Starting phenix.real_space_refine on Wed Feb 14 12:30:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b70_15894/02_2024/8b70_15894_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b70_15894/02_2024/8b70_15894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b70_15894/02_2024/8b70_15894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b70_15894/02_2024/8b70_15894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b70_15894/02_2024/8b70_15894_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b70_15894/02_2024/8b70_15894_updated.pdb" } resolution = 3.3 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= 0.006 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 34 5.16 5 C 6138 2.51 5 N 1456 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 282": "OD1" <-> "OD2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ASP 344": "OD1" <-> "OD2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B GLU 521": "OE1" <-> "OE2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B ARG 573": "NH1" <-> "NH2" Residue "B ASP 595": "OD1" <-> "OD2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 282": "OD1" <-> "OD2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ASP 344": "OD1" <-> "OD2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A ARG 573": "NH1" <-> "NH2" Residue "A ASP 595": "OD1" <-> "OD2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9258 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4444 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 24, 'TRANS': 547} Chain breaks: 2 Chain: "A" Number of atoms: 4444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4444 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 24, 'TRANS': 547} Chain breaks: 2 Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {' K': 1, 'LMT': 3} Classifications: {'RNA': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "A" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 220 Unusual residues: {' K': 1, 'LMT': 5} Classifications: {'RNA': 1, 'undetermined': 6} Link IDs: {None: 6} Time building chain proxies: 5.25, per 1000 atoms: 0.57 Number of scatterers: 9258 At special positions: 0 Unit cell: (112.158, 86.211, 103.788, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 34 16.00 P 4 15.00 O 1624 8.00 N 1456 7.00 C 6138 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 2 sheets defined 69.6% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'B' and resid 26 through 33 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.673A pdb=" N THR B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 87 removed outlier: 4.295A pdb=" N TRP B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Proline residue: B 65 - end of helix removed outlier: 4.145A pdb=" N ILE B 85 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 105 through 136 Processing helix chain 'B' and resid 138 through 160 removed outlier: 4.779A pdb=" N ASP B 142 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS B 144 " --> pdb=" O HIS B 141 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL B 145 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 172 through 194 Processing helix chain 'B' and resid 215 through 228 removed outlier: 4.123A pdb=" N SER B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ALA B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.562A pdb=" N ASN B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 233 through 237' Processing helix chain 'B' and resid 246 through 275 Processing helix chain 'B' and resid 285 through 293 Processing helix chain 'B' and resid 298 through 332 Proline residue: B 323 - end of helix removed outlier: 4.043A pdb=" N ASP B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 348 through 366 Processing helix chain 'B' and resid 370 through 399 Proline residue: B 375 - end of helix Proline residue: B 384 - end of helix Processing helix chain 'B' and resid 404 through 428 Processing helix chain 'B' and resid 430 through 461 Proline residue: B 435 - end of helix removed outlier: 3.584A pdb=" N ILE B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Proline residue: B 441 - end of helix Processing helix chain 'B' and resid 485 through 497 Processing helix chain 'B' and resid 510 through 522 removed outlier: 4.404A pdb=" N LYS B 514 " --> pdb=" O ARG B 510 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 557 removed outlier: 3.603A pdb=" N GLU B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 578 No H-bonds generated for 'chain 'B' and resid 576 through 578' Processing helix chain 'B' and resid 581 through 589 Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 44 through 54 removed outlier: 3.674A pdb=" N THR A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 87 removed outlier: 4.294A pdb=" N TRP A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Proline residue: A 65 - end of helix removed outlier: 4.145A pdb=" N ILE A 85 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 105 through 136 Processing helix chain 'A' and resid 138 through 160 removed outlier: 4.779A pdb=" N ASP A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS A 144 " --> pdb=" O HIS A 141 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL A 145 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 172 through 194 Processing helix chain 'A' and resid 215 through 228 removed outlier: 4.123A pdb=" N SER A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ALA A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.563A pdb=" N ASN A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 237' Processing helix chain 'A' and resid 246 through 275 Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 298 through 332 Proline residue: A 323 - end of helix removed outlier: 4.043A pdb=" N ASP A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 348 through 366 Processing helix chain 'A' and resid 370 through 399 Proline residue: A 375 - end of helix Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 404 through 428 Processing helix chain 'A' and resid 430 through 461 Proline residue: A 435 - end of helix removed outlier: 3.584A pdb=" N ILE A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 485 through 497 Processing helix chain 'A' and resid 510 through 522 removed outlier: 4.405A pdb=" N LYS A 514 " --> pdb=" O ARG A 510 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 557 removed outlier: 3.602A pdb=" N GLU A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 578 No H-bonds generated for 'chain 'A' and resid 576 through 578' Processing helix chain 'A' and resid 581 through 589 Processing sheet with id= A, first strand: chain 'B' and resid 528 through 533 removed outlier: 6.103A pdb=" N SER B 560 " --> pdb=" O VAL B 475 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE B 477 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET B 562 " --> pdb=" O ILE B 477 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU B 564 " --> pdb=" O PRO B 479 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N MET B 597 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE B 565 " --> pdb=" O MET B 597 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA B 599 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLN B 567 " --> pdb=" O ALA B 599 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 601 " --> pdb=" O GLN B 567 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE B 569 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR B 603 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 528 through 533 removed outlier: 6.103A pdb=" N SER A 560 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE A 477 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N MET A 562 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU A 564 " --> pdb=" O PRO A 479 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N MET A 597 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE A 565 " --> pdb=" O MET A 597 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA A 599 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLN A 567 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 601 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE A 569 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR A 603 " --> pdb=" O ILE A 569 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1476 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: 2.86 Time building geometry restraints manager: 4.30 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: 2685 1.34 - 1.46: 2066 1.46 - 1.57: 4655 1.57 - 1.69: 14 1.69 - 1.81: 62 Bond restraints: 9482 Sorted by residual: bond pdb="C3'1 2BA B 901 " pdb="O3'1 2BA B 901 " ideal model delta sigma weight residual 1.418 1.343 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb="C3'1 2BA A1001 " pdb="O3'1 2BA A1001 " ideal model delta sigma weight residual 1.418 1.344 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5' 2BA A1001 " pdb=" O5' 2BA A1001 " ideal model delta sigma weight residual 1.433 1.362 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C5' 2BA B 901 " pdb=" O5' 2BA B 901 " ideal model delta sigma weight residual 1.433 1.362 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C3' 2BA A1001 " pdb=" O3' 2BA A1001 " ideal model delta sigma weight residual 1.410 1.343 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 9477 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.62: 266 105.62 - 112.73: 5438 112.73 - 119.84: 2986 119.84 - 126.95: 4074 126.95 - 134.06: 126 Bond angle restraints: 12890 Sorted by residual: angle pdb=" C LEU B 373 " pdb=" N ILE B 374 " pdb=" CA ILE B 374 " ideal model delta sigma weight residual 120.24 123.22 -2.98 6.30e-01 2.52e+00 2.24e+01 angle pdb=" C LEU A 373 " pdb=" N ILE A 374 " pdb=" CA ILE A 374 " ideal model delta sigma weight residual 120.24 123.20 -2.96 6.30e-01 2.52e+00 2.20e+01 angle pdb=" N ILE A 438 " pdb=" CA ILE A 438 " pdb=" C ILE A 438 " ideal model delta sigma weight residual 111.81 108.52 3.29 8.60e-01 1.35e+00 1.46e+01 angle pdb=" N ILE B 438 " pdb=" CA ILE B 438 " pdb=" C ILE B 438 " ideal model delta sigma weight residual 111.81 108.55 3.26 8.60e-01 1.35e+00 1.44e+01 angle pdb=" C PHE B 382 " pdb=" N ILE B 383 " pdb=" CA ILE B 383 " ideal model delta sigma weight residual 120.33 117.64 2.69 8.00e-01 1.56e+00 1.13e+01 ... (remaining 12885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.25: 5478 26.25 - 52.50: 351 52.50 - 78.75: 93 78.75 - 105.00: 16 105.00 - 131.25: 30 Dihedral angle restraints: 5968 sinusoidal: 2658 harmonic: 3310 Sorted by residual: dihedral pdb=" C1B LMT B 904 " pdb=" C5B LMT B 904 " pdb=" O5B LMT B 904 " pdb=" C6B LMT B 904 " ideal model delta sinusoidal sigma weight residual 175.31 -53.44 -131.25 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C1B LMT A1004 " pdb=" C5B LMT A1004 " pdb=" O5B LMT A1004 " pdb=" C6B LMT A1004 " ideal model delta sinusoidal sigma weight residual 175.31 -53.48 -131.21 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C1B LMT B 904 " pdb=" C5B LMT B 904 " pdb=" O5B LMT B 904 " pdb=" C4B LMT B 904 " ideal model delta sinusoidal sigma weight residual -59.84 67.26 -127.10 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 5965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1324 0.071 - 0.142: 197 0.142 - 0.213: 35 0.213 - 0.284: 24 0.284 - 0.355: 6 Chirality restraints: 1586 Sorted by residual: chirality pdb=" C3' LMT A1004 " pdb=" C2' LMT A1004 " pdb=" C4' LMT A1004 " pdb=" O3' LMT A1004 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" C3' LMT B 904 " pdb=" C2' LMT B 904 " pdb=" C4' LMT B 904 " pdb=" O3' LMT B 904 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C4' LMT A1005 " pdb=" C3' LMT A1005 " pdb=" C5' LMT A1005 " pdb=" O1B LMT A1005 " both_signs ideal model delta sigma weight residual False -2.55 -2.86 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 1583 not shown) Planarity restraints: 1504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 244 " -0.035 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 245 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 244 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO B 245 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 245 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 245 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 153 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" C LEU A 153 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU A 153 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 154 " -0.009 2.00e-02 2.50e+03 ... (remaining 1501 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.75: 1397 2.75 - 3.34: 11163 3.34 - 3.94: 17916 3.94 - 4.54: 25925 4.54 - 5.14: 37268 Nonbonded interactions: 93669 Sorted by model distance: nonbonded pdb=" O3' LMT A1002 " pdb=" O6' LMT A1005 " model vdw 2.148 2.440 nonbonded pdb=" OH TYR A 81 " pdb=" OE1 GLU A 233 " model vdw 2.251 2.440 nonbonded pdb=" OH TYR B 81 " pdb=" OE1 GLU B 233 " model vdw 2.251 2.440 nonbonded pdb=" O3' LMT A1004 " pdb=" O5B LMT A1004 " model vdw 2.321 2.440 nonbonded pdb=" O3' LMT B 904 " pdb=" O5B LMT B 904 " model vdw 2.321 2.440 ... (remaining 93664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 606 or resid 1001 through 1004)) selection = (chain 'B' and (resid 22 through 606 or resid 901 through 904)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.000 Extract box with map and model: 4.460 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.800 Find NCS groups from input model: 0.560 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 9482 Z= 0.464 Angle : 1.018 10.004 12890 Z= 0.446 Chirality : 0.063 0.355 1586 Planarity : 0.005 0.052 1504 Dihedral : 20.776 131.249 3836 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.84 % Allowed : 0.00 % Favored : 99.16 % 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: 1.55 (0.27), residues: 1132 helix: 1.91 (0.19), residues: 796 sheet: -1.86 (0.47), residues: 90 loop : -0.70 (0.47), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 592 HIS 0.002 0.001 HIS B 505 PHE 0.008 0.001 PHE A 382 TYR 0.024 0.001 TYR B 493 ARG 0.002 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 0.984 Fit side-chains REVERT: B 32 MET cc_start: 0.6824 (mtp) cc_final: 0.6581 (mtp) REVERT: B 252 ARG cc_start: 0.5420 (mtt180) cc_final: 0.5098 (mpt-90) REVERT: B 437 LEU cc_start: 0.6776 (mm) cc_final: 0.6523 (mp) REVERT: B 472 LYS cc_start: 0.7690 (mtmt) cc_final: 0.7391 (mttm) REVERT: B 514 LYS cc_start: 0.7550 (mmmt) cc_final: 0.7203 (mmtp) REVERT: B 518 LYS cc_start: 0.6371 (ttpt) cc_final: 0.6056 (tptm) REVERT: A 32 MET cc_start: 0.6736 (mtp) cc_final: 0.6453 (mtp) REVERT: A 243 LYS cc_start: 0.6273 (mmtp) cc_final: 0.5983 (mmmm) REVERT: A 338 MET cc_start: 0.8337 (ptm) cc_final: 0.8004 (ptm) REVERT: A 440 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5909 (mmm) REVERT: A 472 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7372 (mttm) outliers start: 8 outliers final: 1 residues processed: 135 average time/residue: 0.2455 time to fit residues: 44.8702 Evaluate side-chains 92 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 440 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN A 196 GLN A 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9482 Z= 0.224 Angle : 0.697 10.713 12890 Z= 0.309 Chirality : 0.045 0.211 1586 Planarity : 0.005 0.043 1504 Dihedral : 14.289 79.237 1829 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.57 % Allowed : 6.16 % Favored : 92.28 % 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: 1.60 (0.26), residues: 1132 helix: 1.89 (0.19), residues: 790 sheet: -1.53 (0.49), residues: 90 loop : -0.50 (0.46), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 574 HIS 0.005 0.001 HIS A 372 PHE 0.011 0.001 PHE B 366 TYR 0.014 0.001 TYR A 81 ARG 0.004 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.954 Fit side-chains REVERT: B 32 MET cc_start: 0.6842 (mtp) cc_final: 0.6571 (mtp) REVERT: B 141 HIS cc_start: 0.6497 (m-70) cc_final: 0.6177 (m90) REVERT: B 437 LEU cc_start: 0.6882 (mm) cc_final: 0.6581 (mp) REVERT: B 459 GLU cc_start: 0.7130 (pt0) cc_final: 0.6785 (pt0) REVERT: B 472 LYS cc_start: 0.7817 (mtmt) cc_final: 0.7492 (mttm) REVERT: B 514 LYS cc_start: 0.7615 (mmmt) cc_final: 0.7267 (mmtp) REVERT: B 518 LYS cc_start: 0.6483 (ttpt) cc_final: 0.6143 (tptm) REVERT: B 553 LYS cc_start: 0.6009 (ttmt) cc_final: 0.5086 (tttt) REVERT: A 32 MET cc_start: 0.6737 (mtp) cc_final: 0.6466 (mtp) REVERT: A 437 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6897 (mm) REVERT: A 472 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7521 (mttm) outliers start: 15 outliers final: 10 residues processed: 112 average time/residue: 0.2034 time to fit residues: 32.5224 Evaluate side-chains 102 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN A 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9482 Z= 0.195 Angle : 0.584 8.254 12890 Z= 0.273 Chirality : 0.042 0.275 1586 Planarity : 0.005 0.035 1504 Dihedral : 11.171 59.800 1824 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.36 % Allowed : 9.19 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.27), residues: 1132 helix: 1.91 (0.19), residues: 788 sheet: -1.35 (0.51), residues: 90 loop : -0.49 (0.46), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 574 HIS 0.001 0.000 HIS A 575 PHE 0.012 0.001 PHE B 322 TYR 0.013 0.001 TYR B 81 ARG 0.004 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.972 Fit side-chains REVERT: B 32 MET cc_start: 0.6854 (mtp) cc_final: 0.6576 (mtp) REVERT: B 141 HIS cc_start: 0.6541 (m-70) cc_final: 0.6337 (m-70) REVERT: B 437 LEU cc_start: 0.6975 (mm) cc_final: 0.6662 (mp) REVERT: B 459 GLU cc_start: 0.7257 (pt0) cc_final: 0.6970 (pt0) REVERT: B 472 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7511 (mttm) REVERT: B 514 LYS cc_start: 0.7665 (mmmt) cc_final: 0.7309 (mmtp) REVERT: B 553 LYS cc_start: 0.6072 (ttmt) cc_final: 0.5144 (ttpp) REVERT: A 32 MET cc_start: 0.6649 (mtp) cc_final: 0.5972 (mtt) REVERT: A 437 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6967 (mm) REVERT: A 472 LYS cc_start: 0.8001 (mtmt) cc_final: 0.7638 (mttm) outliers start: 13 outliers final: 10 residues processed: 104 average time/residue: 0.2169 time to fit residues: 31.8550 Evaluate side-chains 100 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 0.0470 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9482 Z= 0.155 Angle : 0.542 6.963 12890 Z= 0.254 Chirality : 0.040 0.176 1586 Planarity : 0.004 0.036 1504 Dihedral : 10.033 57.346 1824 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.15 % Allowed : 11.06 % Favored : 87.79 % 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: 1.81 (0.27), residues: 1132 helix: 2.00 (0.19), residues: 790 sheet: -1.24 (0.51), residues: 90 loop : -0.35 (0.46), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 574 HIS 0.001 0.000 HIS B 604 PHE 0.007 0.001 PHE B 516 TYR 0.012 0.001 TYR B 81 ARG 0.005 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.151 Fit side-chains REVERT: B 32 MET cc_start: 0.6849 (mtp) cc_final: 0.6570 (mtp) REVERT: B 141 HIS cc_start: 0.6492 (m-70) cc_final: 0.6203 (m-70) REVERT: B 437 LEU cc_start: 0.7096 (mm) cc_final: 0.6798 (mp) REVERT: B 459 GLU cc_start: 0.7293 (pt0) cc_final: 0.6995 (pt0) REVERT: B 472 LYS cc_start: 0.7877 (mtmt) cc_final: 0.7525 (mttm) REVERT: B 514 LYS cc_start: 0.7683 (mmmt) cc_final: 0.7317 (mmtp) REVERT: B 562 MET cc_start: 0.6873 (ttt) cc_final: 0.6671 (ttt) REVERT: A 437 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6986 (mm) REVERT: A 472 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7567 (mttm) outliers start: 11 outliers final: 7 residues processed: 97 average time/residue: 0.2253 time to fit residues: 31.0289 Evaluate side-chains 92 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN B 460 GLN B 580 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9482 Z= 0.176 Angle : 0.544 6.836 12890 Z= 0.256 Chirality : 0.040 0.190 1586 Planarity : 0.004 0.034 1504 Dihedral : 10.159 58.699 1824 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.36 % Allowed : 11.80 % Favored : 86.85 % 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: 1.76 (0.26), residues: 1132 helix: 1.99 (0.19), residues: 786 sheet: -1.09 (0.52), residues: 90 loop : -0.50 (0.45), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 574 HIS 0.001 0.000 HIS A 575 PHE 0.008 0.001 PHE A 605 TYR 0.013 0.001 TYR A 81 ARG 0.004 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.047 Fit side-chains REVERT: B 32 MET cc_start: 0.6890 (mtp) cc_final: 0.6588 (mtp) REVERT: B 141 HIS cc_start: 0.6444 (m-70) cc_final: 0.6082 (m-70) REVERT: B 402 LYS cc_start: 0.7610 (tttm) cc_final: 0.7394 (tptm) REVERT: B 437 LEU cc_start: 0.7118 (mm) cc_final: 0.6826 (mp) REVERT: B 459 GLU cc_start: 0.7259 (pt0) cc_final: 0.7035 (pt0) REVERT: B 460 GLN cc_start: 0.7544 (tt0) cc_final: 0.7187 (tt0) REVERT: B 472 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7504 (mttm) REVERT: B 514 LYS cc_start: 0.7698 (mmmt) cc_final: 0.7333 (mmtp) REVERT: A 437 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7145 (mm) REVERT: A 459 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6511 (mt-10) REVERT: A 472 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7597 (mttm) outliers start: 13 outliers final: 8 residues processed: 103 average time/residue: 0.2326 time to fit residues: 34.0925 Evaluate side-chains 98 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 64 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9482 Z= 0.156 Angle : 0.532 6.829 12890 Z= 0.250 Chirality : 0.040 0.183 1586 Planarity : 0.004 0.036 1504 Dihedral : 9.869 58.433 1824 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.36 % Allowed : 12.53 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.27), residues: 1132 helix: 2.02 (0.19), residues: 790 sheet: -0.93 (0.53), residues: 90 loop : -0.41 (0.46), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 574 HIS 0.001 0.000 HIS A 372 PHE 0.009 0.001 PHE B 366 TYR 0.011 0.001 TYR A 81 ARG 0.003 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.919 Fit side-chains REVERT: B 32 MET cc_start: 0.6885 (mtp) cc_final: 0.6580 (mtp) REVERT: B 141 HIS cc_start: 0.6460 (m-70) cc_final: 0.6071 (m-70) REVERT: B 402 LYS cc_start: 0.7493 (tttm) cc_final: 0.7272 (tptm) REVERT: B 437 LEU cc_start: 0.7102 (mm) cc_final: 0.6784 (mp) REVERT: B 459 GLU cc_start: 0.7315 (pt0) cc_final: 0.7090 (pt0) REVERT: B 460 GLN cc_start: 0.7594 (tt0) cc_final: 0.7030 (tt0) REVERT: B 472 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7521 (mttm) REVERT: B 514 LYS cc_start: 0.7686 (mmmt) cc_final: 0.7322 (mmtp) REVERT: A 437 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7177 (mm) REVERT: A 472 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7615 (mttm) outliers start: 13 outliers final: 8 residues processed: 102 average time/residue: 0.2164 time to fit residues: 31.0891 Evaluate side-chains 98 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 109 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN A 558 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9482 Z= 0.184 Angle : 0.546 6.808 12890 Z= 0.258 Chirality : 0.040 0.178 1586 Planarity : 0.004 0.035 1504 Dihedral : 9.901 57.467 1824 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.57 % Allowed : 12.21 % Favored : 86.22 % 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: 1.80 (0.26), residues: 1132 helix: 1.99 (0.19), residues: 788 sheet: -0.84 (0.53), residues: 90 loop : -0.49 (0.45), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 574 HIS 0.002 0.000 HIS A 372 PHE 0.007 0.001 PHE B 516 TYR 0.013 0.001 TYR B 81 ARG 0.007 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 1.025 Fit side-chains REVERT: B 32 MET cc_start: 0.6905 (mtp) cc_final: 0.6589 (mtp) REVERT: B 141 HIS cc_start: 0.6428 (m-70) cc_final: 0.6010 (m-70) REVERT: B 355 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5569 (tp) REVERT: B 460 GLN cc_start: 0.7592 (tt0) cc_final: 0.7286 (tm-30) REVERT: B 472 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7671 (mttm) REVERT: B 514 LYS cc_start: 0.7694 (mmmt) cc_final: 0.7331 (mmtp) REVERT: B 536 TYR cc_start: 0.6906 (m-10) cc_final: 0.6388 (m-80) REVERT: B 553 LYS cc_start: 0.6128 (ttmt) cc_final: 0.5067 (ttpp) REVERT: A 32 MET cc_start: 0.6817 (mtp) cc_final: 0.6116 (mtt) REVERT: A 420 MET cc_start: 0.5613 (tmm) cc_final: 0.5368 (tmm) REVERT: A 437 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7165 (mm) REVERT: A 472 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7728 (mttt) outliers start: 15 outliers final: 9 residues processed: 98 average time/residue: 0.2305 time to fit residues: 31.7439 Evaluate side-chains 97 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.0980 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9482 Z= 0.189 Angle : 0.554 7.201 12890 Z= 0.260 Chirality : 0.041 0.202 1586 Planarity : 0.004 0.035 1504 Dihedral : 9.916 57.137 1824 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.57 % Allowed : 12.73 % Favored : 85.70 % 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: 1.74 (0.26), residues: 1132 helix: 1.94 (0.19), residues: 788 sheet: -0.61 (0.54), residues: 92 loop : -0.62 (0.45), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 574 HIS 0.002 0.001 HIS A 372 PHE 0.008 0.001 PHE B 366 TYR 0.013 0.001 TYR B 81 ARG 0.007 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.019 Fit side-chains REVERT: B 32 MET cc_start: 0.6881 (mtp) cc_final: 0.6565 (mtp) REVERT: B 141 HIS cc_start: 0.6422 (m-70) cc_final: 0.5951 (m-70) REVERT: B 355 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5553 (tp) REVERT: B 472 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7689 (mttt) REVERT: B 512 GLN cc_start: 0.6979 (mp10) cc_final: 0.6426 (mt0) REVERT: B 514 LYS cc_start: 0.7671 (mmmt) cc_final: 0.7305 (mmtp) REVERT: B 536 TYR cc_start: 0.6910 (m-10) cc_final: 0.6427 (m-80) REVERT: B 553 LYS cc_start: 0.6201 (ttmt) cc_final: 0.5120 (ttpp) REVERT: A 32 MET cc_start: 0.6856 (mtp) cc_final: 0.6166 (mtt) REVERT: A 355 LEU cc_start: 0.5488 (OUTLIER) cc_final: 0.5252 (tp) REVERT: A 420 MET cc_start: 0.5577 (tmm) cc_final: 0.5336 (tmm) REVERT: A 437 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7207 (mm) REVERT: A 472 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7689 (mttt) outliers start: 15 outliers final: 11 residues processed: 101 average time/residue: 0.2642 time to fit residues: 36.9307 Evaluate side-chains 101 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN B 460 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9482 Z= 0.177 Angle : 0.548 7.002 12890 Z= 0.258 Chirality : 0.040 0.188 1586 Planarity : 0.004 0.035 1504 Dihedral : 9.850 57.730 1824 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.88 % Allowed : 12.63 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.26), residues: 1132 helix: 1.94 (0.19), residues: 788 sheet: -0.62 (0.54), residues: 92 loop : -0.61 (0.45), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 574 HIS 0.002 0.000 HIS A 372 PHE 0.007 0.001 PHE B 366 TYR 0.012 0.001 TYR B 81 ARG 0.007 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 1.041 Fit side-chains REVERT: B 32 MET cc_start: 0.6875 (mtp) cc_final: 0.6569 (mtp) REVERT: B 141 HIS cc_start: 0.6363 (m-70) cc_final: 0.5866 (m-70) REVERT: B 355 LEU cc_start: 0.5769 (OUTLIER) cc_final: 0.5513 (tp) REVERT: B 460 GLN cc_start: 0.7506 (tt0) cc_final: 0.7269 (tt0) REVERT: B 472 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7693 (mttt) REVERT: B 512 GLN cc_start: 0.6981 (mp10) cc_final: 0.6429 (mt0) REVERT: B 514 LYS cc_start: 0.7641 (mmmt) cc_final: 0.7272 (mmtp) REVERT: B 536 TYR cc_start: 0.6977 (m-80) cc_final: 0.6498 (m-80) REVERT: B 553 LYS cc_start: 0.6149 (ttmt) cc_final: 0.5075 (ttpp) REVERT: A 32 MET cc_start: 0.6863 (mtp) cc_final: 0.6575 (mtp) REVERT: A 355 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.5242 (tp) REVERT: A 420 MET cc_start: 0.5570 (tmm) cc_final: 0.5334 (tmm) REVERT: A 437 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7216 (mm) REVERT: A 472 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7658 (mttt) outliers start: 18 outliers final: 12 residues processed: 101 average time/residue: 0.2216 time to fit residues: 31.4744 Evaluate side-chains 104 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9482 Z= 0.212 Angle : 0.572 7.492 12890 Z= 0.270 Chirality : 0.041 0.246 1586 Planarity : 0.005 0.035 1504 Dihedral : 10.063 59.106 1824 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.67 % Allowed : 12.94 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.26), residues: 1132 helix: 1.84 (0.19), residues: 788 sheet: -0.62 (0.54), residues: 92 loop : -0.65 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 574 HIS 0.002 0.001 HIS A 372 PHE 0.010 0.001 PHE B 366 TYR 0.014 0.001 TYR B 81 ARG 0.007 0.000 ARG B 510 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 1.005 Fit side-chains REVERT: B 32 MET cc_start: 0.6859 (mtp) cc_final: 0.6538 (mtp) REVERT: B 355 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5558 (tp) REVERT: B 460 GLN cc_start: 0.7634 (tt0) cc_final: 0.7265 (tm-30) REVERT: B 472 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7747 (mttt) REVERT: B 512 GLN cc_start: 0.7084 (mp10) cc_final: 0.6526 (mt0) REVERT: B 536 TYR cc_start: 0.6996 (m-80) cc_final: 0.6506 (m-80) REVERT: B 553 LYS cc_start: 0.6184 (ttmt) cc_final: 0.5126 (ttpp) REVERT: A 32 MET cc_start: 0.6864 (mtp) cc_final: 0.6573 (mtp) REVERT: A 355 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.5248 (tp) REVERT: A 420 MET cc_start: 0.5572 (tmm) cc_final: 0.5332 (tmm) REVERT: A 437 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7245 (mm) REVERT: A 472 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7601 (mttt) outliers start: 16 outliers final: 13 residues processed: 95 average time/residue: 0.2277 time to fit residues: 30.4367 Evaluate side-chains 99 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 0.0270 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.124768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.107299 restraints weight = 10231.155| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 0.97 r_work: 0.2944 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9482 Z= 0.165 Angle : 0.545 8.493 12890 Z= 0.256 Chirality : 0.040 0.201 1586 Planarity : 0.004 0.036 1504 Dihedral : 9.802 59.529 1824 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.77 % Allowed : 13.05 % Favored : 85.18 % 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: 1.73 (0.26), residues: 1132 helix: 1.92 (0.19), residues: 788 sheet: -0.56 (0.54), residues: 92 loop : -0.58 (0.45), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 574 HIS 0.002 0.000 HIS A 372 PHE 0.008 0.001 PHE B 366 TYR 0.012 0.001 TYR A 81 ARG 0.007 0.000 ARG B 510 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1915.13 seconds wall clock time: 36 minutes 7.94 seconds (2167.94 seconds total)