Starting phenix.real_space_refine on Mon Feb 19 08:34:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1u_15805/02_2024/8b1u_15805_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1u_15805/02_2024/8b1u_15805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1u_15805/02_2024/8b1u_15805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1u_15805/02_2024/8b1u_15805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1u_15805/02_2024/8b1u_15805_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1u_15805/02_2024/8b1u_15805_updated.pdb" } resolution = 3.8 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= 0.004 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: 6 Type Number sf(0) Gaussians P 53 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 15088 2.51 5 N 4249 2.21 5 O 4632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 19": "NH1" <-> "NH2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 423": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B ARG 561": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 653": "NH1" <-> "NH2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 683": "NH1" <-> "NH2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ARG 794": "NH1" <-> "NH2" Residue "B ARG 824": "NH1" <-> "NH2" Residue "B ARG 840": "NH1" <-> "NH2" Residue "B ARG 895": "NH1" <-> "NH2" Residue "B ASP 899": "OD1" <-> "OD2" Residue "B TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1059": "NH1" <-> "NH2" Residue "B TYR 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1077": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1106": "NH1" <-> "NH2" Residue "B ARG 1120": "NH1" <-> "NH2" Residue "B TYR 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ARG 445": "NH1" <-> "NH2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C ARG 525": "NH1" <-> "NH2" Residue "C ARG 530": "NH1" <-> "NH2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 668": "NH1" <-> "NH2" Residue "C PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ARG 709": "NH1" <-> "NH2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 742": "NH1" <-> "NH2" Residue "C TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 799": "NH1" <-> "NH2" Residue "C ARG 804": "NH1" <-> "NH2" Residue "C ARG 839": "NH1" <-> "NH2" Residue "C ARG 858": "NH1" <-> "NH2" Residue "C ARG 877": "NH1" <-> "NH2" Residue "C ARG 896": "NH1" <-> "NH2" Residue "C ARG 900": "NH1" <-> "NH2" Residue "C ARG 902": "NH1" <-> "NH2" Residue "C ARG 935": "NH1" <-> "NH2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C ARG 1001": "NH1" <-> "NH2" Residue "C ARG 1068": "NH1" <-> "NH2" Residue "C PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1118": "NH1" <-> "NH2" Residue "C PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ARG 281": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ARG 360": "NH1" <-> "NH2" Residue "D PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D ARG 526": "NH1" <-> "NH2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D ARG 574": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24127 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 9145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 9145 Classifications: {'peptide': 1141} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 1 Chain: "C" Number of atoms: 8738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8738 Classifications: {'peptide': 1080} Link IDs: {'PCIS': 1, 'PTRANS': 64, 'TRANS': 1014} Chain breaks: 1 Chain: "D" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4644 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 25, 'TRANS': 575} Chain breaks: 1 Chain: "X" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1035 Classifications: {'DNA': 51} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "A" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 533 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.66, per 1000 atoms: 0.52 Number of scatterers: 24127 At special positions: 0 Unit cell: (154.76, 152.64, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 53 15.00 Mg 1 11.99 O 4632 8.00 N 4249 7.00 C 15088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 9.99 Conformation dependent library (CDL) restraints added in 4.4 seconds 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5446 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 15 sheets defined 48.8% alpha, 8.1% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 16.22 Creating SS restraints... Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.722A pdb=" N ILE B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 66 through 89 Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 107 through 123 removed outlier: 5.004A pdb=" N ASP B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU B 123 " --> pdb=" O ARG B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 141 through 144 No H-bonds generated for 'chain 'B' and resid 141 through 144' Processing helix chain 'B' and resid 157 through 171 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.644A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 removed outlier: 3.517A pdb=" N ASP B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 238 Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 324 through 346 removed outlier: 3.859A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 366 through 377 removed outlier: 4.426A pdb=" N THR B 376 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 377 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 427 through 436 Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 511 through 534 Processing helix chain 'B' and resid 561 through 573 Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 591 through 604 Processing helix chain 'B' and resid 609 through 616 Processing helix chain 'B' and resid 625 through 631 Processing helix chain 'B' and resid 635 through 655 Processing helix chain 'B' and resid 658 through 668 Processing helix chain 'B' and resid 670 through 676 Processing helix chain 'B' and resid 680 through 700 removed outlier: 3.967A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 716 removed outlier: 3.969A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 806 Processing helix chain 'B' and resid 837 through 842 Processing helix chain 'B' and resid 850 through 860 Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 949 through 960 removed outlier: 3.543A pdb=" N PHE B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 980 Processing helix chain 'B' and resid 984 through 998 Proline residue: B 988 - end of helix removed outlier: 4.062A pdb=" N THR B 991 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1011 No H-bonds generated for 'chain 'B' and resid 1009 through 1011' Processing helix chain 'B' and resid 1033 through 1043 removed outlier: 4.659A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1049 Processing helix chain 'B' and resid 1090 through 1093 Processing helix chain 'B' and resid 1095 through 1105 Processing helix chain 'B' and resid 1107 through 1125 Processing helix chain 'B' and resid 1131 through 1134 No H-bonds generated for 'chain 'B' and resid 1131 through 1134' Processing helix chain 'B' and resid 1162 through 1173 Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 88 through 102 removed outlier: 3.737A pdb=" N SER C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TRP C 93 " --> pdb=" O GLN C 89 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 122 through 141 Processing helix chain 'C' and resid 143 through 151 removed outlier: 3.595A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 178 removed outlier: 4.613A pdb=" N ALA C 166 " --> pdb=" O ALA C 163 " (cutoff:3.500A) Proline residue: C 167 - end of helix removed outlier: 4.317A pdb=" N GLU C 174 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 198 removed outlier: 4.749A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.814A pdb=" N TRP C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 315 removed outlier: 3.754A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 344 Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 382 through 399 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 415 through 428 Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 467 through 475 Processing helix chain 'C' and resid 477 through 482 Processing helix chain 'C' and resid 487 through 500 removed outlier: 3.838A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 513 Processing helix chain 'C' and resid 524 through 536 Processing helix chain 'C' and resid 556 through 577 removed outlier: 3.837A pdb=" N ALA C 565 " --> pdb=" O GLY C 562 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C 568 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET C 569 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TRP C 574 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 598 removed outlier: 3.505A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Proline residue: C 589 - end of helix removed outlier: 4.715A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 625 Processing helix chain 'C' and resid 634 through 645 Processing helix chain 'C' and resid 708 through 722 removed outlier: 3.597A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 758 Processing helix chain 'C' and resid 769 through 780 Processing helix chain 'C' and resid 791 through 794 Processing helix chain 'C' and resid 807 through 810 No H-bonds generated for 'chain 'C' and resid 807 through 810' Processing helix chain 'C' and resid 834 through 842 Processing helix chain 'C' and resid 844 through 850 Processing helix chain 'C' and resid 875 through 889 Processing helix chain 'C' and resid 894 through 904 Processing helix chain 'C' and resid 911 through 934 removed outlier: 3.743A pdb=" N LEU C 927 " --> pdb=" O GLU C 923 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 990 Processing helix chain 'C' and resid 1013 through 1032 Processing helix chain 'C' and resid 1041 through 1049 Processing helix chain 'C' and resid 1061 through 1076 Processing helix chain 'C' and resid 1088 through 1093 removed outlier: 3.569A pdb=" N ARG C1092 " --> pdb=" O ILE C1088 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1088 through 1093' Processing helix chain 'C' and resid 1099 through 1119 Proline residue: C1115 - end of helix Processing helix chain 'D' and resid 3 through 12 removed outlier: 3.732A pdb=" N GLU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 28 Processing helix chain 'D' and resid 33 through 47 Processing helix chain 'D' and resid 66 through 75 removed outlier: 4.911A pdb=" N SER D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 87 Processing helix chain 'D' and resid 110 through 124 removed outlier: 3.544A pdb=" N CYS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 144 Processing helix chain 'D' and resid 153 through 163 Processing helix chain 'D' and resid 177 through 191 Processing helix chain 'D' and resid 206 through 222 removed outlier: 3.625A pdb=" N GLN D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 231 Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.505A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 319 removed outlier: 4.336A pdb=" N TYR D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA D 317 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 366 through 376 Processing helix chain 'D' and resid 379 through 387 Processing helix chain 'D' and resid 401 through 423 removed outlier: 4.831A pdb=" N ARG D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 437 removed outlier: 3.739A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU D 437 " --> pdb=" O GLN D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 464 removed outlier: 3.725A pdb=" N GLU D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 572 Processing helix chain 'D' and resid 583 through 591 removed outlier: 3.554A pdb=" N SER D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 605 removed outlier: 3.822A pdb=" N SER D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 41 through 65 Processing sheet with id= A, first strand: chain 'B' and resid 18 through 22 removed outlier: 6.500A pdb=" N LEU B 409 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B 21 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 411 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 487 through 490 Processing sheet with id= C, first strand: chain 'B' and resid 865 through 870 removed outlier: 6.681A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA B 870 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 503 " --> pdb=" O ALA B 870 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N CYS B 813 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TRP B 502 " --> pdb=" O CYS B 813 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 815 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N MET B 504 " --> pdb=" O LEU B 815 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL B 817 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN B 737 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL B 558 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 739 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 767 through 769 Processing sheet with id= E, first strand: chain 'B' and resid 901 through 904 removed outlier: 5.375A pdb=" N ARG B1059 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR B 904 " --> pdb=" O ARG B1059 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET B1061 " --> pdb=" O THR B 904 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1017 through 1019 removed outlier: 3.655A pdb=" N PHE B1070 " --> pdb=" O TYR B1077 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 320 through 324 removed outlier: 6.526A pdb=" N LEU C 2 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N LEU C 323 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 4 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE C 236 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR C 5 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU C 238 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N SER C 7 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE C 240 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET C 34 " --> pdb=" O PHE C 212 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N CYS C 214 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU C 36 " --> pdb=" O CYS C 214 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 365 through 367 Processing sheet with id= I, first strand: chain 'C' and resid 781 through 783 removed outlier: 8.623A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU C 727 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N HIS C 377 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 729 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N CYS C 379 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR C 731 " --> pdb=" O CYS C 379 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN C 660 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL C 412 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS C 662 " --> pdb=" O VAL C 412 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 831 through 833 removed outlier: 6.122A pdb=" N GLN C 951 " --> pdb=" O VAL C 832 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 963 through 968 removed outlier: 6.372A pdb=" N GLU C 995 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ARG C 966 " --> pdb=" O GLU C 995 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG C 997 " --> pdb=" O ARG C 966 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ARG C 968 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE C 999 " --> pdb=" O ARG C 968 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 100 through 103 Processing sheet with id= M, first strand: chain 'D' and resid 352 through 355 removed outlier: 8.481A pdb=" N CYS D 353 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 168 " --> pdb=" O CYS D 353 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU D 355 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER D 170 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL D 292 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE D 169 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE D 294 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLY D 171 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLY D 296 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 393 through 396 removed outlier: 6.744A pdb=" N LEU D 577 " --> pdb=" O GLU D 394 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ARG D 396 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU D 579 " --> pdb=" O ARG D 396 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 530 through 532 removed outlier: 7.142A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 9.27 Time building geometry restraints manager: 10.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7168 1.34 - 1.45: 3901 1.45 - 1.57: 13403 1.57 - 1.69: 104 1.69 - 1.81: 174 Bond restraints: 24750 Sorted by residual: bond pdb=" O3A ANP B1501 " pdb=" PB ANP B1501 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" O5' ANP B1501 " pdb=" PA ANP B1501 " ideal model delta sigma weight residual 1.655 1.584 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O3G ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 1.528 1.581 -0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" O2B ANP B1501 " pdb=" PB ANP B1501 " ideal model delta sigma weight residual 1.508 1.556 -0.048 2.00e-02 2.50e+03 5.74e+00 ... (remaining 24745 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.88: 860 105.88 - 112.91: 13167 112.91 - 119.94: 8025 119.94 - 126.97: 11298 126.97 - 134.00: 445 Bond angle restraints: 33795 Sorted by residual: angle pdb=" PB ANP B1501 " pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 126.95 109.92 17.03 3.00e+00 1.11e-01 3.22e+01 angle pdb=" O1B ANP B1501 " pdb=" PB ANP B1501 " pdb=" O2B ANP B1501 " ideal model delta sigma weight residual 120.08 109.49 10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CA LEU C 323 " pdb=" CB LEU C 323 " pdb=" CG LEU C 323 " ideal model delta sigma weight residual 116.30 126.52 -10.22 3.50e+00 8.16e-02 8.53e+00 angle pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " pdb=" O2G ANP B1501 " ideal model delta sigma weight residual 101.05 109.44 -8.39 3.00e+00 1.11e-01 7.83e+00 angle pdb=" C PRO B 174 " pdb=" N LEU B 175 " pdb=" CA LEU B 175 " ideal model delta sigma weight residual 120.51 124.40 -3.89 1.45e+00 4.76e-01 7.18e+00 ... (remaining 33790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 13903 17.67 - 35.35: 608 35.35 - 53.02: 227 53.02 - 70.70: 85 70.70 - 88.37: 10 Dihedral angle restraints: 14833 sinusoidal: 6431 harmonic: 8402 Sorted by residual: dihedral pdb=" CA ASN B1003 " pdb=" C ASN B1003 " pdb=" N GLU B1004 " pdb=" CA GLU B1004 " ideal model delta harmonic sigma weight residual -180.00 -159.76 -20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA TYR D 108 " pdb=" C TYR D 108 " pdb=" N LEU D 109 " pdb=" CA LEU D 109 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ASP C 484 " pdb=" CB ASP C 484 " pdb=" CG ASP C 484 " pdb=" OD1 ASP C 484 " ideal model delta sinusoidal sigma weight residual -30.00 -85.10 55.10 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 14830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3253 0.052 - 0.104: 394 0.104 - 0.155: 61 0.155 - 0.207: 1 0.207 - 0.259: 1 Chirality restraints: 3710 Sorted by residual: chirality pdb=" C3' ANP B1501 " pdb=" C2' ANP B1501 " pdb=" C4' ANP B1501 " pdb=" O3' ANP B1501 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU C 323 " pdb=" CB LEU C 323 " pdb=" CD1 LEU C 323 " pdb=" CD2 LEU C 323 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA ILE C 661 " pdb=" N ILE C 661 " pdb=" C ILE C 661 " pdb=" CB ILE C 661 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 3707 not shown) Planarity restraints: 4257 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO C 658 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 50 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 51 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 381 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO C 382 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " -0.019 5.00e-02 4.00e+02 ... (remaining 4254 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 713 2.72 - 3.26: 23834 3.26 - 3.81: 38726 3.81 - 4.35: 47676 4.35 - 4.90: 79932 Nonbonded interactions: 190881 Sorted by model distance: nonbonded pdb=" OG1 THR B 30 " pdb="MG MG B1502 " model vdw 2.172 2.170 nonbonded pdb=" O2G ANP B1501 " pdb="MG MG B1502 " model vdw 2.202 2.170 nonbonded pdb=" OG SER B1090 " pdb=" OE1 GLN B1153 " model vdw 2.215 2.440 nonbonded pdb=" O ASN B 889 " pdb=" NE2 GLN C 800 " model vdw 2.237 2.520 nonbonded pdb=" O ALA B 361 " pdb=" OG SER B 364 " model vdw 2.250 2.440 ... (remaining 190876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.030 Extract box with map and model: 4.280 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 74.110 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 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 : 0.002 0.143 24750 Z= 0.151 Angle : 0.512 17.029 33795 Z= 0.307 Chirality : 0.035 0.259 3710 Planarity : 0.003 0.053 4257 Dihedral : 12.357 88.373 9387 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.08 % Favored : 98.89 % Rotamer: Outliers : 1.51 % Allowed : 3.06 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -0.66 (0.14), residues: 2872 helix: 0.05 (0.12), residues: 1493 sheet: -0.51 (0.27), residues: 296 loop : -0.94 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 652 HIS 0.002 0.000 HIS B 714 PHE 0.009 0.001 PHE A 46 TYR 0.019 0.001 TYR B1111 ARG 0.003 0.000 ARG B1106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 652 time to evaluate : 2.809 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: B 518 MET cc_start: 0.8491 (mmm) cc_final: 0.8134 (mmm) REVERT: B 960 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7904 (tp30) REVERT: C 252 LYS cc_start: 0.7660 (mttt) cc_final: 0.7436 (pptt) REVERT: C 697 MET cc_start: 0.8153 (mtp) cc_final: 0.7931 (mtp) REVERT: C 897 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8286 (mt) REVERT: C 941 MET cc_start: 0.8006 (ptt) cc_final: 0.7346 (ptt) REVERT: C 955 TRP cc_start: 0.7550 (m100) cc_final: 0.7195 (m100) REVERT: C 973 SER cc_start: 0.7689 (p) cc_final: 0.6912 (t) REVERT: C 1035 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8346 (tp) REVERT: C 1054 ASN cc_start: 0.8275 (m-40) cc_final: 0.7668 (p0) REVERT: C 1079 MET cc_start: 0.7984 (ptm) cc_final: 0.7758 (ptp) REVERT: A 9 ASP cc_start: 0.7536 (p0) cc_final: 0.7302 (p0) REVERT: A 47 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7709 (ttp80) outliers start: 37 outliers final: 4 residues processed: 676 average time/residue: 0.4332 time to fit residues: 431.7581 Evaluate side-chains 262 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 256 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 229 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 266 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN B 181 GLN B 291 GLN B 458 ASN B 484 ASN B 624 ASN ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 GLN ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 GLN B1072 HIS B1103 GLN B1134 HIS B1161 ASN C 137 GLN C 185 HIS C 336 HIS C 390 HIS C 448 HIS C 510 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN ** C 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN D 50 HIS D 247 GLN D 256 HIS D 464 GLN D 469 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24750 Z= 0.275 Angle : 0.588 11.039 33795 Z= 0.297 Chirality : 0.040 0.244 3710 Planarity : 0.004 0.059 4257 Dihedral : 13.632 89.884 3761 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.77 % Allowed : 10.73 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.51 (0.15), residues: 2872 helix: 1.10 (0.13), residues: 1472 sheet: -0.14 (0.27), residues: 305 loop : -0.47 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 502 HIS 0.007 0.001 HIS D 473 PHE 0.024 0.002 PHE C 840 TYR 0.020 0.002 TYR B1111 ARG 0.008 0.001 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 252 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 385 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6755 (mm-30) REVERT: B 518 MET cc_start: 0.8648 (mmm) cc_final: 0.8252 (mmm) REVERT: B 960 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7926 (tp30) REVERT: C 1054 ASN cc_start: 0.8361 (m-40) cc_final: 0.7647 (p0) REVERT: C 1079 MET cc_start: 0.8072 (ptm) cc_final: 0.7842 (ptp) REVERT: D 83 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: D 314 CYS cc_start: 0.7588 (t) cc_final: 0.7305 (t) REVERT: A 9 ASP cc_start: 0.7714 (p0) cc_final: 0.7362 (p0) outliers start: 68 outliers final: 38 residues processed: 308 average time/residue: 0.3597 time to fit residues: 176.4034 Evaluate side-chains 232 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 147 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 266 optimal weight: 8.9990 chunk 287 optimal weight: 0.6980 chunk 237 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 90 optimal weight: 30.0000 chunk 213 optimal weight: 10.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN B 202 GLN B 403 HIS B 484 ASN B 705 HIS B 769 HIS ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 ASN C 87 ASN C 191 GLN C 237 HIS C 448 HIS ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN D 469 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 24750 Z= 0.387 Angle : 0.644 10.196 33795 Z= 0.327 Chirality : 0.042 0.174 3710 Planarity : 0.005 0.044 4257 Dihedral : 13.645 81.317 3755 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.59 % Allowed : 12.40 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.51 (0.15), residues: 2872 helix: 1.05 (0.13), residues: 1481 sheet: 0.04 (0.28), residues: 304 loop : -0.45 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 955 HIS 0.012 0.001 HIS D 473 PHE 0.024 0.002 PHE B 588 TYR 0.026 0.002 TYR B1111 ARG 0.008 0.001 ARG C 668 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 211 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7400 (tp) REVERT: B 960 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7902 (tp30) REVERT: C 667 MET cc_start: 0.8487 (mmp) cc_final: 0.7928 (mmm) REVERT: C 927 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8873 (tt) REVERT: C 1054 ASN cc_start: 0.8401 (m-40) cc_final: 0.7703 (p0) REVERT: C 1079 MET cc_start: 0.8114 (ptm) cc_final: 0.7853 (ptp) REVERT: D 314 CYS cc_start: 0.7980 (t) cc_final: 0.7660 (t) outliers start: 88 outliers final: 47 residues processed: 288 average time/residue: 0.3350 time to fit residues: 157.2626 Evaluate side-chains 237 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 188 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 263 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 267 optimal weight: 3.9990 chunk 283 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 253 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS D 471 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24750 Z= 0.217 Angle : 0.532 10.407 33795 Z= 0.270 Chirality : 0.038 0.293 3710 Planarity : 0.004 0.046 4257 Dihedral : 13.512 87.767 3755 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.69 % Allowed : 14.52 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.84 (0.16), residues: 2872 helix: 1.38 (0.14), residues: 1470 sheet: 0.32 (0.28), residues: 303 loop : -0.42 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 955 HIS 0.005 0.001 HIS C 784 PHE 0.020 0.001 PHE B 257 TYR 0.021 0.001 TYR B1111 ARG 0.006 0.000 ARG C 668 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 213 time to evaluate : 3.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7327 (tp) REVERT: B 199 ARG cc_start: 0.7124 (ttp-170) cc_final: 0.6835 (ttp-170) REVERT: B 518 MET cc_start: 0.8765 (tpp) cc_final: 0.8542 (mpp) REVERT: B 878 TRP cc_start: 0.7488 (t60) cc_final: 0.7274 (t60) REVERT: B 960 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7869 (tp30) REVERT: C 479 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8705 (tt) REVERT: C 667 MET cc_start: 0.8361 (mmp) cc_final: 0.8136 (mmt) REVERT: C 853 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8464 (pp) REVERT: C 897 LEU cc_start: 0.9105 (mt) cc_final: 0.8854 (mt) REVERT: C 927 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8825 (tt) REVERT: C 1054 ASN cc_start: 0.8357 (m-40) cc_final: 0.7671 (p0) REVERT: C 1079 MET cc_start: 0.8040 (ptm) cc_final: 0.7829 (ptp) REVERT: D 160 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7782 (p) REVERT: D 314 CYS cc_start: 0.8053 (t) cc_final: 0.7720 (t) outliers start: 66 outliers final: 41 residues processed: 272 average time/residue: 0.3733 time to fit residues: 167.0402 Evaluate side-chains 233 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 187 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 235 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 210 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 241 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 254 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 GLN B 834 HIS ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24750 Z= 0.180 Angle : 0.504 9.814 33795 Z= 0.255 Chirality : 0.037 0.161 3710 Planarity : 0.004 0.059 4257 Dihedral : 13.400 88.101 3753 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.69 % Allowed : 14.48 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.16), residues: 2872 helix: 1.60 (0.14), residues: 1466 sheet: 0.51 (0.29), residues: 298 loop : -0.36 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 955 HIS 0.004 0.001 HIS B1150 PHE 0.015 0.001 PHE B1172 TYR 0.021 0.001 TYR D 404 ARG 0.007 0.000 ARG B 824 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 203 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7271 (tp) REVERT: B 199 ARG cc_start: 0.7069 (ttp-170) cc_final: 0.6762 (ttp-170) REVERT: B 878 TRP cc_start: 0.7501 (t60) cc_final: 0.7269 (t60) REVERT: B 901 TRP cc_start: 0.8651 (OUTLIER) cc_final: 0.8352 (t60) REVERT: B 960 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7836 (tp30) REVERT: C 712 ASP cc_start: 0.8454 (m-30) cc_final: 0.7988 (t0) REVERT: C 786 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7163 (ttm-80) REVERT: C 853 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8468 (pp) REVERT: C 927 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8777 (tt) REVERT: C 1054 ASN cc_start: 0.8340 (m-40) cc_final: 0.7652 (p0) REVERT: C 1079 MET cc_start: 0.8030 (ptm) cc_final: 0.7813 (ptp) REVERT: D 314 CYS cc_start: 0.8099 (t) cc_final: 0.7774 (t) outliers start: 66 outliers final: 44 residues processed: 259 average time/residue: 0.3361 time to fit residues: 141.3470 Evaluate side-chains 230 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 181 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 901 TRP Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 95 optimal weight: 0.8980 chunk 255 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24750 Z= 0.232 Angle : 0.534 10.521 33795 Z= 0.268 Chirality : 0.038 0.172 3710 Planarity : 0.004 0.046 4257 Dihedral : 13.392 88.723 3752 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.35 % Allowed : 14.16 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.16), residues: 2872 helix: 1.59 (0.14), residues: 1470 sheet: 0.48 (0.29), residues: 300 loop : -0.41 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 955 HIS 0.006 0.001 HIS D 473 PHE 0.015 0.001 PHE B 257 TYR 0.022 0.001 TYR D 404 ARG 0.008 0.000 ARG C1028 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 193 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 824 ARG cc_start: 0.5634 (OUTLIER) cc_final: 0.4984 (mtm180) REVERT: B 901 TRP cc_start: 0.8570 (OUTLIER) cc_final: 0.8284 (t60) REVERT: B 960 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7814 (tp30) REVERT: B 1167 LEU cc_start: 0.8541 (mt) cc_final: 0.8341 (pp) REVERT: C 441 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: C 786 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7151 (ttm-80) REVERT: C 853 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8472 (pp) REVERT: C 927 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8803 (tt) REVERT: C 1054 ASN cc_start: 0.8349 (m-40) cc_final: 0.7576 (p0) REVERT: D 160 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7874 (p) REVERT: D 314 CYS cc_start: 0.8229 (t) cc_final: 0.7729 (t) outliers start: 82 outliers final: 48 residues processed: 265 average time/residue: 0.3286 time to fit residues: 144.4303 Evaluate side-chains 239 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 184 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 901 TRP Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 273 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 161 optimal weight: 0.0020 chunk 207 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 282 optimal weight: 10.0000 chunk 176 optimal weight: 0.1980 chunk 172 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 overall best weight: 2.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN ** C 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24750 Z= 0.203 Angle : 0.518 11.923 33795 Z= 0.258 Chirality : 0.037 0.147 3710 Planarity : 0.003 0.048 4257 Dihedral : 13.319 89.671 3752 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.77 % Allowed : 15.10 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.16), residues: 2872 helix: 1.68 (0.14), residues: 1459 sheet: 0.62 (0.29), residues: 296 loop : -0.35 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 955 HIS 0.005 0.001 HIS D 469 PHE 0.012 0.001 PHE B1172 TYR 0.022 0.001 TYR D 404 ARG 0.006 0.000 ARG C1028 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 193 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 901 TRP cc_start: 0.8668 (OUTLIER) cc_final: 0.8362 (t60) REVERT: B 960 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7661 (mt-10) REVERT: B 968 VAL cc_start: 0.6964 (t) cc_final: 0.6529 (t) REVERT: C 441 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: C 775 ARG cc_start: 0.7362 (tpp80) cc_final: 0.6834 (ttm-80) REVERT: C 786 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7192 (ttm-80) REVERT: C 853 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8429 (pp) REVERT: C 927 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8777 (tt) REVERT: C 1054 ASN cc_start: 0.8337 (m-40) cc_final: 0.7563 (p0) REVERT: D 314 CYS cc_start: 0.8239 (t) cc_final: 0.7675 (t) REVERT: A 9 ASP cc_start: 0.7766 (p0) cc_final: 0.7429 (p0) outliers start: 68 outliers final: 48 residues processed: 254 average time/residue: 0.3223 time to fit residues: 134.8728 Evaluate side-chains 236 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 183 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 901 TRP Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 174 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 458 ASN ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 24750 Z= 0.374 Angle : 0.628 12.665 33795 Z= 0.316 Chirality : 0.041 0.192 3710 Planarity : 0.004 0.042 4257 Dihedral : 13.512 89.001 3752 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.61 % Allowed : 15.67 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.76 (0.16), residues: 2872 helix: 1.32 (0.14), residues: 1457 sheet: 0.43 (0.29), residues: 286 loop : -0.48 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 955 HIS 0.008 0.001 HIS D 473 PHE 0.019 0.002 PHE B 257 TYR 0.024 0.002 TYR D 404 ARG 0.005 0.001 ARG C 530 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 192 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 LEU cc_start: 0.8414 (tp) cc_final: 0.8161 (tt) REVERT: B 152 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7561 (tp) REVERT: B 518 MET cc_start: 0.8992 (mmm) cc_final: 0.8446 (mpp) REVERT: B 960 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7707 (mm-30) REVERT: B 968 VAL cc_start: 0.7030 (t) cc_final: 0.6569 (t) REVERT: C 786 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7262 (ttm-80) REVERT: C 927 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8869 (tt) REVERT: D 83 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: D 184 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8686 (tp) REVERT: D 314 CYS cc_start: 0.8363 (t) cc_final: 0.7796 (t) outliers start: 64 outliers final: 45 residues processed: 251 average time/residue: 0.3282 time to fit residues: 136.3012 Evaluate side-chains 226 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 176 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 256 optimal weight: 6.9990 chunk 270 optimal weight: 0.3980 chunk 246 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 262 optimal weight: 7.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN B 879 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24750 Z= 0.263 Angle : 0.576 11.775 33795 Z= 0.285 Chirality : 0.039 0.210 3710 Planarity : 0.004 0.044 4257 Dihedral : 13.446 88.513 3752 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.49 % Allowed : 16.16 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.84 (0.16), residues: 2872 helix: 1.40 (0.14), residues: 1459 sheet: 0.48 (0.30), residues: 284 loop : -0.47 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 496 HIS 0.005 0.001 HIS D 473 PHE 0.011 0.001 PHE B1172 TYR 0.021 0.001 TYR D 404 ARG 0.005 0.000 ARG C1028 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 179 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7470 (tp) REVERT: B 960 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7688 (mm-30) REVERT: C 775 ARG cc_start: 0.7433 (tpp80) cc_final: 0.6895 (ttm-80) REVERT: C 786 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7211 (ttm-80) REVERT: C 927 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8854 (tt) REVERT: C 955 TRP cc_start: 0.7650 (m100) cc_final: 0.7389 (m100) REVERT: D 83 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: D 314 CYS cc_start: 0.8349 (t) cc_final: 0.7775 (t) REVERT: D 459 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7216 (pp20) REVERT: D 466 ARG cc_start: 0.7507 (mmp80) cc_final: 0.6039 (mmt180) outliers start: 61 outliers final: 43 residues processed: 232 average time/residue: 0.3320 time to fit residues: 127.6622 Evaluate side-chains 222 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 174 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1054 ASN Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 536 MET Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 172 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 132 optimal weight: 0.0570 chunk 193 optimal weight: 7.9990 chunk 291 optimal weight: 10.0000 chunk 268 optimal weight: 0.2980 chunk 232 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24750 Z= 0.184 Angle : 0.542 12.240 33795 Z= 0.267 Chirality : 0.037 0.154 3710 Planarity : 0.004 0.048 4257 Dihedral : 13.320 88.697 3752 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.04 % Allowed : 16.48 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.16), residues: 2872 helix: 1.60 (0.14), residues: 1462 sheet: 0.62 (0.30), residues: 295 loop : -0.41 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1085 HIS 0.006 0.001 HIS D 469 PHE 0.022 0.001 PHE B 257 TYR 0.020 0.001 TYR D 404 ARG 0.004 0.000 ARG C1028 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 189 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 GLU cc_start: 0.7615 (pp20) cc_final: 0.6975 (pp20) REVERT: B 152 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7452 (tp) REVERT: B 518 MET cc_start: 0.8938 (mmm) cc_final: 0.8440 (mpp) REVERT: B 620 MET cc_start: 0.8064 (tpp) cc_final: 0.7480 (tpt) REVERT: B 960 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7717 (mm-30) REVERT: C 775 ARG cc_start: 0.7413 (tpp80) cc_final: 0.6916 (ttm-80) REVERT: C 786 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7171 (ttm-80) REVERT: C 955 TRP cc_start: 0.7639 (m100) cc_final: 0.7342 (m100) REVERT: D 83 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: D 314 CYS cc_start: 0.8195 (t) cc_final: 0.7508 (t) REVERT: D 459 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7149 (pp20) REVERT: A 9 ASP cc_start: 0.7834 (p0) cc_final: 0.7564 (p0) outliers start: 50 outliers final: 38 residues processed: 233 average time/residue: 0.3162 time to fit residues: 122.0676 Evaluate side-chains 225 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1054 ASN Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 184 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 214 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 239 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077244 restraints weight = 61982.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.079885 restraints weight = 39065.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080651 restraints weight = 22545.121| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24750 Z= 0.290 Angle : 0.588 11.023 33795 Z= 0.291 Chirality : 0.039 0.163 3710 Planarity : 0.004 0.048 4257 Dihedral : 13.395 89.481 3752 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.00 % Allowed : 16.73 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.16), residues: 2872 helix: 1.50 (0.14), residues: 1456 sheet: 0.55 (0.30), residues: 294 loop : -0.44 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 496 HIS 0.006 0.001 HIS D 473 PHE 0.013 0.001 PHE B1172 TYR 0.022 0.002 TYR B 749 ARG 0.004 0.000 ARG B 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4235.27 seconds wall clock time: 78 minutes 11.60 seconds (4691.60 seconds total)