Starting phenix.real_space_refine on Wed Jun 26 12:39:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw2_38728/06_2024/8xw2_38728.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw2_38728/06_2024/8xw2_38728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw2_38728/06_2024/8xw2_38728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw2_38728/06_2024/8xw2_38728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw2_38728/06_2024/8xw2_38728.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw2_38728/06_2024/8xw2_38728.pdb" } resolution = 3.59 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= 0.066 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 48 5.16 5 C 6744 2.51 5 N 1650 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "A PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "B PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 10150 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5075 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 34, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5075 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 34, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 6.04, per 1000 atoms: 0.60 Number of scatterers: 10150 At special positions: 0 Unit cell: (91.785, 140.315, 98.115, 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 48 16.00 O 1708 8.00 N 1650 7.00 C 6744 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: 4.18 Conformation dependent library (CDL) restraints added in 1.8 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 2 sheets defined 77.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 3 through 30 removed outlier: 3.501A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.757A pdb=" N LEU A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 92 through 121 removed outlier: 4.119A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 157 through 195 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 242 through 269 Processing helix chain 'A' and resid 290 through 313 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.747A pdb=" N ALA A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 366 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 389 Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.786A pdb=" N ILE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 438 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 456 through 475 Processing helix chain 'A' and resid 477 through 489 Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 512 through 534 removed outlier: 3.615A pdb=" N ALA A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 548 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 565 through 584 Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 590 through 612 removed outlier: 3.724A pdb=" N ILE A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 646 Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 659 through 677 removed outlier: 4.024A pdb=" N VAL A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 703 through 710 removed outlier: 4.109A pdb=" N ASN A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 30 removed outlier: 3.501A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.756A pdb=" N LEU B 80 " --> pdb=" O MET B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 92 through 121 removed outlier: 4.118A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 157 through 195 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 242 through 269 Processing helix chain 'B' and resid 290 through 313 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 360 through 366 removed outlier: 3.746A pdb=" N ALA B 365 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 366 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 389 Processing helix chain 'B' and resid 389 through 400 removed outlier: 3.786A pdb=" N ILE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 438 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 512 through 534 removed outlier: 3.617A pdb=" N ALA B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET B 534 " --> pdb=" O GLY B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 548 Processing helix chain 'B' and resid 554 through 559 Processing helix chain 'B' and resid 565 through 584 Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 590 through 612 removed outlier: 3.724A pdb=" N ILE B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 646 Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 659 through 677 removed outlier: 4.024A pdb=" N VAL B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 703 through 710 removed outlier: 4.108A pdb=" N ASN B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.660A pdb=" N ALA A 322 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.660A pdb=" N ALA B 322 " --> pdb=" O VAL B 239 " (cutoff:3.500A) 691 hydrogen bonds defined for protein. 2049 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: 2.54 Time building geometry restraints manager: 4.59 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: 3094 1.34 - 1.46: 2463 1.46 - 1.58: 4795 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 10440 Sorted by residual: bond pdb=" CG LEU A 441 " pdb=" CD2 LEU A 441 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 bond pdb=" CG LEU B 441 " pdb=" CD2 LEU B 441 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.46e+00 bond pdb=" C ASN A 344 " pdb=" N PRO A 345 " ideal model delta sigma weight residual 1.334 1.319 0.014 8.40e-03 1.42e+04 2.95e+00 bond pdb=" C ASN B 344 " pdb=" N PRO B 345 " ideal model delta sigma weight residual 1.334 1.319 0.014 8.40e-03 1.42e+04 2.89e+00 bond pdb=" CD GLU B 297 " pdb=" OE1 GLU B 297 " ideal model delta sigma weight residual 1.249 1.222 0.027 1.90e-02 2.77e+03 2.06e+00 ... (remaining 10435 not shown) Histogram of bond angle deviations from ideal: 97.47 - 104.78: 222 104.78 - 112.09: 5156 112.09 - 119.40: 3340 119.40 - 126.71: 5300 126.71 - 134.02: 182 Bond angle restraints: 14200 Sorted by residual: angle pdb=" C ALA B 296 " pdb=" N GLU B 297 " pdb=" CA GLU B 297 " ideal model delta sigma weight residual 121.14 113.19 7.95 1.75e+00 3.27e-01 2.07e+01 angle pdb=" C ALA A 296 " pdb=" N GLU A 297 " pdb=" CA GLU A 297 " ideal model delta sigma weight residual 121.14 113.20 7.94 1.75e+00 3.27e-01 2.06e+01 angle pdb=" N GLU A 297 " pdb=" CA GLU A 297 " pdb=" CB GLU A 297 " ideal model delta sigma weight residual 110.40 115.85 -5.45 1.63e+00 3.76e-01 1.12e+01 angle pdb=" N GLU B 297 " pdb=" CA GLU B 297 " pdb=" CB GLU B 297 " ideal model delta sigma weight residual 110.40 115.84 -5.44 1.63e+00 3.76e-01 1.12e+01 angle pdb=" N PRO B 345 " pdb=" CA PRO B 345 " pdb=" C PRO B 345 " ideal model delta sigma weight residual 114.68 111.35 3.33 1.04e+00 9.25e-01 1.03e+01 ... (remaining 14195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5597 17.96 - 35.92: 426 35.92 - 53.87: 83 53.87 - 71.83: 12 71.83 - 89.79: 10 Dihedral angle restraints: 6128 sinusoidal: 2386 harmonic: 3742 Sorted by residual: dihedral pdb=" CA ILE A 108 " pdb=" C ILE A 108 " pdb=" N PHE A 109 " pdb=" CA PHE A 109 " ideal model delta harmonic sigma weight residual -180.00 -160.30 -19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ILE B 108 " pdb=" C ILE B 108 " pdb=" N PHE B 109 " pdb=" CA PHE B 109 " ideal model delta harmonic sigma weight residual -180.00 -160.30 -19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASN B 475 " pdb=" C ASN B 475 " pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta harmonic sigma weight residual -180.00 -162.44 -17.56 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1491 0.088 - 0.176: 109 0.176 - 0.264: 2 0.264 - 0.351: 0 0.351 - 0.439: 2 Chirality restraints: 1604 Sorted by residual: chirality pdb=" CB ILE A 112 " pdb=" CA ILE A 112 " pdb=" CG1 ILE A 112 " pdb=" CG2 ILE A 112 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CB ILE B 112 " pdb=" CA ILE B 112 " pdb=" CG1 ILE B 112 " pdb=" CG2 ILE B 112 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA GLU A 297 " pdb=" N GLU A 297 " pdb=" C GLU A 297 " pdb=" CB GLU A 297 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1601 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 391 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO B 392 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 392 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 392 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 391 " 0.045 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO A 392 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 677 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO B 678 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 678 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 678 " 0.031 5.00e-02 4.00e+02 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 379 2.71 - 3.26: 10994 3.26 - 3.81: 17007 3.81 - 4.35: 19419 4.35 - 4.90: 33328 Nonbonded interactions: 81127 Sorted by model distance: nonbonded pdb=" O PRO A 354 " pdb=" OH TYR A 712 " model vdw 2.169 2.440 nonbonded pdb=" O PRO B 354 " pdb=" OH TYR B 712 " model vdw 2.169 2.440 nonbonded pdb=" OG SER A 216 " pdb=" OE1 GLU A 219 " model vdw 2.206 2.440 nonbonded pdb=" OG SER B 216 " pdb=" OE1 GLU B 219 " model vdw 2.206 2.440 nonbonded pdb=" NE ARG A 343 " pdb=" OE2 GLU B 687 " model vdw 2.236 2.520 ... (remaining 81122 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: 1.350 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: 3.320 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.100 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 0.062 10440 Z= 0.304 Angle : 0.756 7.955 14200 Z= 0.418 Chirality : 0.047 0.439 1604 Planarity : 0.005 0.067 1762 Dihedral : 13.677 89.790 3696 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1248 helix: 1.62 (0.18), residues: 866 sheet: -1.63 (0.86), residues: 34 loop : -2.42 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 624 HIS 0.005 0.001 HIS B 542 PHE 0.023 0.002 PHE A 471 TYR 0.025 0.002 TYR A 294 ARG 0.004 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 SER cc_start: 0.8340 (p) cc_final: 0.8039 (m) REVERT: A 74 ASN cc_start: 0.8548 (p0) cc_final: 0.7948 (p0) REVERT: A 165 MET cc_start: 0.8227 (tpt) cc_final: 0.7867 (tpp) REVERT: A 167 TYR cc_start: 0.7771 (m-80) cc_final: 0.7267 (m-10) REVERT: A 256 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8031 (tm-30) REVERT: A 440 PHE cc_start: 0.7389 (m-80) cc_final: 0.7174 (m-80) REVERT: B 40 SER cc_start: 0.8420 (p) cc_final: 0.8163 (m) REVERT: B 165 MET cc_start: 0.8360 (tpt) cc_final: 0.7896 (tpp) REVERT: B 256 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7835 (tm-30) REVERT: B 437 PHE cc_start: 0.8638 (m-80) cc_final: 0.8428 (m-10) REVERT: B 615 GLN cc_start: 0.6946 (mt0) cc_final: 0.6601 (mt0) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1742 time to fit residues: 58.7481 Evaluate side-chains 173 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN A 472 ASN B 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10440 Z= 0.215 Angle : 0.643 13.620 14200 Z= 0.316 Chirality : 0.043 0.149 1604 Planarity : 0.005 0.056 1762 Dihedral : 4.350 17.764 1360 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.23 % Allowed : 9.45 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1248 helix: 1.79 (0.18), residues: 858 sheet: -1.72 (0.75), residues: 46 loop : -2.74 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 624 HIS 0.006 0.001 HIS A 293 PHE 0.025 0.002 PHE A 428 TYR 0.014 0.001 TYR A 468 ARG 0.003 0.000 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 197 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 SER cc_start: 0.8302 (p) cc_final: 0.8014 (m) REVERT: A 74 ASN cc_start: 0.8563 (p0) cc_final: 0.7949 (p0) REVERT: A 102 TYR cc_start: 0.8720 (m-10) cc_final: 0.8516 (m-80) REVERT: A 165 MET cc_start: 0.8208 (tpt) cc_final: 0.7974 (tpp) REVERT: A 256 GLN cc_start: 0.8333 (tm-30) cc_final: 0.8120 (tm-30) REVERT: A 261 TYR cc_start: 0.8695 (t80) cc_final: 0.8481 (t80) REVERT: A 440 PHE cc_start: 0.7218 (m-80) cc_final: 0.6990 (m-80) REVERT: A 643 MET cc_start: 0.7986 (tmm) cc_final: 0.7656 (tmm) REVERT: B 40 SER cc_start: 0.8342 (p) cc_final: 0.8077 (m) REVERT: B 157 MET cc_start: 0.7997 (mmm) cc_final: 0.7621 (ppp) REVERT: B 165 MET cc_start: 0.8242 (tpt) cc_final: 0.7698 (ttt) REVERT: B 256 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7921 (tm-30) REVERT: B 437 PHE cc_start: 0.8585 (m-80) cc_final: 0.8382 (m-10) REVERT: B 643 MET cc_start: 0.8239 (tmm) cc_final: 0.7998 (tmm) REVERT: B 661 LEU cc_start: 0.8399 (tp) cc_final: 0.8128 (tp) outliers start: 13 outliers final: 6 residues processed: 203 average time/residue: 0.1710 time to fit residues: 52.7911 Evaluate side-chains 176 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 578 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10440 Z= 0.232 Angle : 0.642 14.179 14200 Z= 0.318 Chirality : 0.043 0.168 1604 Planarity : 0.005 0.056 1762 Dihedral : 4.237 18.530 1360 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.70 % Allowed : 12.48 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1248 helix: 1.94 (0.18), residues: 846 sheet: -2.25 (0.75), residues: 36 loop : -2.42 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 624 HIS 0.008 0.001 HIS B 293 PHE 0.026 0.001 PHE A 159 TYR 0.014 0.001 TYR A 468 ARG 0.003 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 SER cc_start: 0.8336 (p) cc_final: 0.7948 (m) REVERT: A 74 ASN cc_start: 0.8567 (p0) cc_final: 0.7940 (p0) REVERT: A 256 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8144 (tm-30) REVERT: A 261 TYR cc_start: 0.8722 (t80) cc_final: 0.8497 (t80) REVERT: A 440 PHE cc_start: 0.7345 (m-80) cc_final: 0.7094 (m-80) REVERT: A 559 MET cc_start: 0.8167 (tpt) cc_final: 0.7750 (tpt) REVERT: B 256 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7902 (tm-30) REVERT: B 378 MET cc_start: 0.8906 (mmp) cc_final: 0.8698 (mmm) REVERT: B 389 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7649 (t80) REVERT: B 437 PHE cc_start: 0.8585 (m-80) cc_final: 0.8375 (m-10) REVERT: B 559 MET cc_start: 0.8190 (tpp) cc_final: 0.6787 (ppp) REVERT: B 643 MET cc_start: 0.8269 (tmm) cc_final: 0.8041 (tmm) outliers start: 18 outliers final: 11 residues processed: 197 average time/residue: 0.1630 time to fit residues: 49.4902 Evaluate side-chains 186 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 672 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10440 Z= 0.233 Angle : 0.620 13.627 14200 Z= 0.306 Chirality : 0.042 0.152 1604 Planarity : 0.005 0.056 1762 Dihedral : 4.153 17.361 1360 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.27 % Allowed : 14.08 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1248 helix: 1.91 (0.18), residues: 872 sheet: -2.40 (0.75), residues: 36 loop : -2.27 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.003 0.001 HIS B 628 PHE 0.025 0.001 PHE A 159 TYR 0.013 0.001 TYR A 468 ARG 0.002 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 SER cc_start: 0.8329 (p) cc_final: 0.7977 (m) REVERT: A 74 ASN cc_start: 0.8551 (p0) cc_final: 0.7924 (p0) REVERT: A 165 MET cc_start: 0.8341 (tpp) cc_final: 0.8119 (tpp) REVERT: A 256 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8134 (tm-30) REVERT: A 440 PHE cc_start: 0.7358 (m-80) cc_final: 0.7115 (m-80) REVERT: A 559 MET cc_start: 0.8283 (tpt) cc_final: 0.8040 (tpt) REVERT: B 157 MET cc_start: 0.8098 (mmm) cc_final: 0.7618 (ppp) REVERT: B 165 MET cc_start: 0.8470 (tpp) cc_final: 0.8075 (tpp) REVERT: B 256 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 389 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7660 (t80) REVERT: B 559 MET cc_start: 0.7807 (tpp) cc_final: 0.6794 (ppp) REVERT: B 643 MET cc_start: 0.8331 (tmm) cc_final: 0.8063 (tmm) outliers start: 24 outliers final: 18 residues processed: 199 average time/residue: 0.1626 time to fit residues: 49.6953 Evaluate side-chains 187 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 672 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 0.0570 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 84 optimal weight: 40.0000 chunk 0 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10440 Z= 0.257 Angle : 0.618 12.591 14200 Z= 0.305 Chirality : 0.042 0.148 1604 Planarity : 0.005 0.056 1762 Dihedral : 4.113 17.030 1360 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.46 % Allowed : 14.93 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1248 helix: 1.97 (0.18), residues: 872 sheet: -2.45 (0.77), residues: 36 loop : -2.30 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 624 HIS 0.004 0.001 HIS B 628 PHE 0.029 0.001 PHE B 159 TYR 0.013 0.001 TYR A 468 ARG 0.001 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 74 ASN cc_start: 0.8549 (p0) cc_final: 0.7920 (p0) REVERT: A 165 MET cc_start: 0.8530 (tpp) cc_final: 0.8320 (tpp) REVERT: A 256 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8125 (tm-30) REVERT: A 440 PHE cc_start: 0.7244 (m-80) cc_final: 0.7001 (m-80) REVERT: B 165 MET cc_start: 0.8487 (tpp) cc_final: 0.8090 (tpp) REVERT: B 169 PHE cc_start: 0.7662 (m-80) cc_final: 0.7423 (m-80) REVERT: B 256 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7894 (tm-30) REVERT: B 389 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7751 (t80) REVERT: B 559 MET cc_start: 0.7747 (tpp) cc_final: 0.6684 (ppp) REVERT: B 643 MET cc_start: 0.8328 (tmm) cc_final: 0.8035 (tmm) outliers start: 26 outliers final: 18 residues processed: 199 average time/residue: 0.1610 time to fit residues: 49.1497 Evaluate side-chains 190 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 672 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10440 Z= 0.211 Angle : 0.613 11.934 14200 Z= 0.303 Chirality : 0.042 0.148 1604 Planarity : 0.005 0.055 1762 Dihedral : 4.100 17.268 1360 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.27 % Allowed : 16.07 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1248 helix: 1.98 (0.18), residues: 872 sheet: -2.45 (0.76), residues: 36 loop : -2.26 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 624 HIS 0.003 0.001 HIS B 628 PHE 0.028 0.001 PHE B 428 TYR 0.010 0.001 TYR A 468 ARG 0.001 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 74 ASN cc_start: 0.8540 (p0) cc_final: 0.7906 (p0) REVERT: A 165 MET cc_start: 0.8607 (tpp) cc_final: 0.8369 (tpp) REVERT: A 256 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 440 PHE cc_start: 0.7240 (m-80) cc_final: 0.6996 (m-80) REVERT: B 165 MET cc_start: 0.8543 (tpp) cc_final: 0.8222 (tpp) REVERT: B 169 PHE cc_start: 0.7546 (m-80) cc_final: 0.7308 (m-80) REVERT: B 256 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7779 (tm-30) REVERT: B 389 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7731 (t80) REVERT: B 559 MET cc_start: 0.7810 (tpp) cc_final: 0.6864 (ptm) REVERT: B 643 MET cc_start: 0.8330 (tmm) cc_final: 0.8000 (tmm) outliers start: 24 outliers final: 17 residues processed: 196 average time/residue: 0.1554 time to fit residues: 47.0752 Evaluate side-chains 186 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 672 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 3.9990 chunk 69 optimal weight: 0.0010 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10440 Z= 0.169 Angle : 0.592 12.094 14200 Z= 0.291 Chirality : 0.040 0.148 1604 Planarity : 0.005 0.054 1762 Dihedral : 4.013 17.623 1360 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.51 % Allowed : 17.20 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1248 helix: 2.05 (0.17), residues: 872 sheet: -2.40 (0.77), residues: 36 loop : -2.20 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 624 HIS 0.002 0.000 HIS B 607 PHE 0.030 0.001 PHE B 428 TYR 0.009 0.001 TYR B 181 ARG 0.003 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ASN cc_start: 0.8536 (p0) cc_final: 0.7901 (p0) REVERT: A 256 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8089 (tm-30) REVERT: A 310 GLU cc_start: 0.8490 (tt0) cc_final: 0.8262 (pt0) REVERT: A 375 ARG cc_start: 0.8844 (tpp80) cc_final: 0.8632 (mmt-90) REVERT: A 440 PHE cc_start: 0.7365 (m-80) cc_final: 0.7110 (m-80) REVERT: B 157 MET cc_start: 0.8158 (mmm) cc_final: 0.7758 (ppp) REVERT: B 165 MET cc_start: 0.8525 (tpp) cc_final: 0.8240 (tpp) REVERT: B 256 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7783 (tm-30) REVERT: B 389 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7669 (t80) REVERT: B 559 MET cc_start: 0.7862 (tpp) cc_final: 0.6940 (ptm) REVERT: B 643 MET cc_start: 0.8301 (tmm) cc_final: 0.8003 (tmm) REVERT: B 661 LEU cc_start: 0.8354 (tp) cc_final: 0.8077 (tp) outliers start: 16 outliers final: 11 residues processed: 195 average time/residue: 0.1569 time to fit residues: 46.5975 Evaluate side-chains 180 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10440 Z= 0.227 Angle : 0.624 13.108 14200 Z= 0.305 Chirality : 0.042 0.144 1604 Planarity : 0.005 0.055 1762 Dihedral : 3.995 17.365 1360 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.80 % Allowed : 17.39 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1248 helix: 2.07 (0.18), residues: 872 sheet: -2.35 (0.79), residues: 36 loop : -2.21 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 525 HIS 0.003 0.001 HIS B 628 PHE 0.031 0.001 PHE B 428 TYR 0.018 0.001 TYR B 181 ARG 0.005 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: A 74 ASN cc_start: 0.8530 (p0) cc_final: 0.7968 (p0) REVERT: A 256 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8031 (tm-30) REVERT: A 310 GLU cc_start: 0.8499 (tt0) cc_final: 0.8281 (pt0) REVERT: A 311 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8296 (pm20) REVERT: A 440 PHE cc_start: 0.7266 (m-80) cc_final: 0.7026 (m-80) REVERT: B 165 MET cc_start: 0.8656 (tpp) cc_final: 0.8403 (tpp) REVERT: B 256 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7819 (tm-30) REVERT: B 389 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7714 (t80) REVERT: B 559 MET cc_start: 0.7844 (tpp) cc_final: 0.6928 (ptm) REVERT: B 661 LEU cc_start: 0.8409 (tp) cc_final: 0.8103 (tp) outliers start: 19 outliers final: 13 residues processed: 185 average time/residue: 0.1696 time to fit residues: 47.9695 Evaluate side-chains 184 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10440 Z= 0.180 Angle : 0.619 15.733 14200 Z= 0.297 Chirality : 0.042 0.176 1604 Planarity : 0.005 0.054 1762 Dihedral : 3.978 17.657 1360 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.61 % Allowed : 17.86 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1248 helix: 2.04 (0.18), residues: 872 sheet: -2.35 (0.78), residues: 36 loop : -2.16 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 525 HIS 0.002 0.000 HIS A 232 PHE 0.032 0.001 PHE B 428 TYR 0.013 0.001 TYR B 181 ARG 0.003 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ASN cc_start: 0.8526 (p0) cc_final: 0.7965 (p0) REVERT: A 165 MET cc_start: 0.8177 (tpp) cc_final: 0.7936 (tpp) REVERT: A 256 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 310 GLU cc_start: 0.8528 (tt0) cc_final: 0.8232 (pt0) REVERT: A 311 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8317 (pm20) REVERT: A 375 ARG cc_start: 0.8865 (tpp80) cc_final: 0.8658 (mmt-90) REVERT: A 440 PHE cc_start: 0.7302 (m-80) cc_final: 0.7077 (m-80) REVERT: A 533 LEU cc_start: 0.9368 (mt) cc_final: 0.9152 (mm) REVERT: B 157 MET cc_start: 0.7962 (mmm) cc_final: 0.7555 (ppp) REVERT: B 169 PHE cc_start: 0.7854 (m-80) cc_final: 0.7579 (m-80) REVERT: B 256 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 310 GLU cc_start: 0.8370 (pt0) cc_final: 0.8138 (pp20) REVERT: B 378 MET cc_start: 0.9155 (mmp) cc_final: 0.8627 (mmm) REVERT: B 389 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7651 (t80) REVERT: B 559 MET cc_start: 0.7871 (tpp) cc_final: 0.6902 (ptm) REVERT: B 643 MET cc_start: 0.8157 (tmm) cc_final: 0.7932 (tmm) outliers start: 17 outliers final: 11 residues processed: 188 average time/residue: 0.1765 time to fit residues: 49.8784 Evaluate side-chains 185 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 586 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.0970 chunk 56 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 0.0770 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10440 Z= 0.189 Angle : 0.638 15.839 14200 Z= 0.304 Chirality : 0.042 0.199 1604 Planarity : 0.005 0.054 1762 Dihedral : 3.941 17.894 1360 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.42 % Allowed : 17.77 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1248 helix: 2.07 (0.18), residues: 872 sheet: -2.30 (0.79), residues: 36 loop : -2.12 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 525 HIS 0.002 0.000 HIS B 628 PHE 0.032 0.001 PHE B 428 TYR 0.014 0.001 TYR B 181 ARG 0.004 0.000 ARG B 682 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 177 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ASN cc_start: 0.8521 (p0) cc_final: 0.7964 (p0) REVERT: A 165 MET cc_start: 0.8214 (tpp) cc_final: 0.7918 (tpp) REVERT: A 256 GLN cc_start: 0.8349 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 310 GLU cc_start: 0.8517 (tt0) cc_final: 0.8307 (pt0) REVERT: A 311 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8382 (pm20) REVERT: A 375 ARG cc_start: 0.8852 (tpp80) cc_final: 0.8629 (mmt-90) REVERT: A 440 PHE cc_start: 0.7317 (m-80) cc_final: 0.7077 (m-80) REVERT: B 157 MET cc_start: 0.8045 (mmm) cc_final: 0.7710 (ppp) REVERT: B 165 MET cc_start: 0.7969 (tpp) cc_final: 0.7593 (tpp) REVERT: B 256 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7845 (tm-30) REVERT: B 378 MET cc_start: 0.9103 (mmp) cc_final: 0.8800 (mmm) REVERT: B 389 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7661 (t80) REVERT: B 559 MET cc_start: 0.7904 (tpp) cc_final: 0.6914 (ptm) outliers start: 15 outliers final: 12 residues processed: 186 average time/residue: 0.1675 time to fit residues: 47.5154 Evaluate side-chains 188 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 174 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 586 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104864 restraints weight = 17240.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107954 restraints weight = 9509.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109842 restraints weight = 6693.234| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10440 Z= 0.173 Angle : 0.628 15.868 14200 Z= 0.298 Chirality : 0.041 0.165 1604 Planarity : 0.005 0.054 1762 Dihedral : 3.910 18.117 1360 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.42 % Allowed : 18.05 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1248 helix: 2.13 (0.18), residues: 860 sheet: -2.29 (0.79), residues: 36 loop : -2.15 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 525 HIS 0.002 0.000 HIS B 607 PHE 0.032 0.001 PHE B 428 TYR 0.012 0.001 TYR B 181 ARG 0.004 0.000 ARG A 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1887.95 seconds wall clock time: 34 minutes 25.44 seconds (2065.44 seconds total)