Starting phenix.real_space_refine on Fri Feb 14 05:34:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yuz_10936/02_2025/6yuz_10936.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yuz_10936/02_2025/6yuz_10936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6yuz_10936/02_2025/6yuz_10936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yuz_10936/02_2025/6yuz_10936.map" model { file = "/net/cci-nas-00/data/ceres_data/6yuz_10936/02_2025/6yuz_10936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yuz_10936/02_2025/6yuz_10936.cif" } resolution = 2.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 48 5.16 5 C 6226 2.51 5 N 1640 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9782 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4834 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 22, 'TRANS': 571} Chain: "C" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4834 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 22, 'TRANS': 571} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.50, per 1000 atoms: 0.66 Number of scatterers: 9782 At special positions: 0 Unit cell: (133.083, 92.907, 104.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 48 16.00 O 1866 8.00 N 1640 7.00 C 6226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.08 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 685 " distance=2.04 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 666 " distance=2.04 Simple disulfide: pdb=" SG CYS C 673 " - pdb=" SG CYS C 685 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 332 " " NAG A 702 " - " ASN A 513 " " NAG A 703 " - " ASN A 575 " " NAG A 704 " - " ASN A 261 " " NAG C 701 " - " ASN C 332 " " NAG C 702 " - " ASN C 513 " " NAG C 703 " - " ASN C 575 " " NAG C 704 " - " ASN C 261 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 16 sheets defined 32.0% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 92 through 111 removed outlier: 4.258A pdb=" N LEU A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.646A pdb=" N ILE A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.578A pdb=" N ILE A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 203 removed outlier: 3.566A pdb=" N LYS A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.597A pdb=" N TYR A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.761A pdb=" N LYS A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.669A pdb=" N ASN A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.984A pdb=" N SER A 507 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 549 through 562 Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.772A pdb=" N ASN A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'C' and resid 93 through 111 removed outlier: 4.258A pdb=" N LEU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 removed outlier: 3.648A pdb=" N ILE C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 removed outlier: 3.579A pdb=" N ILE C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 removed outlier: 3.566A pdb=" N LYS C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 230 through 236 removed outlier: 3.597A pdb=" N TYR C 233 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 234 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 307 removed outlier: 3.761A pdb=" N LYS C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 306 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 420 through 435 removed outlier: 3.671A pdb=" N ASN C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 503 through 507 removed outlier: 3.981A pdb=" N SER C 507 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 519 Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 549 through 562 Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.772A pdb=" N ASN C 566 " --> pdb=" O GLU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 659 Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 125 removed outlier: 6.296A pdb=" N MET A 123 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP A 443 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR A 479 " --> pdb=" O TRP A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 170 removed outlier: 7.284A pdb=" N LYS A 167 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 169 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLY A 176 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 211 removed outlier: 3.587A pdb=" N GLY A 382 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA5, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA6, first strand: chain 'A' and resid 632 through 634 removed outlier: 5.127A pdb=" N ARG A 619 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 649 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE A 647 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER A 623 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY A 645 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 604 through 606 Processing sheet with id=AA8, first strand: chain 'A' and resid 673 through 674 Processing sheet with id=AA9, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.294A pdb=" N MET C 123 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP C 443 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR C 479 " --> pdb=" O TRP C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 167 through 170 removed outlier: 7.285A pdb=" N LYS C 167 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 169 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLY C 176 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 209 through 211 removed outlier: 3.587A pdb=" N GLY C 382 " --> pdb=" O PHE C 311 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AB4, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AB5, first strand: chain 'C' and resid 632 through 634 removed outlier: 5.087A pdb=" N ARG C 619 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 649 " --> pdb=" O ARG C 619 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 647 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER C 623 " --> pdb=" O GLY C 645 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY C 645 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 604 through 606 Processing sheet with id=AB7, first strand: chain 'C' and resid 673 through 674 275 hydrogen bonds defined for protein. 741 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: 2.78 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1604 1.31 - 1.44: 2882 1.44 - 1.56: 5462 1.56 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 10030 Sorted by residual: bond pdb=" C7 NAG C 704 " pdb=" N2 NAG C 704 " ideal model delta sigma weight residual 1.346 1.465 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C7 NAG A 704 " pdb=" N2 NAG A 704 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C7 NAG C 702 " pdb=" N2 NAG C 702 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C7 NAG A 702 " pdb=" N2 NAG A 702 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C7 NAG C 701 " pdb=" N2 NAG C 701 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.39e+01 ... (remaining 10025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 12904 1.06 - 2.13: 495 2.13 - 3.19: 143 3.19 - 4.25: 52 4.25 - 5.32: 26 Bond angle restraints: 13620 Sorted by residual: angle pdb=" CA LEU C 573 " pdb=" C LEU C 573 " pdb=" O LEU C 573 " ideal model delta sigma weight residual 120.84 116.79 4.05 1.08e+00 8.57e-01 1.40e+01 angle pdb=" N THR A 624 " pdb=" CA THR A 624 " pdb=" C THR A 624 " ideal model delta sigma weight residual 111.36 107.61 3.75 1.09e+00 8.42e-01 1.19e+01 angle pdb=" CA LEU A 573 " pdb=" C LEU A 573 " pdb=" O LEU A 573 " ideal model delta sigma weight residual 120.70 117.21 3.49 1.14e+00 7.69e-01 9.39e+00 angle pdb=" CA ASN C 575 " pdb=" CB ASN C 575 " pdb=" CG ASN C 575 " ideal model delta sigma weight residual 112.60 115.65 -3.05 1.00e+00 1.00e+00 9.32e+00 angle pdb=" CA ASN A 625 " pdb=" C ASN A 625 " pdb=" O ASN A 625 " ideal model delta sigma weight residual 120.54 117.42 3.12 1.04e+00 9.25e-01 8.99e+00 ... (remaining 13615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 5624 22.41 - 44.83: 318 44.83 - 67.24: 52 67.24 - 89.66: 16 89.66 - 112.07: 16 Dihedral angle restraints: 6026 sinusoidal: 2542 harmonic: 3484 Sorted by residual: dihedral pdb=" CB CYS A 673 " pdb=" SG CYS A 673 " pdb=" SG CYS A 685 " pdb=" CB CYS A 685 " ideal model delta sinusoidal sigma weight residual -86.00 -26.50 -59.50 1 1.00e+01 1.00e-02 4.73e+01 dihedral pdb=" CB CYS C 673 " pdb=" SG CYS C 673 " pdb=" SG CYS C 685 " pdb=" CB CYS C 685 " ideal model delta sinusoidal sigma weight residual -86.00 -26.52 -59.48 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CA ASN A 261 " pdb=" C ASN A 261 " pdb=" N SER A 262 " pdb=" CA SER A 262 " ideal model delta harmonic sigma weight residual 180.00 152.18 27.82 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 6023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1353 0.071 - 0.142: 124 0.142 - 0.213: 14 0.213 - 0.284: 1 0.284 - 0.355: 2 Chirality restraints: 1494 Sorted by residual: chirality pdb=" CA ARG A 574 " pdb=" N ARG A 574 " pdb=" C ARG A 574 " pdb=" CB ARG A 574 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA ARG C 574 " pdb=" N ARG C 574 " pdb=" C ARG C 574 " pdb=" CB ARG C 574 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ILE A 620 " pdb=" N ILE A 620 " pdb=" C ILE A 620 " pdb=" CB ILE A 620 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1491 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 572 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C HIS A 572 " 0.042 2.00e-02 2.50e+03 pdb=" O HIS A 572 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU A 573 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 336 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO A 337 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 336 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO C 337 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " 0.024 5.00e-02 4.00e+02 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1791 2.77 - 3.30: 9088 3.30 - 3.83: 16306 3.83 - 4.37: 20490 4.37 - 4.90: 33896 Nonbonded interactions: 81571 Sorted by model distance: nonbonded pdb=" OH TYR C 480 " pdb=" O SER C 507 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR A 480 " pdb=" O SER A 507 " model vdw 2.235 3.040 nonbonded pdb=" O SER A 450 " pdb=" OG SER A 505 " model vdw 2.270 3.040 nonbonded pdb=" O SER C 450 " pdb=" OG SER C 505 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR A 151 " pdb=" OE2 GLU A 483 " model vdw 2.292 3.040 ... (remaining 81566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.300 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.006 0.119 10030 Z= 0.389 Angle : 0.576 5.316 13620 Z= 0.333 Chirality : 0.045 0.355 1494 Planarity : 0.003 0.043 1740 Dihedral : 15.649 112.073 3768 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.80 % Favored : 95.95 % Rotamer: Outliers : 2.33 % Allowed : 14.15 % Favored : 83.52 % Cbeta Deviations : 0.09 % 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: -3.67 (0.20), residues: 1184 helix: -3.59 (0.14), residues: 292 sheet: -2.23 (0.42), residues: 132 loop : -2.06 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 264 HIS 0.002 0.001 HIS A 276 PHE 0.009 0.001 PHE C 407 TYR 0.006 0.001 TYR C 579 ARG 0.002 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.067 Fit side-chains REVERT: A 574 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7480 (ptm160) REVERT: A 619 ARG cc_start: 0.7435 (mtp-110) cc_final: 0.7133 (mmm-85) REVERT: A 626 SER cc_start: 0.8141 (m) cc_final: 0.7485 (t) REVERT: C 437 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6875 (mm-30) REVERT: C 574 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7380 (ptm160) outliers start: 25 outliers final: 9 residues processed: 160 average time/residue: 1.3543 time to fit residues: 231.6468 Evaluate side-chains 92 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 574 ARG Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 677 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 244 HIS A 272 GLN A 354 GLN A 358 HIS A 366 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 ASN A 544 GLN A 572 HIS A 609 ASN A 659 GLN C 220 HIS C 244 HIS ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN C 277 GLN C 358 HIS C 366 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN C 544 GLN ** C 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.077848 restraints weight = 16277.982| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.39 r_work: 0.2904 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10030 Z= 0.199 Angle : 0.536 7.136 13620 Z= 0.279 Chirality : 0.044 0.219 1494 Planarity : 0.004 0.041 1740 Dihedral : 7.664 58.651 1487 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.98 % Favored : 94.85 % Rotamer: Outliers : 3.35 % Allowed : 15.46 % Favored : 81.19 % 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: -2.29 (0.22), residues: 1184 helix: -1.08 (0.25), residues: 302 sheet: -1.48 (0.48), residues: 108 loop : -1.78 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 303 HIS 0.005 0.001 HIS A 276 PHE 0.018 0.002 PHE C 407 TYR 0.013 0.001 TYR C 151 ARG 0.004 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7324 (t70) REVERT: A 334 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8827 (p) REVERT: A 574 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7584 (ptt90) REVERT: A 619 ARG cc_start: 0.8120 (mtp-110) cc_final: 0.7479 (mmm-85) REVERT: A 626 SER cc_start: 0.8092 (m) cc_final: 0.7277 (t) REVERT: C 334 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8810 (p) REVERT: C 574 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7497 (ptt90) REVERT: C 579 TYR cc_start: 0.7204 (p90) cc_final: 0.6932 (p90) outliers start: 36 outliers final: 15 residues processed: 118 average time/residue: 1.0952 time to fit residues: 140.5611 Evaluate side-chains 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 574 ARG Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 90 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 277 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 354 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.072046 restraints weight = 16440.397| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.43 r_work: 0.2790 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10030 Z= 0.244 Angle : 0.539 8.290 13620 Z= 0.287 Chirality : 0.045 0.271 1494 Planarity : 0.004 0.038 1740 Dihedral : 6.831 53.391 1482 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.56 % Favored : 95.27 % Rotamer: Outliers : 3.07 % Allowed : 15.55 % Favored : 81.38 % 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: -1.52 (0.23), residues: 1184 helix: 0.08 (0.28), residues: 306 sheet: -1.38 (0.46), residues: 124 loop : -1.46 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 303 HIS 0.008 0.001 HIS C 265 PHE 0.017 0.002 PHE C 407 TYR 0.009 0.001 TYR A 166 ARG 0.004 0.000 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 HIS cc_start: 0.7678 (OUTLIER) cc_final: 0.7367 (t70) REVERT: A 415 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.6971 (mmp) REVERT: A 619 ARG cc_start: 0.8163 (mtp-110) cc_final: 0.7649 (mmm-85) REVERT: A 628 ASP cc_start: 0.7983 (m-30) cc_final: 0.7525 (m-30) REVERT: A 653 LYS cc_start: 0.8787 (ptpp) cc_final: 0.8399 (mtmt) REVERT: A 682 TYR cc_start: 0.8426 (m-10) cc_final: 0.8164 (m-10) REVERT: C 333 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8467 (mptp) REVERT: C 415 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7187 (mmp) REVERT: C 574 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7817 (mtp-110) REVERT: C 619 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7334 (mmm-85) REVERT: C 663 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7790 (mmm160) outliers start: 33 outliers final: 18 residues processed: 114 average time/residue: 1.0805 time to fit residues: 134.2286 Evaluate side-chains 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 574 ARG Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 104 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.095386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.072964 restraints weight = 16338.013| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.44 r_work: 0.2812 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10030 Z= 0.183 Angle : 0.487 10.383 13620 Z= 0.258 Chirality : 0.043 0.230 1494 Planarity : 0.003 0.037 1740 Dihedral : 5.951 42.821 1478 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.07 % Allowed : 15.92 % Favored : 81.01 % 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: -1.18 (0.24), residues: 1184 helix: 0.73 (0.30), residues: 294 sheet: -1.31 (0.47), residues: 124 loop : -1.36 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 303 HIS 0.004 0.001 HIS A 276 PHE 0.014 0.001 PHE C 407 TYR 0.008 0.001 TYR C 582 ARG 0.003 0.000 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 1.118 Fit side-chains REVERT: A 265 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.7404 (t70) REVERT: A 381 MET cc_start: 0.9288 (ttp) cc_final: 0.9024 (ttt) REVERT: A 415 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6971 (mmp) REVERT: A 619 ARG cc_start: 0.8167 (mtp-110) cc_final: 0.7792 (mmm-85) REVERT: A 653 LYS cc_start: 0.8805 (ptpp) cc_final: 0.8439 (mtmt) REVERT: C 333 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8434 (mptp) REVERT: C 606 ASN cc_start: 0.8694 (t0) cc_final: 0.8309 (t0) REVERT: C 610 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8022 (mtm) REVERT: C 663 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7778 (mmm160) outliers start: 33 outliers final: 17 residues processed: 117 average time/residue: 0.9696 time to fit residues: 124.7971 Evaluate side-chains 106 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.069618 restraints weight = 16388.791| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.44 r_work: 0.2743 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10030 Z= 0.321 Angle : 0.582 9.823 13620 Z= 0.305 Chirality : 0.047 0.281 1494 Planarity : 0.004 0.040 1740 Dihedral : 6.345 47.993 1474 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.45 % Allowed : 17.23 % Favored : 79.33 % 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 (0.24), residues: 1184 helix: 0.47 (0.30), residues: 310 sheet: -1.57 (0.47), residues: 132 loop : -1.35 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 303 HIS 0.008 0.002 HIS A 276 PHE 0.018 0.002 PHE A 407 TYR 0.012 0.001 TYR C 166 ARG 0.010 0.001 ARG C 619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 1.121 Fit side-chains REVERT: A 265 HIS cc_start: 0.7710 (OUTLIER) cc_final: 0.7368 (t70) REVERT: A 381 MET cc_start: 0.9257 (ttp) cc_final: 0.8935 (ttt) REVERT: A 415 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7257 (mmp) REVERT: A 444 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8956 (mtm) REVERT: A 619 ARG cc_start: 0.8183 (mtp-110) cc_final: 0.7831 (mmm-85) REVERT: A 653 LYS cc_start: 0.8833 (ptpp) cc_final: 0.8467 (mtmt) REVERT: C 265 HIS cc_start: 0.7285 (OUTLIER) cc_final: 0.6940 (t70) REVERT: C 415 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7398 (mmp) REVERT: C 606 ASN cc_start: 0.8783 (t0) cc_final: 0.8568 (t0) REVERT: C 610 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8092 (mtm) REVERT: C 663 ARG cc_start: 0.8314 (mtt180) cc_final: 0.7805 (mmm160) outliers start: 37 outliers final: 24 residues processed: 114 average time/residue: 0.9865 time to fit residues: 123.5273 Evaluate side-chains 110 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 81 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.093165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.070732 restraints weight = 16347.063| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.43 r_work: 0.2758 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10030 Z= 0.259 Angle : 0.535 11.887 13620 Z= 0.282 Chirality : 0.046 0.306 1494 Planarity : 0.004 0.051 1740 Dihedral : 5.980 45.445 1474 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.89 % Allowed : 18.16 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.24), residues: 1184 helix: 0.74 (0.30), residues: 300 sheet: -1.65 (0.43), residues: 148 loop : -1.24 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 303 HIS 0.006 0.001 HIS A 276 PHE 0.015 0.001 PHE A 407 TYR 0.010 0.001 TYR C 582 ARG 0.005 0.001 ARG C 619 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 1.187 Fit side-chains REVERT: A 265 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.7321 (t70) REVERT: A 381 MET cc_start: 0.9262 (ttp) cc_final: 0.8980 (ttt) REVERT: A 415 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7246 (mmp) REVERT: A 610 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8444 (mtm) REVERT: A 619 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7769 (ttm110) REVERT: A 653 LYS cc_start: 0.8797 (ptpp) cc_final: 0.8466 (mtmt) REVERT: C 265 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6940 (t70) REVERT: C 415 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7346 (mmp) REVERT: C 606 ASN cc_start: 0.8835 (t0) cc_final: 0.8627 (t0) REVERT: C 610 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8112 (mtm) REVERT: C 663 ARG cc_start: 0.8379 (mtt180) cc_final: 0.7813 (mmm160) outliers start: 31 outliers final: 19 residues processed: 107 average time/residue: 1.0149 time to fit residues: 119.0003 Evaluate side-chains 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 104 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.094272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.071569 restraints weight = 16444.523| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.45 r_work: 0.2782 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10030 Z= 0.197 Angle : 0.504 9.551 13620 Z= 0.267 Chirality : 0.044 0.254 1494 Planarity : 0.003 0.053 1740 Dihedral : 5.551 43.202 1472 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.51 % Allowed : 19.09 % Favored : 78.40 % 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: -0.98 (0.24), residues: 1184 helix: 0.95 (0.30), residues: 298 sheet: -1.62 (0.43), residues: 148 loop : -1.15 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 431 HIS 0.005 0.001 HIS A 276 PHE 0.014 0.001 PHE C 407 TYR 0.009 0.001 TYR C 582 ARG 0.011 0.000 ARG C 619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 1.129 Fit side-chains REVERT: A 265 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.7321 (t70) REVERT: A 336 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8735 (mt) REVERT: A 381 MET cc_start: 0.9258 (ttp) cc_final: 0.9004 (ttt) REVERT: A 415 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7164 (mmp) REVERT: A 610 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8532 (mtm) REVERT: A 619 ARG cc_start: 0.8131 (mtp-110) cc_final: 0.7763 (ttm110) REVERT: A 653 LYS cc_start: 0.8823 (ptpp) cc_final: 0.8499 (mtmt) REVERT: C 265 HIS cc_start: 0.7255 (OUTLIER) cc_final: 0.7017 (t70) REVERT: C 336 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8707 (mt) REVERT: C 415 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7280 (mmp) REVERT: C 653 LYS cc_start: 0.8774 (mtpp) cc_final: 0.8140 (mttt) REVERT: C 663 ARG cc_start: 0.8355 (mtt180) cc_final: 0.7793 (mmm160) outliers start: 27 outliers final: 17 residues processed: 108 average time/residue: 1.0176 time to fit residues: 120.7011 Evaluate side-chains 108 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 21 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.072652 restraints weight = 16536.371| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.47 r_work: 0.2801 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10030 Z= 0.168 Angle : 0.497 11.718 13620 Z= 0.262 Chirality : 0.043 0.247 1494 Planarity : 0.003 0.049 1740 Dihedral : 5.176 41.685 1470 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.05 % Allowed : 19.09 % Favored : 78.86 % 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: -0.86 (0.25), residues: 1184 helix: 1.14 (0.30), residues: 296 sheet: -1.58 (0.42), residues: 152 loop : -1.09 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 431 HIS 0.004 0.001 HIS A 276 PHE 0.013 0.001 PHE C 407 TYR 0.009 0.001 TYR C 582 ARG 0.010 0.000 ARG C 619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.135 Fit side-chains REVERT: A 265 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.7319 (t70) REVERT: A 336 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8685 (mt) REVERT: A 381 MET cc_start: 0.9251 (ttp) cc_final: 0.9000 (ttt) REVERT: A 415 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7041 (mmp) REVERT: A 610 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8584 (mtm) REVERT: A 619 ARG cc_start: 0.8119 (mtp-110) cc_final: 0.7747 (ttm110) REVERT: A 653 LYS cc_start: 0.8815 (ptpp) cc_final: 0.8498 (mtmt) REVERT: C 265 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.7034 (t70) REVERT: C 336 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8686 (mt) REVERT: C 415 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7180 (mmp) REVERT: C 610 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8170 (mtm) REVERT: C 663 ARG cc_start: 0.8343 (mtt180) cc_final: 0.7766 (mmm160) outliers start: 22 outliers final: 15 residues processed: 107 average time/residue: 1.0506 time to fit residues: 122.9691 Evaluate side-chains 110 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.071077 restraints weight = 16507.247| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.46 r_work: 0.2762 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10030 Z= 0.231 Angle : 0.525 10.532 13620 Z= 0.278 Chirality : 0.045 0.253 1494 Planarity : 0.004 0.059 1740 Dihedral : 5.272 43.279 1470 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.23 % Allowed : 19.09 % Favored : 78.68 % 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: -0.89 (0.25), residues: 1184 helix: 1.08 (0.30), residues: 296 sheet: -1.63 (0.43), residues: 148 loop : -1.09 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 303 HIS 0.005 0.001 HIS A 276 PHE 0.015 0.001 PHE A 407 TYR 0.010 0.001 TYR A 682 ARG 0.012 0.000 ARG C 619 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 1.177 Fit side-chains REVERT: A 265 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.7109 (t70) REVERT: A 381 MET cc_start: 0.9216 (ttp) cc_final: 0.8942 (ttt) REVERT: A 415 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7151 (mmp) REVERT: A 610 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8504 (mtm) REVERT: A 619 ARG cc_start: 0.8120 (mtp-110) cc_final: 0.7722 (ttm110) REVERT: A 653 LYS cc_start: 0.8834 (ptpp) cc_final: 0.8513 (mtmt) REVERT: C 265 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6975 (t70) REVERT: C 415 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7303 (mmp) REVERT: C 610 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8161 (mtm) REVERT: C 663 ARG cc_start: 0.8367 (mtt180) cc_final: 0.7778 (mmm160) outliers start: 24 outliers final: 16 residues processed: 106 average time/residue: 1.0199 time to fit residues: 118.9103 Evaluate side-chains 106 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 96 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.095342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.072764 restraints weight = 16451.022| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.47 r_work: 0.2800 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10030 Z= 0.158 Angle : 0.496 11.551 13620 Z= 0.262 Chirality : 0.043 0.226 1494 Planarity : 0.003 0.064 1740 Dihedral : 5.036 41.285 1470 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.86 % Allowed : 19.27 % Favored : 78.86 % 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: -0.82 (0.25), residues: 1184 helix: 1.25 (0.30), residues: 296 sheet: -1.61 (0.43), residues: 148 loop : -1.09 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 431 HIS 0.009 0.001 HIS A 265 PHE 0.012 0.001 PHE A 407 TYR 0.009 0.001 TYR C 579 ARG 0.014 0.000 ARG C 619 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.044 Fit side-chains REVERT: A 381 MET cc_start: 0.9242 (ttp) cc_final: 0.8990 (ttt) REVERT: A 415 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7007 (mmp) REVERT: A 619 ARG cc_start: 0.8149 (mtp-110) cc_final: 0.7747 (ttm110) REVERT: A 653 LYS cc_start: 0.8830 (ptpp) cc_final: 0.8485 (mtmt) REVERT: C 415 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7159 (mmp) REVERT: C 610 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8188 (mtm) REVERT: C 663 ARG cc_start: 0.8359 (mtt180) cc_final: 0.7760 (mmm160) outliers start: 20 outliers final: 16 residues processed: 102 average time/residue: 1.0546 time to fit residues: 117.7923 Evaluate side-chains 100 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 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 265 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.071458 restraints weight = 16437.350| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.47 r_work: 0.2771 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10030 Z= 0.208 Angle : 0.510 10.295 13620 Z= 0.270 Chirality : 0.044 0.233 1494 Planarity : 0.004 0.065 1740 Dihedral : 5.108 42.190 1470 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.14 % Allowed : 18.99 % Favored : 78.86 % 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: -0.84 (0.25), residues: 1184 helix: 1.17 (0.30), residues: 298 sheet: -1.61 (0.43), residues: 148 loop : -1.08 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 303 HIS 0.006 0.001 HIS C 276 PHE 0.014 0.001 PHE A 407 TYR 0.011 0.001 TYR A 682 ARG 0.014 0.000 ARG C 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6757.19 seconds wall clock time: 120 minutes 0.01 seconds (7200.01 seconds total)