Starting phenix.real_space_refine on Wed Feb 14 12:58:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8if8_35410/02_2024/8if8_35410.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8if8_35410/02_2024/8if8_35410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8if8_35410/02_2024/8if8_35410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8if8_35410/02_2024/8if8_35410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8if8_35410/02_2024/8if8_35410.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8if8_35410/02_2024/8if8_35410.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 34 5.16 5 C 6093 2.51 5 N 1593 2.21 5 O 1585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 514": "OD1" <-> "OD2" Residue "C ASP 522": "OD1" <-> "OD2" Residue "C TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 549": "OD1" <-> "OD2" Residue "C ASP 565": "OD1" <-> "OD2" Residue "C ASP 613": "OD1" <-> "OD2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 621": "OD1" <-> "OD2" Residue "C PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 128": "OD1" <-> "OD2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 464": "OD1" <-> "OD2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 565": "OD1" <-> "OD2" Residue "B TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 623": "NH1" <-> "NH2" Residue "B PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 628": "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: 9307 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4569 Classifications: {'peptide': 598} Link IDs: {'PTRANS': 34, 'TRANS': 563} Chain breaks: 2 Chain: "B" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4736 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 37, 'TRANS': 582} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.00, per 1000 atoms: 0.54 Number of scatterers: 9307 At special positions: 0 Unit cell: (101.504, 86.528, 116.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 34 16.00 O 1585 8.00 N 1593 7.00 C 6093 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: 3.30 Conformation dependent library (CDL) restraints added in 1.9 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 3 sheets defined 67.0% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'C' and resid 21 through 53 removed outlier: 4.147A pdb=" N VAL C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 88 removed outlier: 3.536A pdb=" N LEU C 67 " --> pdb=" O GLN C 63 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS C 88 " --> pdb=" O TRP C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 113 removed outlier: 3.543A pdb=" N MET C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 142 removed outlier: 3.754A pdb=" N ARG C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP C 141 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 142 " --> pdb=" O ARG C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 172 removed outlier: 3.517A pdb=" N ILE C 164 " --> pdb=" O GLY C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 203 Processing helix chain 'C' and resid 204 through 224 removed outlier: 3.958A pdb=" N SER C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 235 through 249 removed outlier: 3.591A pdb=" N MET C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 270 removed outlier: 3.886A pdb=" N VAL C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C 270 " --> pdb=" O GLY C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 294 removed outlier: 3.542A pdb=" N ARG C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 298 removed outlier: 3.748A pdb=" N GLY C 298 " --> pdb=" O LEU C 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 295 through 298' Processing helix chain 'C' and resid 303 through 331 removed outlier: 4.339A pdb=" N THR C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR C 323 " --> pdb=" O ILE C 319 " (cutoff:3.500A) Proline residue: C 326 - end of helix removed outlier: 3.504A pdb=" N ARG C 330 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 378 Processing helix chain 'C' and resid 381 through 405 removed outlier: 3.531A pdb=" N MET C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 408 No H-bonds generated for 'chain 'C' and resid 406 through 408' Processing helix chain 'C' and resid 416 through 442 removed outlier: 4.030A pdb=" N ARG C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 463 removed outlier: 4.095A pdb=" N MET C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 469 Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 497 through 510 Processing helix chain 'C' and resid 512 through 515 removed outlier: 3.625A pdb=" N ARG C 515 " --> pdb=" O ARG C 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 512 through 515' Processing helix chain 'C' and resid 543 through 546 Processing helix chain 'C' and resid 547 through 559 Processing helix chain 'C' and resid 563 through 572 removed outlier: 3.605A pdb=" N ASP C 572 " --> pdb=" O ILE C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 621 removed outlier: 4.288A pdb=" N ASP C 621 " --> pdb=" O LEU C 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 51 removed outlier: 3.636A pdb=" N LEU B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 62 through 88 removed outlier: 3.665A pdb=" N THR B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 79 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS B 88 " --> pdb=" O TRP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 113 removed outlier: 3.620A pdb=" N MET B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 139 removed outlier: 3.988A pdb=" N ARG B 132 " --> pdb=" O ASP B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 172 removed outlier: 3.534A pdb=" N ILE B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 removed outlier: 3.579A pdb=" N VAL B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 222 removed outlier: 3.555A pdb=" N ALA B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 248 removed outlier: 4.169A pdb=" N ILE B 232 " --> pdb=" O TYR B 228 " (cutoff:3.500A) Proline residue: B 237 - end of helix removed outlier: 4.011A pdb=" N GLY B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 248 " --> pdb=" O TRP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 270 removed outlier: 3.622A pdb=" N VAL B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 294 Processing helix chain 'B' and resid 303 through 320 removed outlier: 3.624A pdb=" N ALA B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.588A pdb=" N ALA B 351 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA B 352 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 378 Processing helix chain 'B' and resid 381 through 405 removed outlier: 3.538A pdb=" N ALA B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 412 through 415 Processing helix chain 'B' and resid 416 through 440 Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 493 through 496 removed outlier: 3.979A pdb=" N LYS B 496 " --> pdb=" O GLY B 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 493 through 496' Processing helix chain 'B' and resid 497 through 510 Processing helix chain 'B' and resid 524 through 529 removed outlier: 3.770A pdb=" N TYR B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 546 Processing helix chain 'B' and resid 547 through 558 Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 563 through 571 Processing sheet with id=AA1, first strand: chain 'C' and resid 532 through 533 removed outlier: 3.683A pdb=" N MET C 584 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 532 through 533 removed outlier: 19.774A pdb=" N VAL B 581 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 16.100A pdb=" N ALA B 597 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N LEU B 583 " --> pdb=" O ARG B 595 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ARG B 595 " --> pdb=" O LEU B 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 532 through 533 588 hydrogen bonds defined for protein. 1719 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: 2.81 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1408 1.32 - 1.44: 2694 1.44 - 1.56: 5389 1.56 - 1.68: 0 1.68 - 1.81: 62 Bond restraints: 9553 Sorted by residual: bond pdb=" CA SER C 224 " pdb=" CB SER C 224 " ideal model delta sigma weight residual 1.530 1.447 0.083 1.58e-02 4.01e+03 2.77e+01 bond pdb=" N GLN B 604 " pdb=" CA GLN B 604 " ideal model delta sigma weight residual 1.462 1.496 -0.034 7.70e-03 1.69e+04 1.95e+01 bond pdb=" CA SER B 361 " pdb=" CB SER B 361 " ideal model delta sigma weight residual 1.530 1.464 0.066 1.93e-02 2.68e+03 1.16e+01 bond pdb=" C TYR B 592 " pdb=" O TYR B 592 " ideal model delta sigma weight residual 1.234 1.196 0.038 1.16e-02 7.43e+03 1.09e+01 bond pdb=" N TYR B 601 " pdb=" CA TYR B 601 " ideal model delta sigma weight residual 1.462 1.487 -0.025 7.70e-03 1.69e+04 1.06e+01 ... (remaining 9548 not shown) Histogram of bond angle deviations from ideal: 95.30 - 103.07: 101 103.07 - 110.85: 3566 110.85 - 118.62: 3920 118.62 - 126.39: 5270 126.39 - 134.16: 216 Bond angle restraints: 13073 Sorted by residual: angle pdb=" N PRO B 605 " pdb=" CA PRO B 605 " pdb=" C PRO B 605 " ideal model delta sigma weight residual 112.47 95.30 17.17 2.06e+00 2.36e-01 6.95e+01 angle pdb=" CA TYR B 601 " pdb=" C TYR B 601 " pdb=" O TYR B 601 " ideal model delta sigma weight residual 119.08 111.61 7.47 9.50e-01 1.11e+00 6.19e+01 angle pdb=" N ARG C 201 " pdb=" CA ARG C 201 " pdb=" C ARG C 201 " ideal model delta sigma weight residual 113.41 105.23 8.18 1.22e+00 6.72e-01 4.49e+01 angle pdb=" CA TYR B 601 " pdb=" C TYR B 601 " pdb=" N PRO B 602 " ideal model delta sigma weight residual 120.52 125.69 -5.17 8.30e-01 1.45e+00 3.87e+01 angle pdb=" N ASN B 606 " pdb=" CA ASN B 606 " pdb=" CB ASN B 606 " ideal model delta sigma weight residual 110.32 100.64 9.68 1.70e+00 3.46e-01 3.24e+01 ... (remaining 13068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5075 17.72 - 35.45: 388 35.45 - 53.17: 72 53.17 - 70.89: 10 70.89 - 88.61: 4 Dihedral angle restraints: 5549 sinusoidal: 2057 harmonic: 3492 Sorted by residual: dihedral pdb=" N ASN B 606 " pdb=" C ASN B 606 " pdb=" CA ASN B 606 " pdb=" CB ASN B 606 " ideal model delta harmonic sigma weight residual 122.80 109.79 13.01 0 2.50e+00 1.60e-01 2.71e+01 dihedral pdb=" CA ALA B 317 " pdb=" C ALA B 317 " pdb=" N ALA B 318 " pdb=" CA ALA B 318 " ideal model delta harmonic sigma weight residual 180.00 155.07 24.93 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" N TRP C 200 " pdb=" C TRP C 200 " pdb=" CA TRP C 200 " pdb=" CB TRP C 200 " ideal model delta harmonic sigma weight residual 122.80 134.65 -11.85 0 2.50e+00 1.60e-01 2.25e+01 ... (remaining 5546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1380 0.080 - 0.161: 134 0.161 - 0.241: 6 0.241 - 0.321: 2 0.321 - 0.402: 5 Chirality restraints: 1527 Sorted by residual: chirality pdb=" CA ASN B 606 " pdb=" N ASN B 606 " pdb=" C ASN B 606 " pdb=" CB ASN B 606 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA TRP C 200 " pdb=" N TRP C 200 " pdb=" C TRP C 200 " pdb=" CB TRP C 200 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA VAL B 600 " pdb=" N VAL B 600 " pdb=" C VAL B 600 " pdb=" CB VAL B 600 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 1524 not shown) Planarity restraints: 1627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 200 " -0.035 2.00e-02 2.50e+03 2.99e-02 2.23e+01 pdb=" CG TRP B 200 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP B 200 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 200 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 200 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 200 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 200 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 155 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C PRO B 155 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO B 155 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE B 156 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 357 " -0.016 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C MET B 357 " 0.059 2.00e-02 2.50e+03 pdb=" O MET B 357 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU B 358 " -0.020 2.00e-02 2.50e+03 ... (remaining 1624 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1822 2.77 - 3.30: 8734 3.30 - 3.83: 15141 3.83 - 4.37: 17613 4.37 - 4.90: 31877 Nonbonded interactions: 75187 Sorted by model distance: nonbonded pdb=" O MET C 402 " pdb=" OG1 THR C 405 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR C 157 " pdb=" OH TYR C 228 " model vdw 2.243 2.440 nonbonded pdb=" O ASP B 514 " pdb=" NE1 TRP B 532 " model vdw 2.285 2.520 nonbonded pdb=" O LEU B 136 " pdb=" OG1 THR B 140 " model vdw 2.318 2.440 nonbonded pdb=" NE1 TRP C 373 " pdb=" OE1 GLU C 434 " model vdw 2.326 2.520 ... (remaining 75182 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 'B' and (resid 21 through 339 or resid 351 through 598 or resid 609 throu \ gh 639 or resid 701)) selection = chain 'C' } 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: 3.070 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: 12.100 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.990 Find NCS groups from input model: 0.550 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.007 0.083 9553 Z= 0.439 Angle : 0.813 17.168 13073 Z= 0.474 Chirality : 0.052 0.402 1527 Planarity : 0.005 0.048 1627 Dihedral : 13.080 88.613 3317 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.27 % 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: -0.00 (0.25), residues: 1210 helix: 1.24 (0.20), residues: 746 sheet: -0.87 (0.74), residues: 54 loop : -2.30 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP B 200 HIS 0.004 0.001 HIS C 540 PHE 0.025 0.002 PHE C 414 TYR 0.044 0.002 TYR B 135 ARG 0.004 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.892 Fit side-chains REVERT: C 415 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7413 (mtp180) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2359 time to fit residues: 31.1638 Evaluate side-chains 79 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9553 Z= 0.223 Angle : 0.594 8.688 13073 Z= 0.299 Chirality : 0.041 0.201 1527 Planarity : 0.005 0.047 1627 Dihedral : 4.456 24.430 1345 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.64 % Allowed : 6.97 % Favored : 92.39 % 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: 0.59 (0.26), residues: 1210 helix: 1.71 (0.20), residues: 750 sheet: -0.77 (0.73), residues: 54 loop : -2.07 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 200 HIS 0.003 0.001 HIS C 540 PHE 0.013 0.001 PHE C 267 TYR 0.022 0.001 TYR B 135 ARG 0.003 0.000 ARG C 615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 1.091 Fit side-chains REVERT: C 415 ARG cc_start: 0.7496 (mtp85) cc_final: 0.7218 (mtp180) REVERT: B 573 LYS cc_start: 0.8848 (ttmm) cc_final: 0.8645 (ttmm) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 0.2339 time to fit residues: 28.9543 Evaluate side-chains 85 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 37 optimal weight: 0.0470 chunk 88 optimal weight: 0.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9553 Z= 0.170 Angle : 0.549 8.004 13073 Z= 0.273 Chirality : 0.040 0.168 1527 Planarity : 0.004 0.042 1627 Dihedral : 4.167 24.213 1345 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.18 % Allowed : 10.83 % Favored : 88.00 % 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: 0.97 (0.26), residues: 1210 helix: 1.99 (0.20), residues: 754 sheet: -0.66 (0.71), residues: 54 loop : -1.89 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 200 HIS 0.005 0.001 HIS C 540 PHE 0.011 0.001 PHE C 267 TYR 0.014 0.001 TYR B 135 ARG 0.002 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.992 Fit side-chains REVERT: B 573 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8649 (ttmm) outliers start: 11 outliers final: 4 residues processed: 96 average time/residue: 0.2102 time to fit residues: 28.8789 Evaluate side-chains 87 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9990 chunk 82 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 0.0570 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 0.0070 chunk 97 optimal weight: 0.8980 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9553 Z= 0.144 Angle : 0.534 7.623 13073 Z= 0.264 Chirality : 0.039 0.159 1527 Planarity : 0.004 0.042 1627 Dihedral : 3.961 23.856 1345 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.07 % Allowed : 11.79 % Favored : 87.14 % 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: 1.27 (0.26), residues: 1210 helix: 2.23 (0.20), residues: 752 sheet: -0.59 (0.70), residues: 54 loop : -1.75 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 PHE 0.011 0.001 PHE C 131 TYR 0.010 0.001 TYR B 135 ARG 0.002 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.092 Fit side-chains REVERT: C 23 ARG cc_start: 0.7161 (mmm-85) cc_final: 0.6836 (mpp-170) REVERT: C 441 LYS cc_start: 0.8380 (mmmt) cc_final: 0.7975 (mtmt) REVERT: C 522 ASP cc_start: 0.7957 (p0) cc_final: 0.7636 (p0) REVERT: B 459 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8079 (mp) outliers start: 10 outliers final: 5 residues processed: 106 average time/residue: 0.2130 time to fit residues: 32.3065 Evaluate side-chains 99 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 0.0370 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 GLN ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS B 535 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9553 Z= 0.329 Angle : 0.611 8.880 13073 Z= 0.303 Chirality : 0.043 0.201 1527 Planarity : 0.005 0.045 1627 Dihedral : 4.222 24.317 1345 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.39 % Allowed : 12.86 % Favored : 85.74 % 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 (0.26), residues: 1210 helix: 1.96 (0.20), residues: 754 sheet: -0.48 (0.73), residues: 54 loop : -1.81 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 PHE 0.016 0.002 PHE C 131 TYR 0.033 0.002 TYR B 135 ARG 0.003 0.000 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.954 Fit side-chains REVERT: C 23 ARG cc_start: 0.7261 (mmm-85) cc_final: 0.6915 (mpp-170) REVERT: C 441 LYS cc_start: 0.8408 (mmmt) cc_final: 0.7947 (mtmt) REVERT: C 522 ASP cc_start: 0.8072 (p0) cc_final: 0.7742 (p0) outliers start: 13 outliers final: 11 residues processed: 98 average time/residue: 0.2281 time to fit residues: 31.6039 Evaluate side-chains 96 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 0.0670 chunk 117 optimal weight: 0.0970 chunk 97 optimal weight: 0.3980 chunk 54 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.0770 chunk 112 optimal weight: 0.8980 overall best weight: 0.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9553 Z= 0.139 Angle : 0.527 7.587 13073 Z= 0.263 Chirality : 0.039 0.186 1527 Planarity : 0.004 0.046 1627 Dihedral : 3.940 23.779 1345 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.75 % Allowed : 13.29 % Favored : 85.96 % 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: 1.38 (0.26), residues: 1210 helix: 2.31 (0.20), residues: 752 sheet: -0.64 (0.70), residues: 56 loop : -1.69 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 200 HIS 0.004 0.001 HIS C 540 PHE 0.011 0.001 PHE B 267 TYR 0.009 0.001 TYR B 150 ARG 0.002 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.995 Fit side-chains REVERT: C 23 ARG cc_start: 0.7120 (mmm-85) cc_final: 0.6735 (mpp-170) REVERT: C 441 LYS cc_start: 0.8311 (mmmt) cc_final: 0.8052 (ttmt) REVERT: C 522 ASP cc_start: 0.7990 (p0) cc_final: 0.7578 (p0) outliers start: 7 outliers final: 6 residues processed: 98 average time/residue: 0.2238 time to fit residues: 31.5449 Evaluate side-chains 96 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.6980 chunk 66 optimal weight: 0.3980 chunk 85 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 71 optimal weight: 0.0670 chunk 53 optimal weight: 0.0980 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9553 Z= 0.147 Angle : 0.520 7.531 13073 Z= 0.257 Chirality : 0.039 0.163 1527 Planarity : 0.004 0.046 1627 Dihedral : 3.785 23.763 1345 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.18 % Allowed : 13.50 % Favored : 85.32 % 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: 1.58 (0.26), residues: 1210 helix: 2.47 (0.19), residues: 753 sheet: -0.60 (0.71), residues: 57 loop : -1.62 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 200 HIS 0.004 0.001 HIS C 540 PHE 0.012 0.001 PHE C 131 TYR 0.010 0.001 TYR B 135 ARG 0.001 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.848 Fit side-chains REVERT: C 23 ARG cc_start: 0.7129 (mmm-85) cc_final: 0.6745 (mpp-170) REVERT: C 441 LYS cc_start: 0.8292 (mmmt) cc_final: 0.8088 (ttmt) REVERT: B 459 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8040 (mp) outliers start: 11 outliers final: 8 residues processed: 106 average time/residue: 0.2278 time to fit residues: 34.1329 Evaluate side-chains 105 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 101 optimal weight: 0.0000 chunk 108 optimal weight: 0.1980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9553 Z= 0.179 Angle : 0.539 7.545 13073 Z= 0.265 Chirality : 0.040 0.178 1527 Planarity : 0.004 0.048 1627 Dihedral : 3.814 23.622 1345 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.18 % Allowed : 14.15 % Favored : 84.67 % 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: 1.62 (0.26), residues: 1210 helix: 2.49 (0.19), residues: 752 sheet: -0.57 (0.71), residues: 57 loop : -1.55 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 PHE 0.012 0.001 PHE C 131 TYR 0.014 0.001 TYR B 135 ARG 0.002 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.093 Fit side-chains REVERT: C 23 ARG cc_start: 0.7157 (mmm-85) cc_final: 0.6766 (mpp-170) REVERT: C 441 LYS cc_start: 0.8323 (mmmt) cc_final: 0.8112 (ttmt) REVERT: C 522 ASP cc_start: 0.7813 (p0) cc_final: 0.7398 (p0) outliers start: 11 outliers final: 8 residues processed: 104 average time/residue: 0.2313 time to fit residues: 33.5457 Evaluate side-chains 102 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 549 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 114 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9553 Z= 0.175 Angle : 0.542 7.871 13073 Z= 0.267 Chirality : 0.040 0.176 1527 Planarity : 0.004 0.049 1627 Dihedral : 3.795 23.649 1345 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.07 % Allowed : 14.47 % Favored : 84.46 % 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: 1.65 (0.26), residues: 1210 helix: 2.51 (0.19), residues: 752 sheet: -0.57 (0.71), residues: 57 loop : -1.55 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 200 HIS 0.004 0.001 HIS C 540 PHE 0.011 0.001 PHE C 131 TYR 0.014 0.001 TYR B 135 ARG 0.002 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.068 Fit side-chains REVERT: C 23 ARG cc_start: 0.7143 (mmm-85) cc_final: 0.6751 (mpp-170) outliers start: 10 outliers final: 10 residues processed: 104 average time/residue: 0.2212 time to fit residues: 32.4851 Evaluate side-chains 105 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 0.0770 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9553 Z= 0.207 Angle : 0.561 7.801 13073 Z= 0.276 Chirality : 0.040 0.186 1527 Planarity : 0.004 0.051 1627 Dihedral : 3.849 23.726 1345 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.29 % Allowed : 14.47 % Favored : 84.24 % 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: 1.53 (0.26), residues: 1210 helix: 2.40 (0.19), residues: 760 sheet: -0.57 (0.71), residues: 57 loop : -1.67 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 PHE 0.012 0.001 PHE C 131 TYR 0.016 0.001 TYR B 135 ARG 0.002 0.000 ARG C 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.975 Fit side-chains REVERT: C 23 ARG cc_start: 0.7149 (mmm-85) cc_final: 0.6767 (mpp-170) outliers start: 12 outliers final: 12 residues processed: 101 average time/residue: 0.2166 time to fit residues: 31.0699 Evaluate side-chains 104 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.128287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.103399 restraints weight = 12308.108| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.05 r_work: 0.3249 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9553 Z= 0.207 Angle : 0.563 8.883 13073 Z= 0.276 Chirality : 0.040 0.184 1527 Planarity : 0.004 0.051 1627 Dihedral : 3.865 23.732 1345 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.29 % Allowed : 14.26 % Favored : 84.46 % 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: 1.53 (0.26), residues: 1210 helix: 2.41 (0.19), residues: 760 sheet: -0.63 (0.71), residues: 57 loop : -1.66 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 PHE 0.012 0.001 PHE C 131 TYR 0.017 0.001 TYR B 135 ARG 0.002 0.000 ARG C 415 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2168.24 seconds wall clock time: 39 minutes 51.31 seconds (2391.31 seconds total)