Starting phenix.real_space_refine on Wed Feb 14 09:55:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcw_12145/02_2024/7bcw_12145_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcw_12145/02_2024/7bcw_12145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcw_12145/02_2024/7bcw_12145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcw_12145/02_2024/7bcw_12145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcw_12145/02_2024/7bcw_12145_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bcw_12145/02_2024/7bcw_12145_updated.pdb" } resolution = 3.5 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= 0.003 sd= 0.041 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: 7 Type Number sf(0) Gaussians V 2 8.30 5 P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 5696 2.51 5 N 1560 2.21 5 O 1705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 127": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B ASP 553": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9025 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4452 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 13, 'TRANS': 560} Chain: "B" Number of atoms: 4452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4452 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 13, 'TRANS': 560} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {' MG': 1, 'ADP': 1, 'POV': 1, 'VO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' MG': 1, 'ADP': 1, 'POV': 1, 'VO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'POV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.43, per 1000 atoms: 0.60 Number of scatterers: 9025 At special positions: 0 Unit cell: (77.738, 79.392, 141.417, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 2 22.97 S 54 16.00 P 6 15.00 Mg 2 11.99 O 1705 8.00 N 1560 7.00 C 5696 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: 3.54 Conformation dependent library (CDL) restraints added in 1.6 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 5 sheets defined 61.6% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 11 through 48 Proline residue: A 18 - end of helix Proline residue: A 22 - end of helix removed outlier: 5.051A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLY A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A 48 " --> pdb=" O MET A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 53 No H-bonds generated for 'chain 'A' and resid 50 through 53' Processing helix chain 'A' and resid 67 through 108 Processing helix chain 'A' and resid 113 through 116 No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 142 through 163 Processing helix chain 'A' and resid 169 through 212 removed outlier: 4.108A pdb=" N ALA A 175 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Proline residue: A 176 - end of helix removed outlier: 3.960A pdb=" N LYS A 187 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 212 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 223 through 270 Proline residue: A 253 - end of helix removed outlier: 3.557A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.696A pdb=" N ASP A 277 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N SER A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 273 through 278' Processing helix chain 'A' and resid 281 through 323 removed outlier: 3.796A pdb=" N MET A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 4.552A pdb=" N ALA A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLN A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 412 through 418 removed outlier: 4.577A pdb=" N GLN A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 460 through 463 No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 513 through 526 Processing helix chain 'A' and resid 562 through 568 Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'B' and resid 9 through 20 Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 25 through 53 removed outlier: 3.659A pdb=" N LEU B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 48 " --> pdb=" O MET B 44 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 67 through 110 removed outlier: 4.070A pdb=" N VAL B 92 " --> pdb=" O CYS B 88 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 116 No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 121 through 140 removed outlier: 3.990A pdb=" N ASP B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 163 Processing helix chain 'B' and resid 169 through 211 removed outlier: 3.843A pdb=" N LEU B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA B 175 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Proline residue: B 176 - end of helix removed outlier: 4.408A pdb=" N LYS B 187 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN B 197 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 removed outlier: 3.599A pdb=" N PHE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 270 Proline residue: B 253 - end of helix removed outlier: 4.138A pdb=" N ALA B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 322 Proline residue: B 297 - end of helix removed outlier: 4.692A pdb=" N ALA B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLN B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 460 through 463 No H-bonds generated for 'chain 'B' and resid 460 through 463' Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 496 Processing helix chain 'B' and resid 513 through 528 removed outlier: 3.893A pdb=" N GLU B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'B' and resid 571 through 577 Processing sheet with id= A, first strand: chain 'A' and resid 342 through 345 Processing sheet with id= B, first strand: chain 'A' and resid 555 through 560 removed outlier: 6.627A pdb=" N VAL A 550 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG A 559 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 548 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 547 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER A 532 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU A 374 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL A 534 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N GLY A 376 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 342 through 345 Processing sheet with id= D, first strand: chain 'B' and resid 556 through 560 removed outlier: 6.700A pdb=" N VAL B 550 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG B 559 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE B 548 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER B 532 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LEU B 374 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 534 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 347 through 349 removed outlier: 3.599A pdb=" N VAL B 347 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N PHE B 349 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ARG B 360 " --> pdb=" O PHE B 349 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 1877 1.33 - 1.47: 3147 1.47 - 1.62: 4013 1.62 - 1.76: 5 1.76 - 1.91: 111 Bond restraints: 9153 Sorted by residual: bond pdb=" C21 POV A 604 " pdb=" O21 POV A 604 " ideal model delta sigma weight residual 1.330 1.404 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C21 POV B 604 " pdb=" O21 POV B 604 " ideal model delta sigma weight residual 1.330 1.404 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C31 POV A 604 " pdb=" O31 POV A 604 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CB MET A 242 " pdb=" CG MET A 242 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.89e+00 bond pdb=" C28 POV B 604 " pdb=" C29 POV B 604 " ideal model delta sigma weight residual 1.497 1.528 -0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 9148 not shown) Histogram of bond angle deviations from ideal: 96.14 - 104.17: 112 104.17 - 112.20: 4847 112.20 - 120.24: 3970 120.24 - 128.27: 3391 128.27 - 136.31: 54 Bond angle restraints: 12374 Sorted by residual: angle pdb=" O13 POV A 604 " pdb=" P POV A 604 " pdb=" O14 POV A 604 " ideal model delta sigma weight residual 121.11 108.59 12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" O11 POV A 604 " pdb=" P POV A 604 " pdb=" O12 POV A 604 " ideal model delta sigma weight residual 97.67 109.98 -12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" O13 POV B 604 " pdb=" P POV B 604 " pdb=" O14 POV B 604 " ideal model delta sigma weight residual 121.11 109.01 12.10 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O11 POV B 604 " pdb=" P POV B 604 " pdb=" O12 POV B 604 " ideal model delta sigma weight residual 97.67 109.66 -11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CB MET B 276 " pdb=" CG MET B 276 " pdb=" SD MET B 276 " ideal model delta sigma weight residual 112.70 122.24 -9.54 3.00e+00 1.11e-01 1.01e+01 ... (remaining 12369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.75: 5373 30.75 - 61.50: 171 61.50 - 92.25: 19 92.25 - 123.00: 0 123.00 - 153.75: 5 Dihedral angle restraints: 5568 sinusoidal: 2248 harmonic: 3320 Sorted by residual: dihedral pdb=" O2A ADP B 602 " pdb=" O3A ADP B 602 " pdb=" PA ADP B 602 " pdb=" PB ADP B 602 " ideal model delta sinusoidal sigma weight residual -60.00 73.70 -133.70 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" O1B ADP B 602 " pdb=" O3A ADP B 602 " pdb=" PB ADP B 602 " pdb=" PA ADP B 602 " ideal model delta sinusoidal sigma weight residual -60.00 73.08 -133.08 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O1B ADP A 602 " pdb=" O3A ADP A 602 " pdb=" PB ADP A 602 " pdb=" PA ADP A 602 " ideal model delta sinusoidal sigma weight residual 300.00 172.88 127.11 1 2.00e+01 2.50e-03 3.85e+01 ... (remaining 5565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 756 0.029 - 0.058: 460 0.058 - 0.087: 167 0.087 - 0.116: 67 0.116 - 0.144: 16 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CA ILE B 400 " pdb=" N ILE B 400 " pdb=" C ILE B 400 " pdb=" CB ILE B 400 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA VAL A 342 " pdb=" N VAL A 342 " pdb=" C VAL A 342 " pdb=" CB VAL A 342 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE B 535 " pdb=" N ILE B 535 " pdb=" C ILE B 535 " pdb=" CB ILE B 535 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1463 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 67 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A 68 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 542 " -0.008 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C ILE A 542 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 542 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU A 543 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 175 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO B 176 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 176 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 176 " 0.018 5.00e-02 4.00e+02 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 43 2.47 - 3.08: 6718 3.08 - 3.69: 13568 3.69 - 4.29: 19553 4.29 - 4.90: 32767 Nonbonded interactions: 72649 Sorted by model distance: nonbonded pdb=" O2 VO4 B 601 " pdb="MG MG B 603 " model vdw 1.868 2.170 nonbonded pdb=" OG SER B 383 " pdb="MG MG B 603 " model vdw 1.889 2.170 nonbonded pdb=" OE1 GLN B 424 " pdb="MG MG B 603 " model vdw 1.942 2.170 nonbonded pdb=" O1B ADP B 602 " pdb="MG MG B 603 " model vdw 1.969 2.170 nonbonded pdb=" OE1 GLN A 424 " pdb="MG MG A 603 " model vdw 2.018 2.170 ... (remaining 72644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 579 or resid 601 through 603 or (resid 604 and ( \ name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C3 or name O11 or name O1 \ 2 or name O13 or name O14 or name O21 or name O22 or name O31)))) selection = (chain 'B' and (resid 6 through 579 or resid 601 through 603 or (resid 604 and ( \ name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C3 or name O11 or name O1 \ 2 or name O13 or name O14 or name O21 or name O22 or name O31)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 7.190 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.850 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.005 0.074 9153 Z= 0.353 Angle : 0.760 12.522 12374 Z= 0.373 Chirality : 0.043 0.144 1466 Planarity : 0.003 0.047 1552 Dihedral : 15.867 153.755 3420 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1144 helix: 1.18 (0.20), residues: 714 sheet: -0.10 (0.60), residues: 68 loop : -1.14 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 91 HIS 0.011 0.001 HIS B 568 PHE 0.014 0.001 PHE A 56 TYR 0.007 0.001 TYR A 83 ARG 0.009 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.046 Fit side-chains REVERT: A 158 ILE cc_start: 0.8858 (pt) cc_final: 0.8652 (mt) REVERT: B 403 ASP cc_start: 0.7550 (t0) cc_final: 0.7211 (t0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2121 time to fit residues: 34.4318 Evaluate side-chains 93 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9153 Z= 0.236 Angle : 0.599 8.382 12374 Z= 0.303 Chirality : 0.041 0.126 1466 Planarity : 0.005 0.040 1552 Dihedral : 10.417 160.908 1314 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.12 % Allowed : 7.57 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1144 helix: 1.31 (0.20), residues: 712 sheet: -0.13 (0.60), residues: 70 loop : -1.09 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 165 HIS 0.007 0.001 HIS B 568 PHE 0.022 0.001 PHE A 43 TYR 0.007 0.001 TYR A 83 ARG 0.005 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.930 Fit side-chains REVERT: B 403 ASP cc_start: 0.7608 (t0) cc_final: 0.7265 (t0) outliers start: 11 outliers final: 2 residues processed: 112 average time/residue: 0.1934 time to fit residues: 31.2520 Evaluate side-chains 97 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 245 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 0.0670 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9153 Z= 0.165 Angle : 0.560 10.385 12374 Z= 0.276 Chirality : 0.040 0.156 1466 Planarity : 0.004 0.037 1552 Dihedral : 10.025 156.611 1314 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.53 % Allowed : 11.35 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1144 helix: 1.38 (0.20), residues: 710 sheet: 0.03 (0.61), residues: 70 loop : -0.96 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 10 HIS 0.005 0.001 HIS B 568 PHE 0.018 0.001 PHE A 319 TYR 0.006 0.001 TYR B 83 ARG 0.003 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.126 Fit side-chains REVERT: B 403 ASP cc_start: 0.7520 (t0) cc_final: 0.7150 (t0) outliers start: 15 outliers final: 9 residues processed: 117 average time/residue: 0.1976 time to fit residues: 34.2137 Evaluate side-chains 102 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 427 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9153 Z= 0.208 Angle : 0.573 8.310 12374 Z= 0.279 Chirality : 0.041 0.137 1466 Planarity : 0.004 0.037 1552 Dihedral : 9.806 151.863 1314 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.25 % Allowed : 12.68 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1144 helix: 1.35 (0.20), residues: 710 sheet: -0.02 (0.61), residues: 70 loop : -0.89 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 10 HIS 0.009 0.001 HIS B 427 PHE 0.019 0.001 PHE A 319 TYR 0.006 0.001 TYR A 83 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.076 Fit side-chains REVERT: A 196 MET cc_start: 0.9050 (tpp) cc_final: 0.8432 (ttt) REVERT: B 403 ASP cc_start: 0.7553 (t0) cc_final: 0.7217 (t0) outliers start: 22 outliers final: 12 residues processed: 116 average time/residue: 0.1889 time to fit residues: 32.4592 Evaluate side-chains 108 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 98 optimal weight: 0.1980 chunk 27 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN A 562 HIS B 427 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9153 Z= 0.161 Angle : 0.548 9.668 12374 Z= 0.268 Chirality : 0.040 0.139 1466 Planarity : 0.004 0.031 1552 Dihedral : 9.560 142.141 1314 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.04 % Allowed : 13.19 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1144 helix: 1.42 (0.20), residues: 710 sheet: 0.07 (0.61), residues: 70 loop : -0.81 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 10 HIS 0.009 0.001 HIS B 427 PHE 0.014 0.001 PHE A 319 TYR 0.006 0.001 TYR A 83 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.019 Fit side-chains REVERT: A 196 MET cc_start: 0.8934 (tpp) cc_final: 0.8005 (ttt) REVERT: B 403 ASP cc_start: 0.7523 (t0) cc_final: 0.7176 (t0) outliers start: 20 outliers final: 13 residues processed: 124 average time/residue: 0.1903 time to fit residues: 34.4745 Evaluate side-chains 114 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 422 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN B 427 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9153 Z= 0.241 Angle : 0.585 9.932 12374 Z= 0.285 Chirality : 0.041 0.138 1466 Planarity : 0.004 0.033 1552 Dihedral : 9.407 129.607 1314 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.56 % Allowed : 14.01 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1144 helix: 1.39 (0.20), residues: 710 sheet: 0.02 (0.61), residues: 70 loop : -0.82 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 10 HIS 0.008 0.001 HIS B 427 PHE 0.012 0.001 PHE A 319 TYR 0.006 0.001 TYR A 83 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.127 Fit side-chains REVERT: B 403 ASP cc_start: 0.7620 (t0) cc_final: 0.7283 (t0) outliers start: 25 outliers final: 20 residues processed: 121 average time/residue: 0.2023 time to fit residues: 35.7407 Evaluate side-chains 123 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 0.0970 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 427 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9153 Z= 0.192 Angle : 0.561 9.937 12374 Z= 0.273 Chirality : 0.040 0.140 1466 Planarity : 0.004 0.030 1552 Dihedral : 9.091 123.611 1314 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.45 % Allowed : 14.72 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1144 helix: 1.42 (0.20), residues: 710 sheet: -0.01 (0.60), residues: 70 loop : -0.77 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 10 HIS 0.008 0.001 HIS B 427 PHE 0.012 0.001 PHE A 319 TYR 0.006 0.001 TYR A 83 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.830 Fit side-chains REVERT: A 535 ILE cc_start: 0.8398 (pt) cc_final: 0.8077 (pt) REVERT: B 403 ASP cc_start: 0.7579 (t0) cc_final: 0.7234 (t0) outliers start: 24 outliers final: 20 residues processed: 121 average time/residue: 0.1955 time to fit residues: 34.2970 Evaluate side-chains 124 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 0.0870 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN B 427 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9153 Z= 0.160 Angle : 0.552 9.977 12374 Z= 0.268 Chirality : 0.040 0.203 1466 Planarity : 0.004 0.030 1552 Dihedral : 8.713 122.283 1314 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.25 % Allowed : 15.44 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1144 helix: 1.45 (0.20), residues: 710 sheet: 0.08 (0.61), residues: 70 loop : -0.69 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 10 HIS 0.008 0.001 HIS B 427 PHE 0.035 0.001 PHE A 288 TYR 0.016 0.001 TYR A 162 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.118 Fit side-chains REVERT: A 237 MET cc_start: 0.8732 (tpt) cc_final: 0.8276 (tpt) REVERT: B 403 ASP cc_start: 0.7552 (t0) cc_final: 0.7218 (t0) outliers start: 22 outliers final: 18 residues processed: 121 average time/residue: 0.1960 time to fit residues: 34.7610 Evaluate side-chains 122 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9153 Z= 0.183 Angle : 0.572 10.177 12374 Z= 0.274 Chirality : 0.041 0.198 1466 Planarity : 0.004 0.031 1552 Dihedral : 8.489 121.024 1314 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.35 % Allowed : 15.54 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1144 helix: 1.45 (0.20), residues: 712 sheet: 0.13 (0.61), residues: 70 loop : -0.69 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 10 HIS 0.010 0.001 HIS B 427 PHE 0.011 0.001 PHE A 319 TYR 0.014 0.001 TYR A 162 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 1.169 Fit side-chains REVERT: A 237 MET cc_start: 0.8775 (tpt) cc_final: 0.8369 (tpt) REVERT: B 403 ASP cc_start: 0.7562 (t0) cc_final: 0.7221 (t0) outliers start: 23 outliers final: 19 residues processed: 119 average time/residue: 0.1954 time to fit residues: 33.8784 Evaluate side-chains 121 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9153 Z= 0.195 Angle : 0.586 10.097 12374 Z= 0.280 Chirality : 0.041 0.202 1466 Planarity : 0.004 0.031 1552 Dihedral : 8.428 120.361 1314 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.04 % Allowed : 16.16 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1144 helix: 1.41 (0.20), residues: 712 sheet: 0.12 (0.61), residues: 70 loop : -0.68 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 10 HIS 0.009 0.001 HIS B 427 PHE 0.034 0.001 PHE A 288 TYR 0.013 0.001 TYR A 162 ARG 0.004 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.123 Fit side-chains REVERT: A 237 MET cc_start: 0.8788 (tpt) cc_final: 0.8464 (tpt) REVERT: B 403 ASP cc_start: 0.7564 (t0) cc_final: 0.7242 (t0) outliers start: 20 outliers final: 19 residues processed: 119 average time/residue: 0.2011 time to fit residues: 35.0408 Evaluate side-chains 122 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.119252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.106502 restraints weight = 14911.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109526 restraints weight = 6635.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111473 restraints weight = 3726.515| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9153 Z= 0.154 Angle : 0.574 9.481 12374 Z= 0.272 Chirality : 0.040 0.193 1466 Planarity : 0.004 0.031 1552 Dihedral : 8.348 119.524 1314 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.04 % Allowed : 16.77 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1144 helix: 1.46 (0.20), residues: 712 sheet: 0.23 (0.62), residues: 70 loop : -0.62 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 10 HIS 0.008 0.001 HIS B 568 PHE 0.011 0.001 PHE A 319 TYR 0.013 0.001 TYR A 162 ARG 0.003 0.000 ARG A 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1757.17 seconds wall clock time: 32 minutes 49.98 seconds (1969.98 seconds total)