Starting phenix.real_space_refine on Thu Mar 14 16:04:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvd_4649/03_2024/6qvd_4649.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvd_4649/03_2024/6qvd_4649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvd_4649/03_2024/6qvd_4649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvd_4649/03_2024/6qvd_4649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvd_4649/03_2024/6qvd_4649.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvd_4649/03_2024/6qvd_4649.pdb" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6094 2.51 5 N 1472 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 199": "NH1" <-> "NH2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 626": "NH1" <-> "NH2" Residue "B PHE 826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 858": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A PHE 826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 858": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9212 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4606 Classifications: {'peptide': 596} Link IDs: {'CIS': 2, 'PTRANS': 26, 'TRANS': 567} Chain breaks: 2 Chain: "A" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4606 Classifications: {'peptide': 596} Link IDs: {'CIS': 2, 'PTRANS': 26, 'TRANS': 567} Chain breaks: 2 Time building chain proxies: 5.10, per 1000 atoms: 0.55 Number of scatterers: 9212 At special positions: 0 Unit cell: (101.65, 95.23, 108.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1576 8.00 N 1472 7.00 C 6094 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: 3.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 66.7% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'B' and resid 115 through 154 removed outlier: 4.768A pdb=" N GLN B 154 " --> pdb=" O TYR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 181 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 190 through 199 removed outlier: 4.359A pdb=" N MET B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 208 through 225 removed outlier: 3.785A pdb=" N PHE B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 213 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 removed outlier: 3.614A pdb=" N PHE B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 280 removed outlier: 3.582A pdb=" N GLY B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 298 through 323 removed outlier: 4.103A pdb=" N ARG B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 377 removed outlier: 3.572A pdb=" N PHE B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 375 " --> pdb=" O GLN B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 removed outlier: 3.791A pdb=" N SER B 383 " --> pdb=" O HIS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 403 removed outlier: 4.557A pdb=" N GLY B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.571A pdb=" N ALA B 447 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 450 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 477 removed outlier: 3.503A pdb=" N ILE B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 472 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 473 " --> pdb=" O TRP B 469 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET B 477 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 506 Processing helix chain 'B' and resid 521 through 538 removed outlier: 4.572A pdb=" N THR B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.948A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 574 Processing helix chain 'B' and resid 576 through 585 Processing helix chain 'B' and resid 621 through 632 Processing helix chain 'B' and resid 654 through 666 Processing helix chain 'B' and resid 833 through 845 Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'A' and resid 116 through 154 removed outlier: 4.768A pdb=" N GLN A 154 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 181 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 190 through 199 removed outlier: 4.360A pdb=" N MET A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 208 through 225 removed outlier: 3.784A pdb=" N PHE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.613A pdb=" N PHE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 280 removed outlier: 3.581A pdb=" N GLY A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 298 through 323 removed outlier: 4.102A pdb=" N ARG A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 377 removed outlier: 3.572A pdb=" N PHE A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 353 " --> pdb=" O PRO A 349 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.792A pdb=" N SER A 383 " --> pdb=" O HIS A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 403 removed outlier: 4.557A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.570A pdb=" N ALA A 447 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 450 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 removed outlier: 3.504A pdb=" N ILE A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 472 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 473 " --> pdb=" O TRP A 469 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 477 " --> pdb=" O VAL A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 506 Processing helix chain 'A' and resid 521 through 538 removed outlier: 4.572A pdb=" N THR A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 3.949A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 574 Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'A' and resid 621 through 632 Processing helix chain 'A' and resid 654 through 666 Processing helix chain 'A' and resid 833 through 845 Processing helix chain 'A' and resid 862 through 871 Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512 Processing sheet with id=AA2, first strand: chain 'B' and resid 636 through 640 removed outlier: 5.569A pdb=" N LEU B 637 " --> pdb=" O SER B 651 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 651 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 639 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 651 " --> pdb=" O ASP B 822 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP B 822 " --> pdb=" O SER B 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853 removed outlier: 6.553A pdb=" N ALA B 849 " --> pdb=" O VAL B 860 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 860 " --> pdb=" O ALA B 849 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 851 " --> pdb=" O ARG B 858 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA5, first strand: chain 'A' and resid 636 through 640 removed outlier: 5.569A pdb=" N LEU A 637 " --> pdb=" O SER A 651 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 651 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 639 " --> pdb=" O LEU A 649 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 651 " --> pdb=" O ASP A 822 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP A 822 " --> pdb=" O SER A 651 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853 removed outlier: 6.553A pdb=" N ALA A 849 " --> pdb=" O VAL A 860 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 860 " --> pdb=" O ALA A 849 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 851 " --> pdb=" O ARG A 858 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1623 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: 2.57 Time building geometry restraints manager: 3.80 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: 1631 1.32 - 1.45: 2434 1.45 - 1.57: 5257 1.57 - 1.69: 4 1.69 - 1.81: 116 Bond restraints: 9442 Sorted by residual: bond pdb=" CB LYS B 518 " pdb=" CG LYS B 518 " ideal model delta sigma weight residual 1.520 1.628 -0.108 3.00e-02 1.11e+03 1.29e+01 bond pdb=" CB LYS A 518 " pdb=" CG LYS A 518 " ideal model delta sigma weight residual 1.520 1.628 -0.108 3.00e-02 1.11e+03 1.29e+01 bond pdb=" CG1 ILE B 516 " pdb=" CD1 ILE B 516 " ideal model delta sigma weight residual 1.513 1.409 0.104 3.90e-02 6.57e+02 7.12e+00 bond pdb=" CG1 ILE A 516 " pdb=" CD1 ILE A 516 " ideal model delta sigma weight residual 1.513 1.410 0.103 3.90e-02 6.57e+02 7.00e+00 bond pdb=" CA TYR B 589 " pdb=" C TYR B 589 " ideal model delta sigma weight residual 1.523 1.556 -0.033 1.34e-02 5.57e+03 5.96e+00 ... (remaining 9437 not shown) Histogram of bond angle deviations from ideal: 94.02 - 103.24: 118 103.24 - 112.46: 4668 112.46 - 121.68: 6102 121.68 - 130.90: 1867 130.90 - 140.12: 75 Bond angle restraints: 12830 Sorted by residual: angle pdb=" C PRO B 588 " pdb=" N TYR B 589 " pdb=" CA TYR B 589 " ideal model delta sigma weight residual 121.54 140.12 -18.58 1.91e+00 2.74e-01 9.47e+01 angle pdb=" C PRO A 588 " pdb=" N TYR A 589 " pdb=" CA TYR A 589 " ideal model delta sigma weight residual 121.54 140.12 -18.58 1.91e+00 2.74e-01 9.46e+01 angle pdb=" N ILE B 510 " pdb=" CA ILE B 510 " pdb=" C ILE B 510 " ideal model delta sigma weight residual 108.82 120.55 -11.73 1.22e+00 6.72e-01 9.25e+01 angle pdb=" N ILE A 510 " pdb=" CA ILE A 510 " pdb=" C ILE A 510 " ideal model delta sigma weight residual 108.82 120.53 -11.71 1.22e+00 6.72e-01 9.21e+01 angle pdb=" N TYR B 589 " pdb=" CA TYR B 589 " pdb=" C TYR B 589 " ideal model delta sigma weight residual 110.80 125.10 -14.30 2.13e+00 2.20e-01 4.51e+01 ... (remaining 12825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 4976 15.62 - 31.24: 396 31.24 - 46.87: 110 46.87 - 62.49: 20 62.49 - 78.11: 6 Dihedral angle restraints: 5508 sinusoidal: 2086 harmonic: 3422 Sorted by residual: dihedral pdb=" CA GLY A 594 " pdb=" C GLY A 594 " pdb=" N TRP A 595 " pdb=" CA TRP A 595 " ideal model delta harmonic sigma weight residual 180.00 125.75 54.25 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA GLY B 594 " pdb=" C GLY B 594 " pdb=" N TRP B 595 " pdb=" CA TRP B 595 " ideal model delta harmonic sigma weight residual 180.00 125.77 54.23 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA LYS B 324 " pdb=" C LYS B 324 " pdb=" N ASP B 325 " pdb=" CA ASP B 325 " ideal model delta harmonic sigma weight residual -180.00 -140.86 -39.14 0 5.00e+00 4.00e-02 6.13e+01 ... (remaining 5505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1194 0.104 - 0.208: 256 0.208 - 0.312: 54 0.312 - 0.416: 10 0.416 - 0.520: 4 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CG LEU B 427 " pdb=" CB LEU B 427 " pdb=" CD1 LEU B 427 " pdb=" CD2 LEU B 427 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" CG LEU A 427 " pdb=" CB LEU A 427 " pdb=" CD1 LEU A 427 " pdb=" CD2 LEU A 427 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CB ILE B 329 " pdb=" CA ILE B 329 " pdb=" CG1 ILE B 329 " pdb=" CG2 ILE B 329 " both_signs ideal model delta sigma weight residual False 2.64 3.07 -0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 1515 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 508 " 0.047 2.00e-02 2.50e+03 9.25e-02 8.56e+01 pdb=" C ASP A 508 " -0.160 2.00e-02 2.50e+03 pdb=" O ASP A 508 " 0.059 2.00e-02 2.50e+03 pdb=" N GLY A 509 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 508 " -0.047 2.00e-02 2.50e+03 9.20e-02 8.47e+01 pdb=" C ASP B 508 " 0.159 2.00e-02 2.50e+03 pdb=" O ASP B 508 " -0.058 2.00e-02 2.50e+03 pdb=" N GLY B 509 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 588 " 0.028 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C PRO B 588 " -0.101 2.00e-02 2.50e+03 pdb=" O PRO B 588 " 0.038 2.00e-02 2.50e+03 pdb=" N TYR B 589 " 0.035 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 895 2.73 - 3.28: 9696 3.28 - 3.82: 16348 3.82 - 4.36: 17975 4.36 - 4.90: 28730 Nonbonded interactions: 73644 Sorted by model distance: nonbonded pdb=" O ILE B 472 " pdb=" OG1 THR B 476 " model vdw 2.193 2.440 nonbonded pdb=" O ILE A 472 " pdb=" OG1 THR A 476 " model vdw 2.194 2.440 nonbonded pdb=" O CYS A 179 " pdb=" OG SER A 183 " model vdw 2.219 2.440 nonbonded pdb=" O CYS B 179 " pdb=" OG SER B 183 " model vdw 2.220 2.440 nonbonded pdb=" O SER B 289 " pdb=" OG1 THR B 293 " model vdw 2.235 2.440 ... (remaining 73639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 5.570 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.950 Find NCS groups from input model: 0.460 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.010 0.108 9442 Z= 0.615 Angle : 1.807 19.518 12830 Z= 0.948 Chirality : 0.096 0.520 1518 Planarity : 0.012 0.093 1568 Dihedral : 12.959 78.110 3308 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.58 % Favored : 90.08 % Rotamer: Outliers : 3.61 % Allowed : 10.62 % Favored : 85.77 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 3.85 % Twisted General : 0.88 % 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: -4.01 (0.20), residues: 1180 helix: -2.27 (0.15), residues: 764 sheet: -0.92 (0.99), residues: 20 loop : -3.28 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.007 TRP A 469 HIS 0.008 0.003 HIS A 389 PHE 0.070 0.007 PHE B 464 TYR 0.046 0.005 TYR B 146 ARG 0.008 0.002 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 209 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.9271 (ptp) cc_final: 0.8957 (ptt) REVERT: B 307 PHE cc_start: 0.9356 (t80) cc_final: 0.8903 (t80) REVERT: B 315 VAL cc_start: 0.9594 (t) cc_final: 0.9358 (m) REVERT: B 339 MET cc_start: 0.8880 (ptp) cc_final: 0.8608 (pmm) REVERT: B 341 PHE cc_start: 0.8529 (t80) cc_final: 0.7624 (t80) REVERT: B 404 PHE cc_start: 0.9225 (m-10) cc_final: 0.8834 (m-80) REVERT: B 464 PHE cc_start: 0.8934 (p90) cc_final: 0.8558 (p90) REVERT: B 468 PHE cc_start: 0.9021 (m-10) cc_final: 0.8714 (m-10) REVERT: B 470 MET cc_start: 0.9282 (ttm) cc_final: 0.8977 (ttm) REVERT: B 494 PHE cc_start: 0.9483 (t80) cc_final: 0.9240 (t80) REVERT: B 559 MET cc_start: 0.9772 (ppp) cc_final: 0.9202 (ppp) REVERT: B 643 LYS cc_start: 0.9606 (pttp) cc_final: 0.9013 (mmmt) REVERT: A 135 MET cc_start: 0.9200 (ptp) cc_final: 0.8909 (ptt) REVERT: A 307 PHE cc_start: 0.9322 (t80) cc_final: 0.8773 (t80) REVERT: A 315 VAL cc_start: 0.9607 (t) cc_final: 0.9378 (m) REVERT: A 339 MET cc_start: 0.9040 (ptp) cc_final: 0.8418 (pmm) REVERT: A 341 PHE cc_start: 0.8824 (t80) cc_final: 0.8351 (t80) REVERT: A 404 PHE cc_start: 0.9420 (m-10) cc_final: 0.9077 (m-80) REVERT: A 427 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8946 (tp) REVERT: A 435 LYS cc_start: 0.9716 (mmtt) cc_final: 0.9429 (tptp) REVERT: A 464 PHE cc_start: 0.8895 (p90) cc_final: 0.8557 (p90) REVERT: A 468 PHE cc_start: 0.8983 (m-10) cc_final: 0.8774 (m-80) REVERT: A 470 MET cc_start: 0.9224 (ttm) cc_final: 0.8800 (ttm) REVERT: A 494 PHE cc_start: 0.9325 (t80) cc_final: 0.8951 (t80) REVERT: A 557 LEU cc_start: 0.9664 (mm) cc_final: 0.9399 (tt) REVERT: A 559 MET cc_start: 0.9823 (ppp) cc_final: 0.9371 (ppp) outliers start: 36 outliers final: 10 residues processed: 233 average time/residue: 0.2020 time to fit residues: 65.3076 Evaluate side-chains 155 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.0000 chunk 107 optimal weight: 2.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9442 Z= 0.237 Angle : 0.906 12.360 12830 Z= 0.469 Chirality : 0.050 0.275 1518 Planarity : 0.006 0.066 1568 Dihedral : 7.226 33.466 1256 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -2.14 (0.23), residues: 1180 helix: -0.71 (0.17), residues: 760 sheet: 0.03 (0.86), residues: 20 loop : -2.77 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 469 HIS 0.004 0.001 HIS A 835 PHE 0.038 0.003 PHE A 464 TYR 0.017 0.002 TYR A 578 ARG 0.009 0.001 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.9143 (ptp) cc_final: 0.8786 (ptt) REVERT: B 341 PHE cc_start: 0.8315 (t80) cc_final: 0.7782 (t80) REVERT: B 404 PHE cc_start: 0.9212 (m-10) cc_final: 0.8836 (m-80) REVERT: B 410 MET cc_start: 0.9043 (tpt) cc_final: 0.8618 (tpt) REVERT: B 464 PHE cc_start: 0.8918 (p90) cc_final: 0.8184 (p90) REVERT: B 468 PHE cc_start: 0.8932 (m-10) cc_final: 0.8524 (m-10) REVERT: B 470 MET cc_start: 0.9274 (ttm) cc_final: 0.8886 (mtt) REVERT: B 494 PHE cc_start: 0.9457 (t80) cc_final: 0.9190 (t80) REVERT: B 568 MET cc_start: 0.9468 (ppp) cc_final: 0.9238 (ppp) REVERT: B 643 LYS cc_start: 0.9587 (pttp) cc_final: 0.9057 (mmmt) REVERT: A 135 MET cc_start: 0.9053 (ptp) cc_final: 0.8665 (ptt) REVERT: A 227 ILE cc_start: 0.8997 (tp) cc_final: 0.8770 (tp) REVERT: A 307 PHE cc_start: 0.9261 (t80) cc_final: 0.8924 (t80) REVERT: A 341 PHE cc_start: 0.8746 (t80) cc_final: 0.8274 (t80) REVERT: A 410 MET cc_start: 0.9043 (tpt) cc_final: 0.8756 (tpt) REVERT: A 436 HIS cc_start: 0.9115 (m-70) cc_final: 0.8857 (m-70) REVERT: A 494 PHE cc_start: 0.9310 (t80) cc_final: 0.8881 (t80) REVERT: A 559 MET cc_start: 0.9791 (ppp) cc_final: 0.9560 (ppp) REVERT: A 564 ILE cc_start: 0.9616 (mm) cc_final: 0.9405 (pt) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1917 time to fit residues: 52.5191 Evaluate side-chains 151 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 HIS B 379 HIS ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 847 HIS A 379 HIS ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 HIS A 847 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9442 Z= 0.259 Angle : 0.848 10.375 12830 Z= 0.440 Chirality : 0.048 0.244 1518 Planarity : 0.006 0.051 1568 Dihedral : 6.697 32.463 1256 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.30 % Allowed : 6.81 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -1.54 (0.24), residues: 1180 helix: -0.15 (0.18), residues: 764 sheet: 0.09 (0.94), residues: 20 loop : -2.77 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 595 HIS 0.005 0.001 HIS A 835 PHE 0.033 0.003 PHE A 365 TYR 0.017 0.002 TYR A 137 ARG 0.003 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 MET cc_start: 0.8677 (mmm) cc_final: 0.8064 (mmm) REVERT: B 339 MET cc_start: 0.9060 (ptp) cc_final: 0.8829 (ptp) REVERT: B 341 PHE cc_start: 0.8297 (t80) cc_final: 0.7731 (t80) REVERT: B 404 PHE cc_start: 0.9310 (m-10) cc_final: 0.8863 (m-80) REVERT: B 410 MET cc_start: 0.9030 (tpt) cc_final: 0.8698 (tpt) REVERT: B 464 PHE cc_start: 0.8992 (p90) cc_final: 0.8339 (p90) REVERT: B 494 PHE cc_start: 0.9471 (t80) cc_final: 0.9160 (t80) REVERT: B 559 MET cc_start: 0.9601 (ppp) cc_final: 0.9364 (ppp) REVERT: B 568 MET cc_start: 0.9465 (ppp) cc_final: 0.9254 (ppp) REVERT: B 643 LYS cc_start: 0.9566 (pttp) cc_final: 0.8985 (mmmt) REVERT: B 836 LYS cc_start: 0.9612 (mttt) cc_final: 0.9312 (tppt) REVERT: A 122 VAL cc_start: 0.9182 (m) cc_final: 0.8965 (m) REVERT: A 339 MET cc_start: 0.9072 (ptp) cc_final: 0.8190 (pmm) REVERT: A 341 PHE cc_start: 0.8599 (t80) cc_final: 0.8091 (t80) REVERT: A 379 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7785 (t-90) REVERT: A 400 VAL cc_start: 0.9265 (m) cc_final: 0.9037 (p) REVERT: A 556 ILE cc_start: 0.9744 (tt) cc_final: 0.9258 (tp) REVERT: A 559 MET cc_start: 0.9764 (ppp) cc_final: 0.9307 (ppp) REVERT: A 836 LYS cc_start: 0.9511 (mttt) cc_final: 0.9208 (tppt) outliers start: 3 outliers final: 1 residues processed: 187 average time/residue: 0.1848 time to fit residues: 49.6626 Evaluate side-chains 141 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 0.0170 chunk 51 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 HIS ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS A 379 HIS A 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9442 Z= 0.194 Angle : 0.800 9.072 12830 Z= 0.408 Chirality : 0.047 0.249 1518 Planarity : 0.005 0.049 1568 Dihedral : 6.192 30.156 1256 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.71 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.12 (0.24), residues: 1180 helix: 0.22 (0.18), residues: 768 sheet: 0.65 (1.00), residues: 20 loop : -2.78 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 595 HIS 0.008 0.002 HIS B 664 PHE 0.028 0.002 PHE A 365 TYR 0.024 0.001 TYR A 146 ARG 0.003 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.9003 (ptp) cc_final: 0.8792 (ptt) REVERT: B 227 ILE cc_start: 0.8897 (mm) cc_final: 0.8676 (tp) REVERT: B 250 MET cc_start: 0.8561 (mmm) cc_final: 0.8038 (mmm) REVERT: B 341 PHE cc_start: 0.8386 (t80) cc_final: 0.7864 (t80) REVERT: B 400 VAL cc_start: 0.9263 (p) cc_final: 0.9044 (p) REVERT: B 404 PHE cc_start: 0.9235 (m-10) cc_final: 0.8767 (m-80) REVERT: B 410 MET cc_start: 0.8953 (tpt) cc_final: 0.8478 (tpt) REVERT: B 466 MET cc_start: 0.9402 (tmm) cc_final: 0.9108 (tmm) REVERT: B 494 PHE cc_start: 0.9418 (t80) cc_final: 0.9166 (t80) REVERT: B 836 LYS cc_start: 0.9574 (mttt) cc_final: 0.9242 (tppt) REVERT: A 122 VAL cc_start: 0.9123 (m) cc_final: 0.8772 (m) REVERT: A 135 MET cc_start: 0.9012 (ptp) cc_final: 0.8756 (ptt) REVERT: A 307 PHE cc_start: 0.9332 (t80) cc_final: 0.9034 (t80) REVERT: A 339 MET cc_start: 0.9019 (ptp) cc_final: 0.8052 (pmm) REVERT: A 341 PHE cc_start: 0.8626 (t80) cc_final: 0.7971 (t80) REVERT: A 404 PHE cc_start: 0.9232 (m-10) cc_final: 0.8850 (m-80) REVERT: A 410 MET cc_start: 0.8930 (tpt) cc_final: 0.8605 (tpt) REVERT: A 414 MET cc_start: 0.6968 (ptm) cc_final: 0.6646 (ptt) REVERT: A 494 PHE cc_start: 0.8724 (m-80) cc_final: 0.8518 (m-80) REVERT: A 556 ILE cc_start: 0.9729 (tt) cc_final: 0.9508 (pt) REVERT: A 559 MET cc_start: 0.9735 (ppp) cc_final: 0.9481 (ppp) REVERT: A 564 ILE cc_start: 0.9657 (mm) cc_final: 0.9365 (mt) REVERT: A 836 LYS cc_start: 0.9466 (mttt) cc_final: 0.9126 (tppt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1862 time to fit residues: 49.4265 Evaluate side-chains 143 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.0040 chunk 97 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS A 369 HIS A 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9442 Z= 0.224 Angle : 0.798 9.629 12830 Z= 0.407 Chirality : 0.047 0.232 1518 Planarity : 0.005 0.045 1568 Dihedral : 6.098 29.471 1256 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.88 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -1.06 (0.24), residues: 1180 helix: 0.32 (0.18), residues: 770 sheet: 0.53 (1.09), residues: 20 loop : -2.89 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 469 HIS 0.009 0.001 HIS B 389 PHE 0.038 0.002 PHE A 468 TYR 0.022 0.002 TYR A 146 ARG 0.002 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 ILE cc_start: 0.9012 (mm) cc_final: 0.8801 (tp) REVERT: B 339 MET cc_start: 0.9023 (ptp) cc_final: 0.7896 (pmm) REVERT: B 341 PHE cc_start: 0.8300 (t80) cc_final: 0.7745 (t80) REVERT: B 400 VAL cc_start: 0.9223 (p) cc_final: 0.8988 (p) REVERT: B 404 PHE cc_start: 0.9182 (m-10) cc_final: 0.8692 (m-80) REVERT: B 410 MET cc_start: 0.8944 (tpt) cc_final: 0.8540 (tpt) REVERT: B 494 PHE cc_start: 0.9431 (t80) cc_final: 0.9144 (t80) REVERT: B 559 MET cc_start: 0.9598 (ppp) cc_final: 0.9362 (ppp) REVERT: B 836 LYS cc_start: 0.9536 (mttt) cc_final: 0.9231 (tppt) REVERT: A 122 VAL cc_start: 0.9083 (m) cc_final: 0.8863 (m) REVERT: A 283 LEU cc_start: 0.8914 (pp) cc_final: 0.8697 (pp) REVERT: A 307 PHE cc_start: 0.9307 (t80) cc_final: 0.8958 (t80) REVERT: A 339 MET cc_start: 0.8976 (ptp) cc_final: 0.8425 (pmm) REVERT: A 341 PHE cc_start: 0.8607 (t80) cc_final: 0.8016 (t80) REVERT: A 559 MET cc_start: 0.9657 (ppp) cc_final: 0.9332 (ppp) REVERT: A 836 LYS cc_start: 0.9478 (mttt) cc_final: 0.9113 (tppt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1833 time to fit residues: 47.2666 Evaluate side-chains 141 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 28 optimal weight: 0.0870 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9442 Z= 0.186 Angle : 0.771 9.472 12830 Z= 0.390 Chirality : 0.046 0.236 1518 Planarity : 0.005 0.044 1568 Dihedral : 5.852 27.502 1256 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.80 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.87 (0.25), residues: 1180 helix: 0.51 (0.19), residues: 772 sheet: 0.88 (1.06), residues: 20 loop : -2.96 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 595 HIS 0.004 0.001 HIS A 436 PHE 0.025 0.002 PHE B 547 TYR 0.018 0.001 TYR B 146 ARG 0.002 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 ILE cc_start: 0.8978 (mm) cc_final: 0.8752 (tp) REVERT: B 283 LEU cc_start: 0.8785 (pp) cc_final: 0.8465 (pp) REVERT: B 306 PHE cc_start: 0.9509 (t80) cc_final: 0.9284 (t80) REVERT: B 307 PHE cc_start: 0.9326 (t80) cc_final: 0.9029 (t80) REVERT: B 339 MET cc_start: 0.8989 (ptp) cc_final: 0.7940 (pmm) REVERT: B 341 PHE cc_start: 0.8338 (t80) cc_final: 0.7846 (t80) REVERT: B 400 VAL cc_start: 0.9212 (p) cc_final: 0.8966 (p) REVERT: B 404 PHE cc_start: 0.9215 (m-10) cc_final: 0.8861 (m-80) REVERT: B 466 MET cc_start: 0.9275 (tmm) cc_final: 0.9044 (tmm) REVERT: B 494 PHE cc_start: 0.9403 (t80) cc_final: 0.9126 (t80) REVERT: B 559 MET cc_start: 0.9606 (ppp) cc_final: 0.9396 (ppp) REVERT: B 836 LYS cc_start: 0.9513 (mttt) cc_final: 0.9172 (tppt) REVERT: B 854 MET cc_start: 0.9434 (ppp) cc_final: 0.9186 (ppp) REVERT: A 307 PHE cc_start: 0.9275 (t80) cc_final: 0.9027 (t80) REVERT: A 339 MET cc_start: 0.8932 (ptp) cc_final: 0.8431 (pmm) REVERT: A 341 PHE cc_start: 0.8662 (t80) cc_final: 0.8031 (t80) REVERT: A 400 VAL cc_start: 0.9298 (p) cc_final: 0.9085 (m) REVERT: A 404 PHE cc_start: 0.9314 (m-10) cc_final: 0.9067 (m-80) REVERT: A 466 MET cc_start: 0.9393 (tmm) cc_final: 0.9187 (tmm) REVERT: A 468 PHE cc_start: 0.8568 (m-80) cc_final: 0.8293 (m-80) REVERT: A 485 MET cc_start: 0.9384 (pmm) cc_final: 0.8989 (pmm) REVERT: A 494 PHE cc_start: 0.8765 (m-80) cc_final: 0.8534 (m-80) REVERT: A 559 MET cc_start: 0.9610 (ppp) cc_final: 0.9269 (ppp) REVERT: A 836 LYS cc_start: 0.9458 (mttt) cc_final: 0.9082 (tppt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1887 time to fit residues: 49.6698 Evaluate side-chains 146 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.0040 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9442 Z= 0.194 Angle : 0.784 9.683 12830 Z= 0.393 Chirality : 0.047 0.231 1518 Planarity : 0.005 0.039 1568 Dihedral : 5.762 26.717 1256 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.63 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1180 helix: 0.61 (0.19), residues: 772 sheet: 1.17 (1.07), residues: 20 loop : -2.97 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 469 HIS 0.005 0.001 HIS A 237 PHE 0.030 0.002 PHE B 288 TYR 0.018 0.001 TYR A 206 ARG 0.001 0.000 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 PHE cc_start: 0.8789 (t80) cc_final: 0.8556 (t80) REVERT: B 339 MET cc_start: 0.9003 (ptp) cc_final: 0.7985 (pmm) REVERT: B 341 PHE cc_start: 0.8371 (t80) cc_final: 0.7863 (t80) REVERT: B 400 VAL cc_start: 0.9208 (p) cc_final: 0.8952 (p) REVERT: B 404 PHE cc_start: 0.9182 (m-10) cc_final: 0.8744 (m-80) REVERT: B 410 MET cc_start: 0.8812 (tpt) cc_final: 0.8487 (tpt) REVERT: B 414 MET cc_start: 0.7548 (ptm) cc_final: 0.6824 (ptt) REVERT: B 477 MET cc_start: 0.8603 (ppp) cc_final: 0.8297 (tmm) REVERT: B 494 PHE cc_start: 0.9379 (t80) cc_final: 0.9099 (t80) REVERT: B 559 MET cc_start: 0.9585 (ppp) cc_final: 0.9368 (ppp) REVERT: B 836 LYS cc_start: 0.9497 (mttt) cc_final: 0.9164 (mmtm) REVERT: B 854 MET cc_start: 0.9480 (ppp) cc_final: 0.9230 (ppp) REVERT: A 122 VAL cc_start: 0.8981 (m) cc_final: 0.8756 (m) REVERT: A 235 PHE cc_start: 0.8866 (t80) cc_final: 0.8631 (t80) REVERT: A 307 PHE cc_start: 0.9300 (t80) cc_final: 0.8954 (t80) REVERT: A 339 MET cc_start: 0.8893 (ptp) cc_final: 0.8416 (pmm) REVERT: A 341 PHE cc_start: 0.8688 (t80) cc_final: 0.8082 (t80) REVERT: A 410 MET cc_start: 0.8937 (tpt) cc_final: 0.8713 (tpt) REVERT: A 468 PHE cc_start: 0.8654 (m-80) cc_final: 0.8365 (m-80) REVERT: A 494 PHE cc_start: 0.8809 (m-80) cc_final: 0.8599 (m-80) REVERT: A 559 MET cc_start: 0.9623 (ppp) cc_final: 0.9309 (ppp) REVERT: A 836 LYS cc_start: 0.9451 (mttt) cc_final: 0.9081 (tppt) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1826 time to fit residues: 50.0367 Evaluate side-chains 150 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9442 Z= 0.188 Angle : 0.792 9.180 12830 Z= 0.397 Chirality : 0.047 0.228 1518 Planarity : 0.005 0.043 1568 Dihedral : 5.626 25.949 1256 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.97 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 1180 helix: 0.60 (0.19), residues: 770 sheet: 1.41 (1.08), residues: 20 loop : -2.97 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 595 HIS 0.004 0.001 HIS A 436 PHE 0.024 0.002 PHE B 547 TYR 0.017 0.001 TYR B 296 ARG 0.001 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 ILE cc_start: 0.8839 (tp) cc_final: 0.8554 (tp) REVERT: B 339 MET cc_start: 0.8991 (ptp) cc_final: 0.7988 (pmm) REVERT: B 341 PHE cc_start: 0.8461 (t80) cc_final: 0.7975 (t80) REVERT: B 400 VAL cc_start: 0.9110 (p) cc_final: 0.8883 (p) REVERT: B 404 PHE cc_start: 0.9189 (m-10) cc_final: 0.8749 (m-80) REVERT: B 410 MET cc_start: 0.8810 (tpt) cc_final: 0.8427 (tpt) REVERT: B 414 MET cc_start: 0.7357 (ptm) cc_final: 0.6778 (ptt) REVERT: B 470 MET cc_start: 0.8968 (tmm) cc_final: 0.8635 (tmm) REVERT: B 477 MET cc_start: 0.8550 (ppp) cc_final: 0.8288 (tmm) REVERT: B 494 PHE cc_start: 0.9367 (t80) cc_final: 0.9099 (t80) REVERT: B 559 MET cc_start: 0.9605 (ppp) cc_final: 0.9400 (ppp) REVERT: B 836 LYS cc_start: 0.9476 (mttt) cc_final: 0.9168 (mmtm) REVERT: B 854 MET cc_start: 0.9488 (ppp) cc_final: 0.9228 (ppp) REVERT: A 307 PHE cc_start: 0.9311 (t80) cc_final: 0.8993 (t80) REVERT: A 339 MET cc_start: 0.8841 (ptp) cc_final: 0.8409 (pmm) REVERT: A 341 PHE cc_start: 0.8651 (t80) cc_final: 0.8106 (t80) REVERT: A 466 MET cc_start: 0.9392 (tmm) cc_final: 0.8919 (tmm) REVERT: A 468 PHE cc_start: 0.8592 (m-80) cc_final: 0.8184 (m-80) REVERT: A 494 PHE cc_start: 0.8810 (m-80) cc_final: 0.8569 (m-80) REVERT: A 559 MET cc_start: 0.9625 (ppp) cc_final: 0.9313 (ppp) REVERT: A 836 LYS cc_start: 0.9420 (mttt) cc_final: 0.9050 (tppt) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1894 time to fit residues: 52.4994 Evaluate side-chains 146 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 46 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9442 Z= 0.185 Angle : 0.791 9.290 12830 Z= 0.394 Chirality : 0.047 0.225 1518 Planarity : 0.005 0.039 1568 Dihedral : 5.594 26.090 1256 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.05 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.25), residues: 1180 helix: 0.70 (0.19), residues: 770 sheet: 1.37 (1.05), residues: 20 loop : -2.95 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 469 HIS 0.013 0.001 HIS B 436 PHE 0.037 0.002 PHE B 306 TYR 0.016 0.001 TYR B 146 ARG 0.001 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 339 MET cc_start: 0.9024 (ptp) cc_final: 0.8003 (pmm) REVERT: B 341 PHE cc_start: 0.8472 (t80) cc_final: 0.7991 (t80) REVERT: B 400 VAL cc_start: 0.9096 (p) cc_final: 0.8833 (p) REVERT: B 414 MET cc_start: 0.7260 (ptm) cc_final: 0.7058 (ptt) REVERT: B 470 MET cc_start: 0.8927 (tmm) cc_final: 0.8648 (tmm) REVERT: B 494 PHE cc_start: 0.9359 (t80) cc_final: 0.9066 (t80) REVERT: B 559 MET cc_start: 0.9635 (ppp) cc_final: 0.9422 (ppp) REVERT: B 836 LYS cc_start: 0.9468 (mttt) cc_final: 0.9157 (mmtm) REVERT: B 854 MET cc_start: 0.9488 (ppp) cc_final: 0.9229 (ppp) REVERT: A 219 LEU cc_start: 0.9470 (mt) cc_final: 0.9202 (pp) REVERT: A 235 PHE cc_start: 0.8728 (t80) cc_final: 0.8525 (t80) REVERT: A 283 LEU cc_start: 0.8925 (pp) cc_final: 0.8604 (pp) REVERT: A 307 PHE cc_start: 0.9303 (t80) cc_final: 0.8980 (t80) REVERT: A 339 MET cc_start: 0.8742 (ptp) cc_final: 0.8348 (pmm) REVERT: A 341 PHE cc_start: 0.8643 (t80) cc_final: 0.8084 (t80) REVERT: A 468 PHE cc_start: 0.8608 (m-80) cc_final: 0.8224 (m-80) REVERT: A 494 PHE cc_start: 0.8825 (m-80) cc_final: 0.8597 (m-80) REVERT: A 559 MET cc_start: 0.9633 (ppp) cc_final: 0.9326 (ppp) REVERT: A 836 LYS cc_start: 0.9412 (mttt) cc_final: 0.9041 (tppt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1589 time to fit residues: 42.2973 Evaluate side-chains 143 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 0.0970 chunk 57 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9442 Z= 0.183 Angle : 0.793 10.220 12830 Z= 0.394 Chirality : 0.047 0.223 1518 Planarity : 0.005 0.041 1568 Dihedral : 5.532 27.801 1256 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.97 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1180 helix: 0.78 (0.19), residues: 770 sheet: 1.57 (1.06), residues: 20 loop : -2.90 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 595 HIS 0.007 0.001 HIS A 436 PHE 0.031 0.002 PHE A 288 TYR 0.016 0.001 TYR B 296 ARG 0.001 0.000 ARG B 300 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 LEU cc_start: 0.9527 (mt) cc_final: 0.9176 (pp) REVERT: B 339 MET cc_start: 0.8999 (ptp) cc_final: 0.8049 (pmm) REVERT: B 341 PHE cc_start: 0.8418 (t80) cc_final: 0.7945 (t80) REVERT: B 400 VAL cc_start: 0.9071 (p) cc_final: 0.8833 (p) REVERT: B 410 MET cc_start: 0.8796 (tpt) cc_final: 0.8479 (tpt) REVERT: B 414 MET cc_start: 0.7225 (ptm) cc_final: 0.6803 (ptt) REVERT: B 470 MET cc_start: 0.8829 (tmm) cc_final: 0.8447 (tmm) REVERT: B 494 PHE cc_start: 0.9354 (t80) cc_final: 0.9068 (t80) REVERT: B 836 LYS cc_start: 0.9455 (mttt) cc_final: 0.9133 (mmtm) REVERT: B 854 MET cc_start: 0.9492 (ppp) cc_final: 0.8827 (ppp) REVERT: A 219 LEU cc_start: 0.9457 (mt) cc_final: 0.9166 (pp) REVERT: A 307 PHE cc_start: 0.9339 (t80) cc_final: 0.9035 (t80) REVERT: A 339 MET cc_start: 0.8730 (ptp) cc_final: 0.8350 (pmm) REVERT: A 341 PHE cc_start: 0.8509 (t80) cc_final: 0.7959 (t80) REVERT: A 401 ILE cc_start: 0.9432 (pt) cc_final: 0.9056 (pt) REVERT: A 468 PHE cc_start: 0.8680 (m-80) cc_final: 0.8204 (m-80) REVERT: A 494 PHE cc_start: 0.8861 (m-80) cc_final: 0.8589 (m-80) REVERT: A 559 MET cc_start: 0.9638 (ppp) cc_final: 0.9326 (ppp) REVERT: A 836 LYS cc_start: 0.9380 (mttt) cc_final: 0.8987 (mptt) REVERT: A 854 MET cc_start: 0.9610 (ppp) cc_final: 0.9184 (ppp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1928 time to fit residues: 51.2350 Evaluate side-chains 145 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.0370 chunk 86 optimal weight: 0.0980 chunk 13 optimal weight: 0.1980 chunk 26 optimal weight: 0.0870 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 HIS B 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.069359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.053301 restraints weight = 61089.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.055054 restraints weight = 43512.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.056397 restraints weight = 33627.180| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9442 Z= 0.185 Angle : 0.812 12.026 12830 Z= 0.402 Chirality : 0.047 0.220 1518 Planarity : 0.005 0.042 1568 Dihedral : 5.417 29.519 1256 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.31 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.57 (0.25), residues: 1180 helix: 0.76 (0.19), residues: 760 sheet: 1.62 (1.06), residues: 20 loop : -2.83 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 595 HIS 0.006 0.001 HIS A 436 PHE 0.029 0.002 PHE B 547 TYR 0.014 0.001 TYR B 146 ARG 0.001 0.000 ARG B 663 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1969.93 seconds wall clock time: 36 minutes 14.42 seconds (2174.42 seconds total)