Starting phenix.real_space_refine on Mon Feb 19 07:19:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1t_15804/02_2024/8b1t_15804_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1t_15804/02_2024/8b1t_15804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1t_15804/02_2024/8b1t_15804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1t_15804/02_2024/8b1t_15804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1t_15804/02_2024/8b1t_15804_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1t_15804/02_2024/8b1t_15804_updated.pdb" } resolution = 3.4 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 15000 2.51 5 N 4224 2.21 5 O 4604 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 PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 275": "OE1" <-> "OE2" Residue "B PHE 289": "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 TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 849": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "D TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 10": "OD1" <-> "OD2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 27": "NH1" <-> "NH2" 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: 23986 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: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 392 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} 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: 12.24, per 1000 atoms: 0.51 Number of scatterers: 23986 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 4604 8.00 N 4224 7.00 C 15000 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: 9.54 Conformation dependent library (CDL) restraints added in 4.0 seconds 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5412 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 15 sheets defined 48.8% alpha, 8.3% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 11.71 Creating SS restraints... Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.732A pdb=" N ILE B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.946A 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: 5.217A pdb=" N ASP B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 6.075A 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: 3.612A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 removed outlier: 3.519A pdb=" N ASP B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.342A 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: 3.943A 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: 4.411A pdb=" N THR B 376 " --> pdb=" O ALA B 373 " (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 removed outlier: 3.532A pdb=" N ALA B 570 " --> pdb=" O GLN B 566 " (cutoff:3.500A) 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: 3.970A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 716 removed outlier: 3.867A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 806 removed outlier: 3.609A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 842 removed outlier: 3.561A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 860 Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 949 through 961 removed outlier: 3.605A 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: 3.953A 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 1014 through 1016 No H-bonds generated for 'chain 'B' and resid 1014 through 1016' Processing helix chain 'B' and resid 1033 through 1043 removed outlier: 4.732A 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: 3.693A pdb=" N SER C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP C 93 " --> pdb=" O GLN C 89 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 122 through 141 Processing helix chain 'C' and resid 143 through 151 removed outlier: 3.717A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 178 removed outlier: 4.606A pdb=" N ALA C 166 " --> pdb=" O ALA C 163 " (cutoff:3.500A) Proline residue: C 167 - end of helix removed outlier: 4.243A pdb=" N GLU C 174 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 198 removed outlier: 4.909A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.188A 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: 3.703A pdb=" N TRP C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 316 removed outlier: 3.539A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.664A 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 removed outlier: 3.635A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) 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 474 Processing helix chain 'C' and resid 477 through 482 Processing helix chain 'C' and resid 487 through 500 removed outlier: 3.865A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.847A 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: 3.891A pdb=" N ALA C 565 " --> pdb=" O GLY C 562 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 568 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET C 569 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TRP C 574 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 598 removed outlier: 3.537A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Proline residue: C 589 - end of helix removed outlier: 4.691A 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 removed outlier: 3.521A pdb=" N ASP C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 643 " --> pdb=" O ASP C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 722 removed outlier: 3.607A 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 804 through 810 Proline residue: C 808 - end of helix Processing helix chain 'C' and resid 834 through 842 Processing helix chain 'C' and resid 844 through 851 Processing helix chain 'C' and resid 875 through 889 Processing helix chain 'C' and resid 894 through 904 Processing helix chain 'C' and resid 910 through 934 removed outlier: 3.800A pdb=" N LEU C 927 " --> pdb=" O GLU C 923 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 991 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: 3.722A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) 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: 3.769A pdb=" N GLU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 3.990A 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 48 Processing helix chain 'D' and resid 66 through 75 removed outlier: 4.884A pdb=" N SER D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 5.050A 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: 3.514A 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: 3.644A pdb=" N GLN D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 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: 3.605A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 318 removed outlier: 4.349A pdb=" N TYR D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA D 317 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 removed outlier: 3.559A pdb=" N ARG D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) 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: 4.853A pdb=" N ARG D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 437 removed outlier: 3.668A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU D 437 " --> pdb=" O GLN D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 464 removed outlier: 3.731A 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: 3.619A pdb=" N SER D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 605 removed outlier: 3.835A 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 51 Processing sheet with id= A, first strand: chain 'B' and resid 18 through 22 removed outlier: 6.516A pdb=" N LEU B 409 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE B 21 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU B 411 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.464A 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: 6.566A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA B 870 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 503 " --> pdb=" O ALA B 870 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS B 813 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N TRP B 502 " --> pdb=" O CYS B 813 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 815 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N MET B 504 " --> pdb=" O LEU B 815 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL B 817 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN B 737 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B 558 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 6.240A 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 905 removed outlier: 5.471A pdb=" N ARG B1059 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR B 904 " --> pdb=" O ARG B1059 " (cutoff:3.500A) removed outlier: 6.242A 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: 3.631A 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: 6.477A pdb=" N LEU C 2 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LEU C 323 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 4 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE C 236 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR C 5 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU C 238 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER C 7 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE C 240 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N MET C 34 " --> pdb=" O PHE C 212 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N CYS C 214 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 5.569A 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: 8.637A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU C 727 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N HIS C 377 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE C 729 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N CYS C 379 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR C 731 " --> pdb=" O CYS C 379 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASN C 660 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL C 412 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 6.626A 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: 6.174A 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: 6.415A pdb=" N GLU C 995 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG C 966 " --> pdb=" O GLU C 995 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ARG C 997 " --> pdb=" O ARG C 966 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ARG C 968 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE C 999 " --> pdb=" O ARG C 968 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 52 through 54 Processing sheet with id= M, first strand: chain 'D' and resid 352 through 355 removed outlier: 8.450A pdb=" N CYS D 353 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL D 168 " --> pdb=" O CYS D 353 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU D 355 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N SER D 170 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL D 292 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE D 169 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE D 294 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLY D 171 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 5.860A 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: 6.640A pdb=" N LEU D 577 " --> pdb=" O GLU D 394 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG D 396 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 6.406A 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: 7.115A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2676 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: 9.78 Time building geometry restraints manager: 10.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7353 1.33 - 1.45: 3755 1.45 - 1.57: 13221 1.57 - 1.69: 105 1.69 - 1.81: 173 Bond restraints: 24607 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 5.13e+01 bond pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" O5' ANP B1501 " pdb=" PA ANP B1501 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3G ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 1.528 1.580 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" O2G ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 1.530 1.576 -0.046 2.00e-02 2.50e+03 5.39e+00 ... (remaining 24602 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.82: 835 105.82 - 112.88: 13094 112.88 - 119.93: 8038 119.93 - 126.98: 11198 126.98 - 134.04: 437 Bond angle restraints: 33602 Sorted by residual: angle pdb=" PB ANP B1501 " pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 126.95 108.71 18.24 3.00e+00 1.11e-01 3.70e+01 angle pdb=" O1B ANP B1501 " pdb=" PB ANP B1501 " pdb=" O2B ANP B1501 " ideal model delta sigma weight residual 120.08 109.58 10.50 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C SER B 449 " pdb=" N ALA B 450 " pdb=" CA ALA B 450 " ideal model delta sigma weight residual 120.60 125.29 -4.69 1.53e+00 4.27e-01 9.39e+00 angle pdb=" CA LEU C 323 " pdb=" CB LEU C 323 " pdb=" CG LEU C 323 " ideal model delta sigma weight residual 116.30 126.89 -10.59 3.50e+00 8.16e-02 9.15e+00 angle pdb=" N LEU B 175 " pdb=" CA LEU B 175 " pdb=" C LEU B 175 " ideal model delta sigma weight residual 109.60 113.05 -3.45 1.15e+00 7.56e-01 8.99e+00 ... (remaining 33597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 13619 16.89 - 33.78: 737 33.78 - 50.67: 272 50.67 - 67.57: 99 67.57 - 84.46: 13 Dihedral angle restraints: 14740 sinusoidal: 6390 harmonic: 8350 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 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+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 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PHE B 127 " pdb=" C PHE B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 14737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3181 0.050 - 0.101: 419 0.101 - 0.151: 87 0.151 - 0.202: 1 0.202 - 0.252: 1 Chirality restraints: 3689 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 -2.61 0.25 2.00e-01 2.50e+01 1.59e+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 7.59e-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 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 3686 not shown) Planarity restraints: 4231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO C 658 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 381 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO C 382 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 658 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO B 659 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 659 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 659 " -0.020 5.00e-02 4.00e+02 ... (remaining 4228 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 194 2.63 - 3.20: 21111 3.20 - 3.77: 36495 3.77 - 4.33: 50200 4.33 - 4.90: 82610 Nonbonded interactions: 190610 Sorted by model distance: nonbonded pdb=" OG1 THR B 30 " pdb="MG MG B1502 " model vdw 2.065 2.170 nonbonded pdb=" NH1 ARG B 682 " pdb=" O ARG B 728 " model vdw 2.212 2.520 nonbonded pdb=" OD2 ASP B1044 " pdb=" NE2 GLN B1112 " model vdw 2.223 2.520 nonbonded pdb=" OG SER B1090 " pdb=" OE1 GLN B1153 " model vdw 2.224 2.440 nonbonded pdb=" OD2 ASP B 388 " pdb=" NZ LYS B 745 " model vdw 2.232 2.520 ... (remaining 190605 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.220 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 70.060 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.003 0.143 24607 Z= 0.197 Angle : 0.540 18.237 33602 Z= 0.320 Chirality : 0.036 0.252 3689 Planarity : 0.004 0.045 4231 Dihedral : 13.043 84.457 9328 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.05 % Favored : 98.91 % Rotamer: Outliers : 1.44 % Allowed : 3.90 % Favored : 94.67 % 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: -0.96 (0.14), residues: 2855 helix: -0.22 (0.12), residues: 1481 sheet: -0.71 (0.27), residues: 311 loop : -1.03 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 652 HIS 0.003 0.001 HIS B 171 PHE 0.010 0.001 PHE C 857 TYR 0.018 0.001 TYR B1111 ARG 0.004 0.000 ARG C 433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 452 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 289 PHE cc_start: 0.8704 (m-80) cc_final: 0.8383 (m-80) REVERT: B 604 MET cc_start: 0.8116 (tpt) cc_final: 0.7771 (tpt) REVERT: B 672 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: B 709 ARG cc_start: 0.7607 (tpp80) cc_final: 0.7327 (mtm-85) REVERT: B 1079 LEU cc_start: 0.9360 (tp) cc_final: 0.9143 (tt) REVERT: C 42 MET cc_start: 0.8972 (tpt) cc_final: 0.8596 (tpt) REVERT: C 556 LEU cc_start: 0.8817 (mt) cc_final: 0.8537 (mt) REVERT: C 617 GLN cc_start: 0.8214 (tp40) cc_final: 0.7989 (tp40) REVERT: C 924 MET cc_start: 0.8470 (mmp) cc_final: 0.8232 (mmp) REVERT: D 78 LEU cc_start: 0.6377 (mm) cc_final: 0.6129 (tp) REVERT: D 136 LEU cc_start: 0.8316 (tp) cc_final: 0.7905 (tt) outliers start: 35 outliers final: 5 residues processed: 480 average time/residue: 0.4456 time to fit residues: 312.5703 Evaluate side-chains 189 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 122 optimal weight: 0.0270 chunk 75 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 264 optimal weight: 4.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- 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 440 HIS B 458 ASN B 484 ASN B 594 GLN B 650 GLN B 769 HIS B 835 GLN B 843 GLN B 848 GLN B1018 GLN B1057 GLN B1072 HIS B1103 GLN B1134 HIS B1161 ASN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 237 HIS C 336 HIS C 510 ASN C 541 GLN C 660 ASN C 749 GLN C 881 ASN C 920 GLN C 979 GLN C1054 ASN D 22 GLN D 251 GLN D 256 HIS D 399 GLN D 523 GLN D 556 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24607 Z= 0.297 Angle : 0.551 11.128 33602 Z= 0.282 Chirality : 0.040 0.170 3689 Planarity : 0.004 0.051 4231 Dihedral : 13.753 88.081 3741 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.87 % Allowed : 8.58 % Favored : 88.55 % 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: 0.15 (0.15), residues: 2855 helix: 0.79 (0.13), residues: 1484 sheet: -0.21 (0.28), residues: 308 loop : -0.67 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 265 HIS 0.005 0.001 HIS C 6 PHE 0.017 0.002 PHE B 461 TYR 0.018 0.002 TYR B1111 ARG 0.006 0.001 ARG D 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 189 time to evaluate : 2.696 Fit side-chains revert: symmetry clash REVERT: B 310 PHE cc_start: 0.7894 (m-10) cc_final: 0.7684 (m-10) REVERT: B 332 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8371 (mt) REVERT: B 655 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7797 (mpp80) REVERT: B 672 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: B 709 ARG cc_start: 0.7715 (tpp80) cc_final: 0.7347 (mtm-85) REVERT: B 815 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8894 (pp) REVERT: B 1078 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8577 (tt) REVERT: C 835 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6761 (tm-30) REVERT: C 924 MET cc_start: 0.8532 (mmp) cc_final: 0.8239 (mmp) REVERT: D 78 LEU cc_start: 0.6530 (mm) cc_final: 0.6243 (tp) REVERT: D 275 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7368 (p0) REVERT: D 384 THR cc_start: 0.8357 (p) cc_final: 0.8061 (t) REVERT: D 407 MET cc_start: 0.7776 (ttp) cc_final: 0.7513 (tmm) REVERT: D 462 MET cc_start: 0.7481 (mmm) cc_final: 0.7001 (mmp) REVERT: D 470 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7429 (mtm110) outliers start: 70 outliers final: 32 residues processed: 245 average time/residue: 0.3220 time to fit residues: 130.0381 Evaluate side-chains 197 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1078 ASN Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain D residue 523 GLN Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.5980 chunk 82 optimal weight: 8.9990 chunk 219 optimal weight: 0.9980 chunk 179 optimal weight: 0.0670 chunk 72 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 285 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 881 ASN C 920 GLN C1054 ASN C1108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24607 Z= 0.176 Angle : 0.475 10.786 33602 Z= 0.245 Chirality : 0.037 0.153 3689 Planarity : 0.003 0.049 4231 Dihedral : 13.563 87.615 3741 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.30 % Allowed : 9.73 % Favored : 87.98 % 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: 0.72 (0.15), residues: 2855 helix: 1.27 (0.13), residues: 1482 sheet: 0.19 (0.28), residues: 306 loop : -0.46 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 265 HIS 0.003 0.001 HIS C 6 PHE 0.018 0.001 PHE B 257 TYR 0.021 0.001 TYR C 138 ARG 0.004 0.000 ARG D 445 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 173 time to evaluate : 2.484 Fit side-chains REVERT: B 310 PHE cc_start: 0.7894 (m-10) cc_final: 0.7622 (m-10) REVERT: B 332 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8385 (mt) REVERT: B 568 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7130 (tpp80) REVERT: B 655 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7811 (mpp80) REVERT: B 709 ARG cc_start: 0.7671 (tpp80) cc_final: 0.7306 (mtm-85) REVERT: C 835 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6778 (tm-30) REVERT: C 924 MET cc_start: 0.8507 (mmp) cc_final: 0.8198 (mmp) REVERT: D 78 LEU cc_start: 0.6520 (mm) cc_final: 0.6252 (tp) REVERT: D 462 MET cc_start: 0.7568 (mmm) cc_final: 0.7023 (mmp) REVERT: D 470 ARG cc_start: 0.7744 (ttt180) cc_final: 0.7344 (mtm110) outliers start: 56 outliers final: 33 residues processed: 217 average time/residue: 0.3325 time to fit residues: 118.2167 Evaluate side-chains 188 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1161 ASN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 52 CYS Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 265 optimal weight: 9.9990 chunk 281 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 705 HIS ** C1054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN D 523 GLN D 542 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 24607 Z= 0.538 Angle : 0.656 10.777 33602 Z= 0.336 Chirality : 0.044 0.213 3689 Planarity : 0.005 0.055 4231 Dihedral : 13.862 85.737 3738 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.36 % Allowed : 10.34 % Favored : 86.29 % 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: 0.17 (0.15), residues: 2855 helix: 0.75 (0.13), residues: 1483 sheet: -0.05 (0.29), residues: 300 loop : -0.62 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 616 HIS 0.009 0.002 HIS C 6 PHE 0.026 0.002 PHE C 125 TYR 0.020 0.002 TYR C 310 ARG 0.004 0.001 ARG B 613 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 160 time to evaluate : 2.672 Fit side-chains revert: symmetry clash REVERT: B 310 PHE cc_start: 0.7898 (m-10) cc_final: 0.7605 (m-10) REVERT: B 332 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8543 (mt) REVERT: B 490 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8127 (m) REVERT: B 655 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8134 (mpp80) REVERT: B 709 ARG cc_start: 0.7680 (tpp80) cc_final: 0.7152 (mtm-85) REVERT: B 1140 TYR cc_start: 0.8309 (m-10) cc_final: 0.8045 (m-80) REVERT: C 661 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8757 (mm) REVERT: C 924 MET cc_start: 0.8574 (mmp) cc_final: 0.8244 (mmp) REVERT: D 239 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8754 (p) REVERT: D 275 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7604 (p0) REVERT: D 462 MET cc_start: 0.7646 (mmm) cc_final: 0.7091 (mmp) REVERT: D 470 ARG cc_start: 0.7630 (ttt180) cc_final: 0.7358 (mtm110) outliers start: 82 outliers final: 49 residues processed: 228 average time/residue: 0.3608 time to fit residues: 135.8458 Evaluate side-chains 201 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 146 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1161 ASN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 52 CYS Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 128 HIS Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 523 GLN Chi-restraints excluded: chain D residue 592 THR Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 7.9990 chunk 159 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 252 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 834 HIS ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN D 65 HIS D 300 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24607 Z= 0.173 Angle : 0.480 9.453 33602 Z= 0.250 Chirality : 0.037 0.165 3689 Planarity : 0.003 0.052 4231 Dihedral : 13.609 88.394 3734 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.05 % Allowed : 12.35 % Favored : 85.60 % 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: 0.77 (0.16), residues: 2855 helix: 1.31 (0.14), residues: 1481 sheet: 0.11 (0.29), residues: 304 loop : -0.41 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 993 HIS 0.002 0.001 HIS C 448 PHE 0.019 0.001 PHE B 257 TYR 0.017 0.001 TYR B1111 ARG 0.004 0.000 ARG D 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 171 time to evaluate : 2.732 Fit side-chains REVERT: B 310 PHE cc_start: 0.7786 (m-10) cc_final: 0.7544 (m-10) REVERT: B 354 MET cc_start: 0.7918 (mtt) cc_final: 0.7545 (mpt) REVERT: B 655 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8022 (mpp80) REVERT: B 709 ARG cc_start: 0.7608 (tpp80) cc_final: 0.7261 (mtm-85) REVERT: B 1140 TYR cc_start: 0.8261 (m-10) cc_final: 0.7960 (m-80) REVERT: C 661 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8547 (mm) REVERT: C 924 MET cc_start: 0.8460 (mmp) cc_final: 0.8134 (mmp) REVERT: D 239 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8509 (p) REVERT: D 275 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7587 (p0) REVERT: D 462 MET cc_start: 0.7642 (mmm) cc_final: 0.7101 (mmp) REVERT: D 470 ARG cc_start: 0.7646 (ttt180) cc_final: 0.7342 (mtm110) outliers start: 50 outliers final: 26 residues processed: 210 average time/residue: 0.3291 time to fit residues: 114.5847 Evaluate side-chains 180 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1161 ASN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 52 CYS Chi-restraints excluded: chain D residue 128 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 20.0000 chunk 253 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 281 optimal weight: 9.9990 chunk 233 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN C1054 ASN D 300 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 24607 Z= 0.463 Angle : 0.619 9.714 33602 Z= 0.316 Chirality : 0.043 0.203 3689 Planarity : 0.005 0.048 4231 Dihedral : 13.735 86.940 3734 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.75 % Allowed : 12.84 % Favored : 84.41 % 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: 0.38 (0.15), residues: 2855 helix: 0.96 (0.13), residues: 1476 sheet: -0.02 (0.29), residues: 297 loop : -0.55 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 993 HIS 0.008 0.001 HIS C 843 PHE 0.023 0.002 PHE C 125 TYR 0.022 0.002 TYR B 173 ARG 0.005 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 150 time to evaluate : 2.903 Fit side-chains REVERT: B 310 PHE cc_start: 0.7859 (m-10) cc_final: 0.7614 (m-10) REVERT: B 332 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8519 (mt) REVERT: B 354 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7699 (mpt) REVERT: B 655 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8135 (mpp80) REVERT: B 709 ARG cc_start: 0.7680 (tpp80) cc_final: 0.7176 (mtm-85) REVERT: B 900 ASN cc_start: 0.6342 (OUTLIER) cc_final: 0.5680 (t0) REVERT: B 947 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.5892 (ptp90) REVERT: C 661 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8771 (mm) REVERT: C 835 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7056 (tm-30) REVERT: C 924 MET cc_start: 0.8547 (mmp) cc_final: 0.8218 (mmp) REVERT: D 239 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8675 (p) REVERT: D 275 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7664 (p0) REVERT: D 407 MET cc_start: 0.8049 (tmm) cc_final: 0.7661 (tmm) REVERT: D 462 MET cc_start: 0.7721 (mmm) cc_final: 0.7131 (mmp) REVERT: D 470 ARG cc_start: 0.7688 (ttt180) cc_final: 0.7269 (mtm110) outliers start: 67 outliers final: 45 residues processed: 206 average time/residue: 0.3341 time to fit residues: 113.0638 Evaluate side-chains 196 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 143 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 900 ASN Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1102 MET Chi-restraints excluded: chain B residue 1161 ASN Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 52 CYS Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 128 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 0.0060 chunk 31 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 280 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24607 Z= 0.145 Angle : 0.474 9.501 33602 Z= 0.245 Chirality : 0.037 0.160 3689 Planarity : 0.003 0.048 4231 Dihedral : 13.442 89.296 3734 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.85 % Allowed : 13.54 % Favored : 84.61 % 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: 0.92 (0.16), residues: 2855 helix: 1.45 (0.14), residues: 1481 sheet: 0.22 (0.29), residues: 301 loop : -0.39 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 265 HIS 0.002 0.001 HIS B 714 PHE 0.018 0.001 PHE B 257 TYR 0.018 0.001 TYR B1111 ARG 0.004 0.000 ARG D 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 166 time to evaluate : 2.501 Fit side-chains REVERT: B 310 PHE cc_start: 0.7793 (m-10) cc_final: 0.7569 (m-10) REVERT: B 354 MET cc_start: 0.7941 (mtt) cc_final: 0.7596 (mpt) REVERT: B 655 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8000 (mpp80) REVERT: B 709 ARG cc_start: 0.7535 (tpp80) cc_final: 0.7144 (mtm-85) REVERT: B 1140 TYR cc_start: 0.8250 (m-80) cc_final: 0.8012 (m-10) REVERT: C 158 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8718 (tp) REVERT: C 661 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8576 (mm) REVERT: C 924 MET cc_start: 0.8430 (mmp) cc_final: 0.8104 (mmp) REVERT: D 239 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8363 (p) REVERT: D 275 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7532 (p0) REVERT: D 407 MET cc_start: 0.8083 (tmm) cc_final: 0.7621 (tmm) REVERT: D 462 MET cc_start: 0.7607 (mmm) cc_final: 0.6997 (mmp) REVERT: D 470 ARG cc_start: 0.7605 (ttt180) cc_final: 0.7284 (mtm110) outliers start: 45 outliers final: 33 residues processed: 203 average time/residue: 0.3303 time to fit residues: 112.0865 Evaluate side-chains 185 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1102 MET Chi-restraints excluded: chain B residue 1161 ASN Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 128 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 55 optimal weight: 0.2980 chunk 54 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 191 optimal weight: 0.3980 chunk 138 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24607 Z= 0.229 Angle : 0.493 9.652 33602 Z= 0.253 Chirality : 0.038 0.150 3689 Planarity : 0.003 0.045 4231 Dihedral : 13.397 89.063 3734 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.05 % Allowed : 13.79 % Favored : 84.16 % 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: 0.97 (0.16), residues: 2855 helix: 1.49 (0.14), residues: 1474 sheet: 0.20 (0.29), residues: 304 loop : -0.33 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 710 HIS 0.003 0.001 HIS C 843 PHE 0.017 0.001 PHE C 193 TYR 0.016 0.001 TYR B1111 ARG 0.003 0.000 ARG D 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 153 time to evaluate : 2.694 Fit side-chains REVERT: B 310 PHE cc_start: 0.7814 (m-10) cc_final: 0.7570 (m-10) REVERT: B 354 MET cc_start: 0.7930 (mtt) cc_final: 0.7542 (mpt) REVERT: B 655 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8086 (mpp80) REVERT: B 709 ARG cc_start: 0.7626 (tpp80) cc_final: 0.7149 (mtm-85) REVERT: B 1140 TYR cc_start: 0.8253 (m-80) cc_final: 0.8004 (m-10) REVERT: C 158 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8729 (tp) REVERT: C 236 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8290 (mt) REVERT: C 661 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8656 (mm) REVERT: C 924 MET cc_start: 0.8466 (mmp) cc_final: 0.8141 (mmp) REVERT: D 239 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8433 (p) REVERT: D 275 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7560 (p0) REVERT: D 407 MET cc_start: 0.8107 (tmm) cc_final: 0.7635 (tmm) REVERT: D 462 MET cc_start: 0.7578 (mmm) cc_final: 0.6947 (mmp) REVERT: D 470 ARG cc_start: 0.7597 (ttt180) cc_final: 0.7269 (mtm110) outliers start: 50 outliers final: 37 residues processed: 191 average time/residue: 0.3193 time to fit residues: 102.2898 Evaluate side-chains 190 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 147 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1102 MET Chi-restraints excluded: chain B residue 1161 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 128 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 0.3980 chunk 268 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 247 optimal weight: 0.5980 chunk 260 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24607 Z= 0.229 Angle : 0.499 9.692 33602 Z= 0.255 Chirality : 0.038 0.176 3689 Planarity : 0.003 0.044 4231 Dihedral : 13.380 88.723 3733 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.09 % Allowed : 13.91 % Favored : 84.00 % 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: 0.98 (0.16), residues: 2855 helix: 1.47 (0.14), residues: 1479 sheet: 0.24 (0.29), residues: 310 loop : -0.31 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 710 HIS 0.005 0.001 HIS C 563 PHE 0.016 0.001 PHE C 193 TYR 0.016 0.001 TYR B1111 ARG 0.002 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 147 time to evaluate : 2.727 Fit side-chains REVERT: B 310 PHE cc_start: 0.7812 (m-10) cc_final: 0.7570 (m-10) REVERT: B 354 MET cc_start: 0.7928 (mtt) cc_final: 0.7525 (mpt) REVERT: B 655 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8071 (mpp80) REVERT: B 709 ARG cc_start: 0.7630 (tpp80) cc_final: 0.7113 (mtm-85) REVERT: B 947 ARG cc_start: 0.6038 (OUTLIER) cc_final: 0.5807 (ptp90) REVERT: B 1140 TYR cc_start: 0.8249 (m-80) cc_final: 0.7981 (m-80) REVERT: C 158 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8724 (tp) REVERT: C 236 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8285 (mt) REVERT: C 661 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8645 (mm) REVERT: C 924 MET cc_start: 0.8465 (mmp) cc_final: 0.8132 (mmp) REVERT: D 239 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8472 (p) REVERT: D 275 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7543 (p0) REVERT: D 462 MET cc_start: 0.7512 (mmm) cc_final: 0.6872 (mmp) REVERT: D 470 ARG cc_start: 0.7594 (ttt180) cc_final: 0.7259 (mtm110) outliers start: 51 outliers final: 37 residues processed: 186 average time/residue: 0.3482 time to fit residues: 106.3734 Evaluate side-chains 188 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 144 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1161 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 128 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 5.9990 chunk 276 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 266 optimal weight: 9.9990 chunk 230 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN D 518 ASN ** 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: 0.8223 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24607 Z= 0.203 Angle : 0.489 9.698 33602 Z= 0.250 Chirality : 0.037 0.159 3689 Planarity : 0.003 0.045 4231 Dihedral : 13.348 88.940 3733 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.85 % Allowed : 14.20 % Favored : 83.96 % 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: 1.02 (0.16), residues: 2855 helix: 1.50 (0.14), residues: 1482 sheet: 0.32 (0.29), residues: 307 loop : -0.30 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 710 HIS 0.004 0.001 HIS C 563 PHE 0.017 0.001 PHE C 193 TYR 0.016 0.001 TYR B1111 ARG 0.003 0.000 ARG D 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 149 time to evaluate : 2.790 Fit side-chains REVERT: B 310 PHE cc_start: 0.7803 (m-10) cc_final: 0.7566 (m-10) REVERT: B 354 MET cc_start: 0.7989 (mtt) cc_final: 0.7609 (mpt) REVERT: B 655 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8006 (mpp80) REVERT: B 709 ARG cc_start: 0.7617 (tpp80) cc_final: 0.7097 (mtm-85) REVERT: B 1140 TYR cc_start: 0.8245 (m-80) cc_final: 0.7878 (m-80) REVERT: C 158 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8703 (tp) REVERT: C 236 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8269 (mt) REVERT: C 661 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8643 (mm) REVERT: C 924 MET cc_start: 0.8450 (mmp) cc_final: 0.8124 (mmp) REVERT: D 239 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8461 (p) REVERT: D 275 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7530 (p0) REVERT: D 462 MET cc_start: 0.7499 (mmm) cc_final: 0.6857 (mmp) REVERT: D 470 ARG cc_start: 0.7606 (ttt180) cc_final: 0.7275 (mtm110) outliers start: 45 outliers final: 37 residues processed: 183 average time/residue: 0.3383 time to fit residues: 102.6160 Evaluate side-chains 188 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1161 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 128 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 8.9990 chunk 245 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.110974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.084165 restraints weight = 46522.605| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.35 r_work: 0.3027 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 24607 Z= 0.249 Angle : 0.648 59.187 33602 Z= 0.371 Chirality : 0.040 0.688 3689 Planarity : 0.003 0.045 4231 Dihedral : 13.358 88.920 3733 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.81 % Allowed : 14.32 % Favored : 83.87 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.16), residues: 2855 helix: 1.50 (0.14), residues: 1478 sheet: 0.32 (0.29), residues: 307 loop : -0.30 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 710 HIS 0.003 0.001 HIS C 563 PHE 0.016 0.001 PHE C 193 TYR 0.016 0.001 TYR B1111 ARG 0.004 0.000 ARG C 706 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4471.23 seconds wall clock time: 82 minutes 25.92 seconds (4945.92 seconds total)