Starting phenix.real_space_refine on Sat Aug 3 05:54:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6o_37330/08_2024/8w6o_37330.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6o_37330/08_2024/8w6o_37330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6o_37330/08_2024/8w6o_37330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6o_37330/08_2024/8w6o_37330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6o_37330/08_2024/8w6o_37330.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6o_37330/08_2024/8w6o_37330.cif" } resolution = 2.9 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= -0.004 sd= 0.143 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 S 50 5.16 5 Na 4 4.78 5 C 4823 2.51 5 N 1076 2.21 5 O 1194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 11": "NH1" <-> "NH2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7147 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3497 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 27, 'TRANS': 420} Chain breaks: 5 Chain: "B" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3590 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 28, 'TRANS': 430} Chain breaks: 5 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' NA': 2, 'CLR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' NA': 2, 'CLR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.32, per 1000 atoms: 0.60 Number of scatterers: 7147 At special positions: 0 Unit cell: (82.612, 94.569, 78.264, 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) S 50 16.00 Na 4 11.00 O 1194 8.00 N 1076 7.00 C 4823 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: 2.84 Conformation dependent library (CDL) restraints added in 1.3 seconds 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 1 sheets defined 73.3% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.815A pdb=" N VAL A 17 " --> pdb=" O PHE A 13 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 19 " --> pdb=" O PHE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 51 removed outlier: 3.664A pdb=" N CYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TYR A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 Proline residue: A 67 - end of helix removed outlier: 3.607A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 102 removed outlier: 3.677A pdb=" N SER A 98 " --> pdb=" O CYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.690A pdb=" N THR A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 159 removed outlier: 3.847A pdb=" N MET A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 233 through 252 removed outlier: 4.079A pdb=" N ARG A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.534A pdb=" N PHE A 265 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 308 removed outlier: 3.590A pdb=" N PHE A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.581A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 344 through 362 removed outlier: 3.559A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 392 removed outlier: 3.628A pdb=" N VAL A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 396 Processing helix chain 'A' and resid 423 through 431 removed outlier: 3.548A pdb=" N PHE A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.012A pdb=" N ILE A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 removed outlier: 3.867A pdb=" N TRP A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.670A pdb=" N GLY A 466 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 467 " --> pdb=" O PRO A 464 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 468 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.534A pdb=" N ILE A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A 480 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 485 " --> pdb=" O VAL A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 508 removed outlier: 3.613A pdb=" N ILE A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Proline residue: A 499 - end of helix Proline residue: A 503 - end of helix removed outlier: 3.681A pdb=" N GLU A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 523 removed outlier: 3.643A pdb=" N ILE A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) Proline residue: A 518 - end of helix Processing helix chain 'A' and resid 533 through 539 removed outlier: 3.569A pdb=" N ALA A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 572 removed outlier: 3.576A pdb=" N MET A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.528A pdb=" N PHE A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 21 removed outlier: 3.929A pdb=" N VAL B 17 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR B 19 " --> pdb=" O PHE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 51 removed outlier: 3.507A pdb=" N GLU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 Proline residue: B 67 - end of helix Processing helix chain 'B' and resid 83 through 102 removed outlier: 3.615A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 98 " --> pdb=" O CYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.935A pdb=" N ARG B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 135 removed outlier: 3.893A pdb=" N LEU B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 160 removed outlier: 3.734A pdb=" N MET B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 233 through 252 removed outlier: 4.109A pdb=" N ARG B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 238 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 273 removed outlier: 3.574A pdb=" N PHE B 265 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 308 removed outlier: 3.598A pdb=" N PHE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Proline residue: B 290 - end of helix removed outlier: 3.562A pdb=" N ILE B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 362 removed outlier: 3.558A pdb=" N VAL B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.802A pdb=" N VAL B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 431 Processing helix chain 'B' and resid 433 through 452 removed outlier: 4.059A pdb=" N ILE B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 removed outlier: 4.101A pdb=" N TRP B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 467 removed outlier: 3.706A pdb=" N GLY B 466 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 467 " --> pdb=" O PRO B 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 463 through 467' Processing helix chain 'B' and resid 469 through 485 Processing helix chain 'B' and resid 489 through 508 removed outlier: 3.585A pdb=" N ILE B 494 " --> pdb=" O ASN B 490 " (cutoff:3.500A) Proline residue: B 499 - end of helix Proline residue: B 503 - end of helix Processing helix chain 'B' and resid 511 through 523 removed outlier: 3.684A pdb=" N ILE B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 516 " --> pdb=" O PRO B 512 " (cutoff:3.500A) Proline residue: B 518 - end of helix removed outlier: 3.554A pdb=" N LEU B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 539 removed outlier: 3.553A pdb=" N ALA B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 572 removed outlier: 4.225A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS B 570 " --> pdb=" O MET B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.503A pdb=" N PHE B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 401 removed outlier: 4.726A pdb=" N SER A 419 " --> pdb=" O ALA A 401 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1113 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: 1.97 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1935 1.34 - 1.46: 1350 1.46 - 1.57: 3982 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 7349 Sorted by residual: bond pdb=" C PRO B 534 " pdb=" N PRO B 535 " ideal model delta sigma weight residual 1.334 1.367 -0.033 1.51e-02 4.39e+03 4.66e+00 bond pdb=" C PRO A 534 " pdb=" N PRO A 535 " ideal model delta sigma weight residual 1.334 1.364 -0.030 1.51e-02 4.39e+03 4.02e+00 bond pdb=" C LEU A 26 " pdb=" N PRO A 27 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.66e+00 bond pdb=" C LEU B 24 " pdb=" N PRO B 25 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.59e+00 bond pdb=" C LEU A 24 " pdb=" N PRO A 25 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.53e+00 ... (remaining 7344 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.96: 308 106.96 - 113.73: 4176 113.73 - 120.51: 3002 120.51 - 127.28: 2450 127.28 - 134.06: 124 Bond angle restraints: 10060 Sorted by residual: angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 111.81 107.36 4.45 8.60e-01 1.35e+00 2.68e+01 angle pdb=" N GLU A 36 " pdb=" CA GLU A 36 " pdb=" C GLU A 36 " ideal model delta sigma weight residual 114.56 108.13 6.43 1.27e+00 6.20e-01 2.56e+01 angle pdb=" N TYR B 379 " pdb=" CA TYR B 379 " pdb=" C TYR B 379 " ideal model delta sigma weight residual 109.81 119.72 -9.91 2.21e+00 2.05e-01 2.01e+01 angle pdb=" N PRO A 534 " pdb=" CA PRO A 534 " pdb=" C PRO A 534 " ideal model delta sigma weight residual 110.70 116.05 -5.35 1.22e+00 6.72e-01 1.92e+01 angle pdb=" C VAL A 118 " pdb=" N ASN A 119 " pdb=" CA ASN A 119 " ideal model delta sigma weight residual 121.80 132.49 -10.69 2.44e+00 1.68e-01 1.92e+01 ... (remaining 10055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 3968 17.83 - 35.66: 328 35.66 - 53.48: 47 53.48 - 71.31: 6 71.31 - 89.14: 3 Dihedral angle restraints: 4352 sinusoidal: 1718 harmonic: 2634 Sorted by residual: dihedral pdb=" CA ASN B 119 " pdb=" C ASN B 119 " pdb=" N PRO B 120 " pdb=" CA PRO B 120 " ideal model delta harmonic sigma weight residual 180.00 136.33 43.67 0 5.00e+00 4.00e-02 7.63e+01 dihedral pdb=" CA ALA A 121 " pdb=" C ALA A 121 " pdb=" N TRP A 122 " pdb=" CA TRP A 122 " ideal model delta harmonic sigma weight residual -180.00 -145.39 -34.61 0 5.00e+00 4.00e-02 4.79e+01 dihedral pdb=" CA PRO B 27 " pdb=" C PRO B 27 " pdb=" N ILE B 28 " pdb=" CA ILE B 28 " ideal model delta harmonic sigma weight residual 180.00 147.24 32.76 0 5.00e+00 4.00e-02 4.29e+01 ... (remaining 4349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 995 0.068 - 0.136: 211 0.136 - 0.205: 27 0.205 - 0.273: 0 0.273 - 0.341: 1 Chirality restraints: 1234 Sorted by residual: chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA SER A 502 " pdb=" N SER A 502 " pdb=" C SER A 502 " pdb=" CB SER A 502 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CB ILE B 343 " pdb=" CA ILE B 343 " pdb=" CG1 ILE B 343 " pdb=" CG2 ILE B 343 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 1231 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " 0.081 5.00e-02 4.00e+02 1.23e-01 2.40e+01 pdb=" N PRO A 27 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 26 " -0.079 5.00e-02 4.00e+02 1.20e-01 2.32e+01 pdb=" N PRO B 27 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 534 " -0.062 5.00e-02 4.00e+02 9.17e-02 1.35e+01 pdb=" N PRO B 535 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO B 535 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 535 " -0.051 5.00e-02 4.00e+02 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1494 2.78 - 3.31: 6490 3.31 - 3.84: 11635 3.84 - 4.37: 14042 4.37 - 4.90: 24547 Nonbonded interactions: 58208 Sorted by model distance: nonbonded pdb=" O CYS B 243 " pdb=" OG SER B 247 " model vdw 2.246 3.040 nonbonded pdb=" O CYS A 243 " pdb=" OG SER A 247 " model vdw 2.259 3.040 nonbonded pdb=" O LEU B 567 " pdb=" OG1 THR B 571 " model vdw 2.280 3.040 nonbonded pdb=" O LEU A 567 " pdb=" OG1 THR A 571 " model vdw 2.284 3.040 nonbonded pdb=" O SER A 519 " pdb=" OG1 THR A 523 " model vdw 2.304 3.040 ... (remaining 58203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 11 through 73 or resid 83 through 159 or resid 232 through \ 363 or resid 382 through 405 or resid 416 through 587 or resid 701 through 703) \ ) } 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: 0.010 Normalize map: mean=0, sd=1: 0.720 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.800 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 0.061 7349 Z= 0.334 Angle : 1.037 10.693 10060 Z= 0.551 Chirality : 0.055 0.341 1234 Planarity : 0.011 0.123 1176 Dihedral : 13.102 89.139 2636 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.57 % Favored : 92.98 % Rotamer: Outliers : 0.13 % Allowed : 7.13 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.36 % 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: -4.81 (0.21), residues: 883 helix: -2.70 (0.14), residues: 624 sheet: None (None), residues: 0 loop : -4.00 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 122 HIS 0.013 0.003 HIS B 105 PHE 0.022 0.002 PHE A 287 TYR 0.016 0.002 TYR B 39 ARG 0.002 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.810 Fit side-chains REVERT: A 72 MET cc_start: 0.6259 (mmm) cc_final: 0.5676 (mpt) REVERT: A 232 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7987 (tttp) REVERT: B 72 MET cc_start: 0.6438 (mmt) cc_final: 0.6171 (mpt) REVERT: B 552 LYS cc_start: 0.7643 (tptt) cc_final: 0.7116 (ttpt) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 1.0951 time to fit residues: 154.1085 Evaluate side-chains 102 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 HIS A 338 GLN A 558 ASN B 119 ASN B 156 GLN B 234 HIS B 338 GLN B 558 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7349 Z= 0.208 Angle : 0.720 10.120 10060 Z= 0.360 Chirality : 0.044 0.227 1234 Planarity : 0.008 0.111 1176 Dihedral : 5.617 37.071 1063 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.91 % Favored : 92.98 % Rotamer: Outliers : 1.91 % Allowed : 12.36 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.24 % 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: -2.24 (0.27), residues: 883 helix: -0.67 (0.19), residues: 635 sheet: None (None), residues: 0 loop : -3.51 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 572 HIS 0.008 0.002 HIS B 105 PHE 0.011 0.001 PHE B 15 TYR 0.014 0.001 TYR A 418 ARG 0.003 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.809 Fit side-chains REVERT: A 72 MET cc_start: 0.6168 (mmm) cc_final: 0.5665 (mpt) REVERT: A 232 LYS cc_start: 0.8224 (ttmm) cc_final: 0.7928 (tttp) REVERT: B 378 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6549 (pm20) REVERT: B 390 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8373 (mt) REVERT: B 552 LYS cc_start: 0.7600 (tptt) cc_final: 0.7239 (mtpt) outliers start: 15 outliers final: 4 residues processed: 113 average time/residue: 1.1229 time to fit residues: 134.4265 Evaluate side-chains 103 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 0.0570 chunk 80 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 0.0040 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.3910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 HIS A 338 GLN B 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7349 Z= 0.167 Angle : 0.672 11.374 10060 Z= 0.332 Chirality : 0.042 0.240 1234 Planarity : 0.007 0.105 1176 Dihedral : 5.178 35.551 1063 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.34 % Favored : 93.54 % Rotamer: Outliers : 1.91 % Allowed : 13.89 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.29), residues: 883 helix: 0.27 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -3.23 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 572 HIS 0.007 0.001 HIS B 31 PHE 0.009 0.001 PHE B 15 TYR 0.017 0.001 TYR A 418 ARG 0.006 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 0.807 Fit side-chains REVERT: A 72 MET cc_start: 0.6156 (mmm) cc_final: 0.5656 (mpt) REVERT: A 232 LYS cc_start: 0.8146 (ttmm) cc_final: 0.7822 (tttp) REVERT: B 378 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6477 (pm20) REVERT: B 552 LYS cc_start: 0.7424 (tptt) cc_final: 0.7176 (mtpt) outliers start: 15 outliers final: 4 residues processed: 115 average time/residue: 1.0811 time to fit residues: 131.9537 Evaluate side-chains 101 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 378 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 0.0030 chunk 81 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7349 Z= 0.193 Angle : 0.677 12.565 10060 Z= 0.335 Chirality : 0.043 0.241 1234 Planarity : 0.007 0.104 1176 Dihedral : 5.123 35.331 1063 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 2.42 % Allowed : 14.78 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.63 (0.30), residues: 883 helix: 0.58 (0.22), residues: 634 sheet: None (None), residues: 0 loop : -3.07 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 572 HIS 0.007 0.002 HIS B 31 PHE 0.011 0.001 PHE B 15 TYR 0.017 0.001 TYR A 418 ARG 0.004 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.764 Fit side-chains REVERT: A 72 MET cc_start: 0.6067 (mmm) cc_final: 0.5582 (mpt) REVERT: A 232 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7820 (tttp) REVERT: A 338 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6179 (mp-120) REVERT: B 378 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6465 (pm20) REVERT: B 390 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8356 (mt) REVERT: B 552 LYS cc_start: 0.7515 (tptt) cc_final: 0.7086 (ttpt) outliers start: 19 outliers final: 9 residues processed: 113 average time/residue: 1.1168 time to fit residues: 134.0343 Evaluate side-chains 110 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7349 Z= 0.166 Angle : 0.644 10.401 10060 Z= 0.319 Chirality : 0.042 0.235 1234 Planarity : 0.007 0.102 1176 Dihedral : 4.905 34.754 1063 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.57 % Favored : 93.32 % Rotamer: Outliers : 2.29 % Allowed : 15.92 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.33 (0.31), residues: 883 helix: 0.84 (0.22), residues: 630 sheet: None (None), residues: 0 loop : -2.98 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.008 0.001 HIS B 31 PHE 0.010 0.001 PHE B 15 TYR 0.016 0.001 TYR A 418 ARG 0.004 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.824 Fit side-chains REVERT: A 72 MET cc_start: 0.6033 (mmm) cc_final: 0.5559 (mpt) REVERT: A 232 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7697 (tptp) REVERT: A 338 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6109 (mp-120) REVERT: B 128 MET cc_start: 0.9096 (mtp) cc_final: 0.8846 (mtp) REVERT: B 378 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6303 (pm20) REVERT: B 390 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8325 (mt) REVERT: B 552 LYS cc_start: 0.7482 (tptt) cc_final: 0.7082 (ttpt) outliers start: 18 outliers final: 10 residues processed: 121 average time/residue: 0.9825 time to fit residues: 126.5959 Evaluate side-chains 111 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 428 GLN B 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7349 Z= 0.288 Angle : 0.735 10.132 10060 Z= 0.366 Chirality : 0.047 0.245 1234 Planarity : 0.007 0.105 1176 Dihedral : 5.334 34.827 1063 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % Rotamer: Outliers : 3.18 % Allowed : 16.18 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.24 % 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: -0.41 (0.30), residues: 883 helix: 0.76 (0.22), residues: 632 sheet: None (None), residues: 0 loop : -3.00 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 585 HIS 0.008 0.002 HIS A 105 PHE 0.016 0.002 PHE A 15 TYR 0.019 0.002 TYR B 418 ARG 0.003 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.748 Fit side-chains REVERT: A 72 MET cc_start: 0.6140 (mmm) cc_final: 0.5659 (mpt) REVERT: A 338 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6269 (mp-120) REVERT: B 128 MET cc_start: 0.9090 (mtp) cc_final: 0.8772 (mtp) REVERT: B 378 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6399 (pm20) REVERT: B 552 LYS cc_start: 0.7622 (tptt) cc_final: 0.7142 (ttpt) outliers start: 25 outliers final: 15 residues processed: 110 average time/residue: 1.0333 time to fit residues: 120.9716 Evaluate side-chains 103 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 452 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.0570 chunk 72 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 0.0670 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 HIS B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7349 Z= 0.181 Angle : 0.661 11.093 10060 Z= 0.328 Chirality : 0.043 0.235 1234 Planarity : 0.007 0.102 1176 Dihedral : 5.044 33.985 1063 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.46 % Favored : 93.43 % Rotamer: Outliers : 2.42 % Allowed : 17.07 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.18 (0.31), residues: 883 helix: 0.95 (0.22), residues: 627 sheet: None (None), residues: 0 loop : -2.89 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.008 0.001 HIS B 31 PHE 0.011 0.001 PHE B 15 TYR 0.020 0.001 TYR B 418 ARG 0.003 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.750 Fit side-chains REVERT: A 72 MET cc_start: 0.5984 (mmm) cc_final: 0.5615 (mpt) REVERT: A 232 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7596 (tptp) REVERT: A 338 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6234 (mp-120) REVERT: B 128 MET cc_start: 0.9104 (mtp) cc_final: 0.8604 (mtp) REVERT: B 552 LYS cc_start: 0.7523 (tptt) cc_final: 0.7072 (ttpt) outliers start: 19 outliers final: 13 residues processed: 112 average time/residue: 1.0349 time to fit residues: 123.3905 Evaluate side-chains 108 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 HIS B 156 GLN B 346 GLN B 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7349 Z= 0.202 Angle : 0.676 9.907 10060 Z= 0.337 Chirality : 0.044 0.238 1234 Planarity : 0.007 0.103 1176 Dihedral : 5.039 33.513 1063 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.25 % Favored : 92.64 % Rotamer: Outliers : 2.93 % Allowed : 16.82 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.31), residues: 883 helix: 0.93 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -2.89 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 585 HIS 0.008 0.001 HIS B 31 PHE 0.012 0.001 PHE B 15 TYR 0.021 0.002 TYR B 418 ARG 0.003 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 0.723 Fit side-chains REVERT: A 72 MET cc_start: 0.5964 (mmm) cc_final: 0.5606 (mpt) REVERT: A 338 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6222 (mp-120) REVERT: B 275 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: B 552 LYS cc_start: 0.7531 (tptt) cc_final: 0.7084 (ttpt) outliers start: 23 outliers final: 16 residues processed: 108 average time/residue: 0.9729 time to fit residues: 112.1435 Evaluate side-chains 110 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 452 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 HIS B 156 GLN B 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7349 Z= 0.214 Angle : 0.685 9.100 10060 Z= 0.341 Chirality : 0.044 0.236 1234 Planarity : 0.007 0.102 1176 Dihedral : 5.100 33.708 1063 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 3.18 % Allowed : 16.18 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.16 (0.31), residues: 883 helix: 0.93 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -2.89 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 585 HIS 0.008 0.001 HIS B 31 PHE 0.012 0.001 PHE B 15 TYR 0.019 0.002 TYR B 418 ARG 0.003 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 1.887 Fit side-chains REVERT: A 72 MET cc_start: 0.5955 (mmm) cc_final: 0.5617 (mpt) REVERT: A 232 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7654 (tptp) REVERT: A 338 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6234 (mp-120) REVERT: B 275 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: B 552 LYS cc_start: 0.7543 (tptt) cc_final: 0.7091 (ttpt) outliers start: 25 outliers final: 16 residues processed: 109 average time/residue: 1.1127 time to fit residues: 130.1047 Evaluate side-chains 108 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 539 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.0030 chunk 81 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 HIS B 156 GLN B 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7349 Z= 0.188 Angle : 0.665 8.085 10060 Z= 0.333 Chirality : 0.043 0.235 1234 Planarity : 0.007 0.102 1176 Dihedral : 4.987 33.220 1063 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 2.68 % Allowed : 16.69 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.09 (0.31), residues: 883 helix: 0.98 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -2.85 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 572 HIS 0.007 0.001 HIS B 31 PHE 0.011 0.001 PHE B 15 TYR 0.019 0.001 TYR B 418 ARG 0.002 0.000 ARG A 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 0.705 Fit side-chains REVERT: A 17 VAL cc_start: 0.8429 (m) cc_final: 0.8185 (t) REVERT: A 72 MET cc_start: 0.5901 (mmm) cc_final: 0.5598 (mpt) REVERT: A 232 LYS cc_start: 0.8081 (ttmm) cc_final: 0.7561 (tptt) REVERT: A 338 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6234 (mp-120) REVERT: B 275 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: B 390 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8418 (mt) REVERT: B 552 LYS cc_start: 0.7517 (tptt) cc_final: 0.7072 (ttpt) outliers start: 21 outliers final: 16 residues processed: 107 average time/residue: 1.0384 time to fit residues: 118.1522 Evaluate side-chains 109 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 539 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 HIS B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.145753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.133058 restraints weight = 8475.659| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 0.82 r_work: 0.3392 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7349 Z= 0.213 Angle : 0.685 8.701 10060 Z= 0.343 Chirality : 0.045 0.234 1234 Planarity : 0.007 0.102 1176 Dihedral : 5.080 33.071 1063 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.25 % Favored : 92.64 % Rotamer: Outliers : 2.93 % Allowed : 16.56 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.13 (0.31), residues: 883 helix: 0.98 (0.22), residues: 627 sheet: None (None), residues: 0 loop : -2.86 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 585 HIS 0.008 0.001 HIS B 31 PHE 0.013 0.001 PHE B 15 TYR 0.018 0.002 TYR B 418 ARG 0.002 0.000 ARG A 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2676.66 seconds wall clock time: 47 minutes 49.75 seconds (2869.75 seconds total)