Starting phenix.real_space_refine on Sun Jul 27 23:49:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yuz_10936/07_2025/6yuz_10936.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yuz_10936/07_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_10936/07_2025/6yuz_10936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yuz_10936/07_2025/6yuz_10936.map" model { file = "/net/cci-nas-00/data/ceres_data/6yuz_10936/07_2025/6yuz_10936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yuz_10936/07_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-5711/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: 6.96, per 1000 atoms: 0.71 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: 3.06 Conformation dependent library (CDL) restraints added in 1.7 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: 1.07 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: 2.46 Time building geometry restraints manager: 3.49 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: 0.04 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.630 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.640 ------------------------------------------------------------------------------- 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 10044 Z= 0.328 Angle : 0.614 9.429 13656 Z= 0.340 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01196 ( 8) link_NAG-ASN : angle 4.96484 ( 24) hydrogen bonds : bond 0.30368 ( 275) hydrogen bonds : angle 8.82422 ( 741) SS BOND : bond 0.01938 ( 6) SS BOND : angle 1.60833 ( 12) covalent geometry : bond 0.00606 (10030) covalent geometry : angle 0.57613 (13620) *********************** 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 : 1.173 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: 1.5840 time to fit residues: 271.9904 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 : 1.598 ------------------------------------------------------------------------------- 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: 5.9990 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 = 44)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.077841 restraints weight = 16277.982| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.39 r_work: 0.2910 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 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 10044 Z= 0.137 Angle : 0.555 7.152 13656 Z= 0.283 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 8) link_NAG-ASN : angle 3.46605 ( 24) hydrogen bonds : bond 0.04180 ( 275) hydrogen bonds : angle 4.70176 ( 741) SS BOND : bond 0.00557 ( 6) SS BOND : angle 0.64712 ( 12) covalent geometry : bond 0.00305 (10030) covalent geometry : angle 0.53553 (13620) *********************** 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 : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.7300 (t70) REVERT: A 334 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8820 (p) REVERT: A 574 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7562 (ptt90) REVERT: A 619 ARG cc_start: 0.8109 (mtp-110) cc_final: 0.7455 (mmm-85) REVERT: A 626 SER cc_start: 0.8079 (m) cc_final: 0.7266 (t) REVERT: C 334 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8806 (p) REVERT: C 574 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7477 (ptt90) REVERT: C 579 TYR cc_start: 0.7187 (p90) cc_final: 0.6912 (p90) outliers start: 36 outliers final: 15 residues processed: 118 average time/residue: 1.1472 time to fit residues: 147.5920 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 : 1.180 ------------------------------------------------------------------------------- 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: 4.9990 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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** A 578 HIS C 195 ASN C 265 HIS C 354 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.093093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.070508 restraints weight = 16535.314| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.43 r_work: 0.2753 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10044 Z= 0.211 Angle : 0.601 8.843 13656 Z= 0.315 Chirality : 0.047 0.302 1494 Planarity : 0.004 0.038 1740 Dihedral : 7.069 55.974 1482 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.98 % Favored : 94.85 % Rotamer: Outliers : 2.98 % Allowed : 15.46 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1184 helix: 0.11 (0.29), residues: 296 sheet: -1.25 (0.51), residues: 108 loop : -1.51 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 303 HIS 0.011 0.002 HIS C 265 PHE 0.018 0.002 PHE C 407 TYR 0.010 0.002 TYR C 582 ARG 0.005 0.001 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 8) link_NAG-ASN : angle 3.08442 ( 24) hydrogen bonds : bond 0.05112 ( 275) hydrogen bonds : angle 4.51597 ( 741) SS BOND : bond 0.00215 ( 6) SS BOND : angle 0.82448 ( 12) covalent geometry : bond 0.00491 (10030) covalent geometry : angle 0.58762 (13620) *********************** 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 121 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 HIS cc_start: 0.7666 (OUTLIER) cc_final: 0.7346 (t70) REVERT: A 415 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7220 (mmp) REVERT: A 619 ARG cc_start: 0.8198 (mtp-110) cc_final: 0.7691 (mmm-85) REVERT: A 628 ASP cc_start: 0.7982 (m-30) cc_final: 0.7531 (m-30) REVERT: A 653 LYS cc_start: 0.8797 (ptpp) cc_final: 0.8404 (mtmt) REVERT: C 123 MET cc_start: 0.9388 (mtt) cc_final: 0.9184 (mtt) REVERT: C 415 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7298 (mmp) REVERT: C 574 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7808 (mtp-110) REVERT: C 606 ASN cc_start: 0.8671 (t0) cc_final: 0.8307 (t0) REVERT: C 663 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7782 (mmm160) outliers start: 32 outliers final: 19 residues processed: 110 average time/residue: 1.2117 time to fit residues: 144.8771 Evaluate side-chains 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 312 SER Chi-restraints excluded: chain C residue 316 VAL 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: 0.8980 chunk 20 optimal weight: 0.8980 chunk 116 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.093933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.071479 restraints weight = 16194.800| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.42 r_work: 0.2782 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10044 Z= 0.149 Angle : 0.528 9.027 13656 Z= 0.275 Chirality : 0.045 0.252 1494 Planarity : 0.004 0.047 1740 Dihedral : 6.225 45.723 1478 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.63 % Allowed : 16.48 % Favored : 79.89 % 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: -1.33 (0.24), residues: 1184 helix: 0.56 (0.30), residues: 298 sheet: -1.57 (0.43), residues: 152 loop : -1.39 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 303 HIS 0.005 0.001 HIS A 276 PHE 0.015 0.001 PHE C 407 TYR 0.009 0.001 TYR A 582 ARG 0.008 0.000 ARG C 619 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 8) link_NAG-ASN : angle 3.10593 ( 24) hydrogen bonds : bond 0.04027 ( 275) hydrogen bonds : angle 4.22115 ( 741) SS BOND : bond 0.00161 ( 6) SS BOND : angle 0.57096 ( 12) covalent geometry : bond 0.00344 (10030) covalent geometry : angle 0.51175 (13620) *********************** 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 129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 1.062 Fit side-chains REVERT: A 265 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7390 (t70) REVERT: A 381 MET cc_start: 0.9267 (ttt) cc_final: 0.8994 (ttt) REVERT: A 415 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7172 (mmp) REVERT: A 610 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8388 (mtm) REVERT: A 619 ARG cc_start: 0.8189 (mtp-110) cc_final: 0.7735 (mmm-85) REVERT: A 653 LYS cc_start: 0.8793 (ptpp) cc_final: 0.8458 (mtmt) REVERT: C 265 HIS cc_start: 0.7297 (OUTLIER) cc_final: 0.6971 (t70) REVERT: C 333 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8457 (mptp) REVERT: C 415 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7220 (mmp) REVERT: C 606 ASN cc_start: 0.8724 (t0) cc_final: 0.8363 (t0) REVERT: C 610 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8070 (mtm) REVERT: C 663 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7828 (mmm160) outliers start: 39 outliers final: 18 residues processed: 119 average time/residue: 1.0026 time to fit residues: 130.4825 Evaluate side-chains 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 610 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 265 HIS 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 437 GLU 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: 7.9990 chunk 111 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 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 = 0.3257 r_free = 0.3257 target = 0.091463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.068812 restraints weight = 16375.874| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.42 r_work: 0.2722 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10044 Z= 0.255 Angle : 0.643 11.980 13656 Z= 0.330 Chirality : 0.050 0.352 1494 Planarity : 0.004 0.042 1740 Dihedral : 6.538 49.673 1474 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.91 % Allowed : 16.11 % Favored : 79.98 % 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: -1.39 (0.24), residues: 1184 helix: 0.35 (0.29), residues: 308 sheet: -1.59 (0.48), residues: 132 loop : -1.39 (0.22), residues: 744 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 0.019 0.002 PHE C 407 TYR 0.012 0.002 TYR C 166 ARG 0.008 0.001 ARG C 619 Details of bonding type rmsd link_NAG-ASN : bond 0.01359 ( 8) link_NAG-ASN : angle 3.74383 ( 24) hydrogen bonds : bond 0.05010 ( 275) hydrogen bonds : angle 4.38955 ( 741) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.93506 ( 12) covalent geometry : bond 0.00601 (10030) covalent geometry : angle 0.62372 (13620) *********************** 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 125 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 1.256 Fit side-chains REVERT: A 265 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7350 (t70) REVERT: A 381 MET cc_start: 0.9250 (ttt) cc_final: 0.8962 (ttt) REVERT: A 415 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7394 (mmp) REVERT: A 610 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8282 (mpp) REVERT: A 619 ARG cc_start: 0.8163 (mtp-110) cc_final: 0.7802 (mmm-85) REVERT: A 653 LYS cc_start: 0.8838 (ptpp) cc_final: 0.8503 (mtmt) REVERT: C 415 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7385 (mmp) REVERT: C 606 ASN cc_start: 0.8873 (t0) cc_final: 0.8650 (t0) REVERT: C 610 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8039 (mtm) REVERT: C 663 ARG cc_start: 0.8415 (mtt180) cc_final: 0.7760 (mmm160) outliers start: 42 outliers final: 25 residues processed: 112 average time/residue: 1.2286 time to fit residues: 152.4480 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 : 2.013 ------------------------------------------------------------------------------- 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 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 437 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 500 ILE 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 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 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: 1.9990 chunk 116 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 0.0570 chunk 90 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 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 = 0.3322 r_free = 0.3322 target = 0.095395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.072939 restraints weight = 16316.520| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.45 r_work: 0.2803 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10044 Z= 0.108 Angle : 0.495 9.027 13656 Z= 0.260 Chirality : 0.043 0.238 1494 Planarity : 0.003 0.039 1740 Dihedral : 5.767 43.274 1474 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.61 % Allowed : 18.06 % 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: -1.07 (0.24), residues: 1184 helix: 0.91 (0.30), residues: 296 sheet: -1.59 (0.42), residues: 152 loop : -1.23 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 431 HIS 0.003 0.001 HIS C 276 PHE 0.012 0.001 PHE C 407 TYR 0.009 0.001 TYR C 582 ARG 0.007 0.000 ARG C 619 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 8) link_NAG-ASN : angle 2.35029 ( 24) hydrogen bonds : bond 0.03456 ( 275) hydrogen bonds : angle 4.02532 ( 741) SS BOND : bond 0.00186 ( 6) SS BOND : angle 0.48718 ( 12) covalent geometry : bond 0.00239 (10030) covalent geometry : angle 0.48503 (13620) *********************** 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 114 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 1.252 Fit side-chains REVERT: A 265 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.7354 (t70) REVERT: A 381 MET cc_start: 0.9238 (ttt) cc_final: 0.9013 (ttt) REVERT: A 415 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7060 (mmp) REVERT: A 610 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8288 (mpp) REVERT: A 619 ARG cc_start: 0.8131 (mtp-110) cc_final: 0.7737 (ttm110) REVERT: A 653 LYS cc_start: 0.8794 (ptpp) cc_final: 0.8466 (mtmt) REVERT: C 265 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.7190 (t70) REVERT: C 333 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8466 (mptp) REVERT: C 415 MET cc_start: 0.7905 (mpp) cc_final: 0.7153 (mmp) REVERT: C 606 ASN cc_start: 0.8834 (t0) cc_final: 0.8625 (t0) REVERT: C 610 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8114 (mtm) REVERT: C 653 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8185 (mttt) REVERT: C 663 ARG cc_start: 0.8358 (mtt180) cc_final: 0.7800 (mmm160) outliers start: 28 outliers final: 15 residues processed: 105 average time/residue: 1.0434 time to fit residues: 121.1218 Evaluate side-chains 103 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 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 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 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 654 ASN 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: 1.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** C 265 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 = 0.3265 r_free = 0.3265 target = 0.091785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.068906 restraints weight = 16468.125| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.44 r_work: 0.2727 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10044 Z= 0.225 Angle : 0.592 12.300 13656 Z= 0.309 Chirality : 0.048 0.288 1494 Planarity : 0.004 0.054 1740 Dihedral : 5.983 47.075 1472 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.79 % Allowed : 18.44 % Favored : 78.77 % 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: -1.22 (0.24), residues: 1184 helix: 0.64 (0.30), residues: 298 sheet: -1.56 (0.47), residues: 132 loop : -1.31 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 303 HIS 0.007 0.002 HIS A 276 PHE 0.017 0.002 PHE A 407 TYR 0.010 0.001 TYR A 682 ARG 0.010 0.001 ARG C 619 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 8) link_NAG-ASN : angle 2.58189 ( 24) hydrogen bonds : bond 0.04671 ( 275) hydrogen bonds : angle 4.26776 ( 741) SS BOND : bond 0.00247 ( 6) SS BOND : angle 0.89298 ( 12) covalent geometry : bond 0.00530 (10030) covalent geometry : angle 0.58256 (13620) *********************** 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 113 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 1.082 Fit side-chains REVERT: A 265 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7353 (t70) REVERT: A 381 MET cc_start: 0.9220 (ttt) cc_final: 0.8965 (ttt) REVERT: A 415 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7367 (mmp) REVERT: A 610 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8338 (mpp) REVERT: A 619 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7787 (ttm110) REVERT: A 653 LYS cc_start: 0.8872 (ptpp) cc_final: 0.8487 (mtmt) REVERT: C 265 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.7064 (t70) REVERT: C 415 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7447 (mmp) REVERT: C 606 ASN cc_start: 0.8948 (t0) cc_final: 0.8738 (t0) REVERT: C 610 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8158 (mtm) REVERT: C 653 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8229 (mttt) REVERT: C 663 ARG cc_start: 0.8368 (mtt180) cc_final: 0.7788 (mmm160) outliers start: 30 outliers final: 18 residues processed: 107 average time/residue: 0.9748 time to fit residues: 114.5416 Evaluate side-chains 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 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 415 MET Chi-restraints excluded: chain A residue 610 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 21 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 chunk 97 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.095023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.072586 restraints weight = 16435.983| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.45 r_work: 0.2803 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10044 Z= 0.105 Angle : 0.487 9.274 13656 Z= 0.256 Chirality : 0.043 0.230 1494 Planarity : 0.003 0.054 1740 Dihedral : 5.364 42.172 1471 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.96 % Allowed : 18.90 % Favored : 79.14 % 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: -0.97 (0.24), residues: 1184 helix: 1.07 (0.31), residues: 294 sheet: -1.62 (0.43), residues: 148 loop : -1.17 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 431 HIS 0.008 0.001 HIS C 265 PHE 0.012 0.001 PHE A 407 TYR 0.009 0.001 TYR C 582 ARG 0.013 0.000 ARG C 619 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 8) link_NAG-ASN : angle 1.89822 ( 24) hydrogen bonds : bond 0.03412 ( 275) hydrogen bonds : angle 4.00181 ( 741) SS BOND : bond 0.00132 ( 6) SS BOND : angle 0.41040 ( 12) covalent geometry : bond 0.00230 (10030) covalent geometry : angle 0.48055 (13620) *********************** 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 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.180 Fit side-chains REVERT: A 265 HIS cc_start: 0.7609 (OUTLIER) cc_final: 0.7326 (t70) REVERT: A 381 MET cc_start: 0.9222 (ttt) cc_final: 0.9006 (ttt) REVERT: A 415 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7063 (mmp) REVERT: A 619 ARG cc_start: 0.8131 (mtp-110) cc_final: 0.7741 (ttm110) REVERT: A 653 LYS cc_start: 0.8825 (ptpp) cc_final: 0.8483 (mtmt) REVERT: C 265 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.7144 (t70) REVERT: C 415 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7191 (mmp) REVERT: C 610 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8171 (mtm) REVERT: C 653 LYS cc_start: 0.8792 (mtpp) cc_final: 0.8206 (mttt) REVERT: C 663 ARG cc_start: 0.8319 (mtt180) cc_final: 0.7789 (mmm160) outliers start: 21 outliers final: 14 residues processed: 103 average time/residue: 1.0054 time to fit residues: 113.5359 Evaluate side-chains 98 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 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 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 415 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 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: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 215 HIS C 265 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.069536 restraints weight = 16440.267| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.44 r_work: 0.2741 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10044 Z= 0.183 Angle : 0.559 12.528 13656 Z= 0.291 Chirality : 0.046 0.261 1494 Planarity : 0.004 0.064 1740 Dihedral : 5.537 44.542 1471 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.05 % Allowed : 19.18 % Favored : 78.77 % 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: -1.03 (0.24), residues: 1184 helix: 0.91 (0.30), residues: 294 sheet: -1.62 (0.43), residues: 148 loop : -1.17 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 303 HIS 0.006 0.001 HIS A 276 PHE 0.015 0.001 PHE C 407 TYR 0.011 0.001 TYR A 682 ARG 0.013 0.001 ARG C 619 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 8) link_NAG-ASN : angle 2.24621 ( 24) hydrogen bonds : bond 0.04240 ( 275) hydrogen bonds : angle 4.14714 ( 741) SS BOND : bond 0.00221 ( 6) SS BOND : angle 0.74461 ( 12) covalent geometry : bond 0.00431 (10030) covalent geometry : angle 0.55088 (13620) *********************** 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 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 1.716 Fit side-chains REVERT: A 265 HIS cc_start: 0.7525 (OUTLIER) cc_final: 0.7134 (t70) REVERT: A 381 MET cc_start: 0.9195 (ttt) cc_final: 0.8962 (ttt) REVERT: A 415 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7282 (mmp) REVERT: A 619 ARG cc_start: 0.8116 (mtp-110) cc_final: 0.7735 (ttm110) REVERT: A 628 ASP cc_start: 0.8103 (m-30) cc_final: 0.7541 (m-30) REVERT: A 653 LYS cc_start: 0.8872 (ptpp) cc_final: 0.8517 (mtmt) REVERT: C 265 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.7071 (t70) REVERT: C 415 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7374 (mmp) REVERT: C 610 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8205 (mtm) REVERT: C 663 ARG cc_start: 0.8400 (mtt180) cc_final: 0.7808 (mmm160) outliers start: 22 outliers final: 13 residues processed: 102 average time/residue: 1.2044 time to fit residues: 133.7731 Evaluate side-chains 99 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: 0.9980 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 265 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 = 0.3308 r_free = 0.3308 target = 0.094438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.072063 restraints weight = 16478.406| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.45 r_work: 0.2785 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10044 Z= 0.114 Angle : 0.500 10.107 13656 Z= 0.263 Chirality : 0.043 0.229 1494 Planarity : 0.004 0.065 1740 Dihedral : 5.207 42.283 1470 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.68 % Allowed : 19.37 % 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: -0.94 (0.24), residues: 1184 helix: 1.06 (0.30), residues: 298 sheet: -1.61 (0.43), residues: 148 loop : -1.15 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 431 HIS 0.006 0.001 HIS A 265 PHE 0.015 0.001 PHE C 266 TYR 0.009 0.001 TYR C 582 ARG 0.014 0.000 ARG C 619 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 8) link_NAG-ASN : angle 1.89338 ( 24) hydrogen bonds : bond 0.03559 ( 275) hydrogen bonds : angle 4.02401 ( 741) SS BOND : bond 0.00142 ( 6) SS BOND : angle 0.42405 ( 12) covalent geometry : bond 0.00256 (10030) covalent geometry : angle 0.49408 (13620) ********************** 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 102 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 1.222 Fit side-chains REVERT: A 381 MET cc_start: 0.9211 (ttt) cc_final: 0.8988 (ttt) REVERT: A 415 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7042 (mmp) REVERT: A 619 ARG cc_start: 0.8132 (mtp-110) cc_final: 0.7730 (ttm110) REVERT: A 653 LYS cc_start: 0.8833 (ptpp) cc_final: 0.8491 (mtmt) REVERT: C 415 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7236 (mmp) REVERT: C 610 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8203 (mtm) REVERT: C 663 ARG cc_start: 0.8375 (mtt180) cc_final: 0.7795 (mmm160) outliers start: 18 outliers final: 14 residues processed: 99 average time/residue: 1.1977 time to fit residues: 130.9448 Evaluate side-chains 99 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: 0.9990 chunk 104 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 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 = 0.3313 r_free = 0.3313 target = 0.094676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.072193 restraints weight = 16421.242| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.46 r_work: 0.2793 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10044 Z= 0.117 Angle : 0.501 11.666 13656 Z= 0.262 Chirality : 0.043 0.215 1494 Planarity : 0.003 0.064 1740 Dihedral : 4.976 40.656 1470 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.58 % Allowed : 19.46 % 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: -0.84 (0.24), residues: 1184 helix: 1.22 (0.30), residues: 296 sheet: -1.61 (0.43), residues: 148 loop : -1.10 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 431 HIS 0.004 0.001 HIS C 276 PHE 0.013 0.001 PHE C 407 TYR 0.011 0.001 TYR C 682 ARG 0.014 0.000 ARG C 619 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 8) link_NAG-ASN : angle 1.74047 ( 24) hydrogen bonds : bond 0.03503 ( 275) hydrogen bonds : angle 3.95424 ( 741) SS BOND : bond 0.00133 ( 6) SS BOND : angle 0.49197 ( 12) covalent geometry : bond 0.00265 (10030) covalent geometry : angle 0.49604 (13620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7399.28 seconds wall clock time: 131 minutes 32.51 seconds (7892.51 seconds total)