate side-chains 155 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 2.692 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.2264 time to fit residues: 9.4677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 161 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 275 optimal weight: 0.7980 chunk 228 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 22 optimal weight: 0.0170 chunk 91 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN B 391 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24088 Z= 0.174 Angle : 0.761 22.033 32818 Z= 0.323 Chirality : 0.111 4.823 4071 Planarity : 0.003 0.053 4078 Dihedral : 8.391 138.678 4767 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.12 % Allowed : 17.01 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2795 helix: 2.10 (0.21), residues: 658 sheet: 0.28 (0.19), residues: 631 loop : -0.91 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 409 HIS 0.003 0.001 HIS A 39 PHE 0.014 0.001 PHE C 829 TYR 0.016 0.001 TYR B 864 ARG 0.005 0.000 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 172 average time/residue: 0.3178 time to fit residues: 91.9639 Evaluate side-chains 157 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 2.924 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 15 average time/residue: 0.2202 time to fit residues: 9.9167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 157 optimal weight: 0.1980 chunk 201 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 274 optimal weight: 0.4980 chunk 171 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24088 Z= 0.184 Angle : 0.753 22.037 32818 Z= 0.319 Chirality : 0.111 4.827 4071 Planarity : 0.003 0.056 4078 Dihedral : 8.178 140.740 4767 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.80 % Allowed : 17.45 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2795 helix: 2.16 (0.21), residues: 659 sheet: 0.34 (0.20), residues: 621 loop : -0.88 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 409 HIS 0.003 0.001 HIS A 39 PHE 0.028 0.001 PHE B 111 TYR 0.016 0.001 TYR B 864 ARG 0.004 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 171 average time/residue: 0.3238 time to fit residues: 93.1261 Evaluate side-chains 157 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 2.740 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.2016 time to fit residues: 8.0039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 174 optimal weight: 0.3980 chunk 187 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 181 HIS ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24088 Z= 0.259 Angle : 0.769 22.066 32818 Z= 0.330 Chirality : 0.111 4.836 4071 Planarity : 0.003 0.054 4078 Dihedral : 8.151 142.234 4767 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.96 % Allowed : 17.85 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2795 helix: 2.09 (0.21), residues: 664 sheet: 0.30 (0.19), residues: 640 loop : -0.87 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 409 HIS 0.004 0.001 HIS C1062 PHE 0.021 0.001 PHE B 155 TYR 0.017 0.001 TYR B 701 ARG 0.004 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 159 average time/residue: 0.3289 time to fit residues: 88.0715 Evaluate side-chains 153 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 2.924 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.2210 time to fit residues: 9.3446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 0.9990 chunk 240 optimal weight: 0.8980 chunk 255 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 78 optimal weight: 0.5980 chunk 231 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24088 Z= 0.234 Angle : 0.765 21.861 32818 Z= 0.329 Chirality : 0.110 4.823 4071 Planarity : 0.003 0.058 4078 Dihedral : 8.069 143.138 4767 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.48 % Allowed : 18.45 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2795 helix: 2.06 (0.21), residues: 664 sheet: 0.33 (0.19), residues: 639 loop : -0.85 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 63 HIS 0.003 0.001 HIS C1062 PHE 0.019 0.001 PHE B 366 TYR 0.020 0.001 TYR B 701 ARG 0.004 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 156 average time/residue: 0.3407 time to fit residues: 88.5019 Evaluate side-chains 144 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 2.761 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.2434 time to fit residues: 5.8946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 188 optimal weight: 0.1980 chunk 283 optimal weight: 0.4980 chunk 261 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 240 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24088 Z= 0.197 Angle : 0.757 21.990 32818 Z= 0.323 Chirality : 0.111 4.838 4071 Planarity : 0.003 0.058 4078 Dihedral : 7.924 144.267 4767 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.36 % Allowed : 18.84 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2795 helix: 2.10 (0.21), residues: 665 sheet: 0.40 (0.20), residues: 633 loop : -0.85 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 63 HIS 0.003 0.001 HIS C1062 PHE 0.017 0.001 PHE B 366 TYR 0.023 0.001 TYR B 701 ARG 0.003 0.000 ARG B 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 152 average time/residue: 0.3493 time to fit residues: 88.9054 Evaluate side-chains 148 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 2.680 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.2224 time to fit residues: 5.9549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 0.0010 chunk 208 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 226 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 232 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 198 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.095692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.063112 restraints weight = 68737.973| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.68 r_work: 0.2957 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24088 Z= 0.188 Angle : 0.755 22.000 32818 Z= 0.323 Chirality : 0.111 4.839 4071 Planarity : 0.003 0.058 4078 Dihedral : 7.802 144.938 4767 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.28 % Allowed : 19.00 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2795 helix: 2.15 (0.21), residues: 664 sheet: 0.48 (0.20), residues: 631 loop : -0.87 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 63 HIS 0.003 0.000 HIS C1062 PHE 0.017 0.001 PHE B 366 TYR 0.030 0.001 TYR B 701 ARG 0.003 0.000 ARG A 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4450.81 seconds wall clock time: 83 minutes 52.30 seconds (5032.30 seconds total)