Starting phenix.real_space_refine on Wed Sep 17 16:43:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yuz_10936/09_2025/6yuz_10936.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yuz_10936/09_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_10936/09_2025/6yuz_10936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yuz_10936/09_2025/6yuz_10936.map" model { file = "/net/cci-nas-00/data/ceres_data/6yuz_10936/09_2025/6yuz_10936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yuz_10936/09_2025/6yuz_10936.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.90, per 1000 atoms: 0.30 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: 1.00 Conformation dependent library (CDL) restraints added in 394.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.42 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: 1.64 Time building geometry restraints manager: 1.33 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: 0.02 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: 2.740 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.040 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:7.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.520 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 621 TYR 0.006 0.001 TYR C 579 PHE 0.009 0.001 PHE C 407 TRP 0.004 0.001 TRP C 264 HIS 0.002 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00606 (10030) covalent geometry : angle 0.57613 (13620) SS BOND : bond 0.01938 ( 6) SS BOND : angle 1.60833 ( 12) hydrogen bonds : bond 0.30368 ( 275) hydrogen bonds : angle 8.82422 ( 741) link_NAG-ASN : bond 0.01196 ( 8) link_NAG-ASN : angle 4.96484 ( 24) *********************** 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 : 0.412 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: 0.7379 (ptm160) outliers start: 25 outliers final: 9 residues processed: 160 average time/residue: 0.6622 time to fit residues: 112.7874 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 : 0.393 ------------------------------------------------------------------------------- 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 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 277 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 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 659 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.072822 restraints weight = 16276.724| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.40 r_work: 0.2815 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 10044 Z= 0.197 Angle : 0.609 7.682 13656 Z= 0.315 Chirality : 0.047 0.261 1494 Planarity : 0.004 0.041 1740 Dihedral : 7.977 58.724 1487 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.49 % Favored : 94.34 % 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 : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.22), residues: 1184 helix: -1.08 (0.25), residues: 302 sheet: -1.62 (0.45), residues: 124 loop : -1.65 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 456 TYR 0.014 0.002 TYR C 166 PHE 0.021 0.002 PHE C 407 TRP 0.011 0.001 TRP A 303 HIS 0.010 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00453 (10030) covalent geometry : angle 0.59416 (13620) SS BOND : bond 0.00105 ( 6) SS BOND : angle 0.73605 ( 12) hydrogen bonds : bond 0.05020 ( 275) hydrogen bonds : angle 4.77872 ( 741) link_NAG-ASN : bond 0.00690 ( 8) link_NAG-ASN : angle 3.25229 ( 24) *********************** 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 : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7337 (t70) REVERT: A 415 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.6735 (mmp) REVERT: A 574 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7641 (ptt90) REVERT: A 619 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7594 (mmm-85) REVERT: C 415 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.6956 (mmp) REVERT: C 437 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8195 (mt-10) REVERT: C 574 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7580 (ptt90) REVERT: C 663 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7686 (mmm160) outliers start: 36 outliers final: 17 residues processed: 118 average time/residue: 0.5453 time to fit residues: 69.4301 Evaluate side-chains 103 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 415 MET 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 415 MET Chi-restraints excluded: chain C residue 449 ASP 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 110 optimal weight: 0.0570 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN ** 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 = 0.3378 r_free = 0.3378 target = 0.098400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.076258 restraints weight = 16363.614| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.39 r_work: 0.2874 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10044 Z= 0.102 Angle : 0.494 7.859 13656 Z= 0.256 Chirality : 0.043 0.235 1494 Planarity : 0.003 0.040 1740 Dihedral : 6.911 58.770 1482 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.97 % Favored : 95.86 % Rotamer: Outliers : 2.51 % Allowed : 15.64 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.23), residues: 1184 helix: 0.15 (0.28), residues: 306 sheet: -1.27 (0.46), residues: 122 loop : -1.47 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 619 TYR 0.008 0.001 TYR C 582 PHE 0.014 0.001 PHE A 407 TRP 0.010 0.001 TRP C 303 HIS 0.003 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00219 (10030) covalent geometry : angle 0.47642 (13620) SS BOND : bond 0.00175 ( 6) SS BOND : angle 0.64201 ( 12) hydrogen bonds : bond 0.03663 ( 275) hydrogen bonds : angle 4.25093 ( 741) link_NAG-ASN : bond 0.00571 ( 8) link_NAG-ASN : angle 3.13776 ( 24) *********************** 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 113 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 265 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.7385 (t70) REVERT: A 415 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6547 (mmp) REVERT: A 574 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7667 (ptt90) REVERT: A 610 MET cc_start: 0.8449 (mmm) cc_final: 0.7955 (mpt) REVERT: A 619 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7607 (mmm-85) REVERT: A 653 LYS cc_start: 0.8783 (ptpp) cc_final: 0.8400 (mtmt) REVERT: A 682 TYR cc_start: 0.8544 (m-80) cc_final: 0.8304 (m-10) REVERT: C 333 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8409 (mptp) REVERT: C 334 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8852 (p) REVERT: C 415 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.6846 (mmp) REVERT: C 437 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8244 (mt-10) REVERT: C 449 ASP cc_start: 0.7575 (m-30) cc_final: 0.6990 (OUTLIER) REVERT: C 574 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7755 (mtp-110) REVERT: C 585 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8606 (pt0) REVERT: C 619 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.7281 (mmm-85) REVERT: C 663 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7693 (mmm160) outliers start: 27 outliers final: 15 residues processed: 106 average time/residue: 0.5718 time to fit residues: 65.5221 Evaluate side-chains 108 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 159 THR Chi-restraints excluded: chain C residue 243 THR 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 574 ARG Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 664 ASP 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 23 optimal weight: 7.9990 chunk 58 optimal weight: 0.0980 chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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** A 578 HIS C 195 ASN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 HIS ** 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 = 0.3272 r_free = 0.3272 target = 0.092005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.069279 restraints weight = 16462.691| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.39 r_work: 0.2742 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10044 Z= 0.261 Angle : 0.637 11.367 13656 Z= 0.329 Chirality : 0.050 0.349 1494 Planarity : 0.005 0.040 1740 Dihedral : 7.089 49.916 1482 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.83 % Favored : 94.00 % Rotamer: Outliers : 3.07 % Allowed : 16.57 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.24), residues: 1184 helix: 0.24 (0.29), residues: 308 sheet: -1.61 (0.47), residues: 140 loop : -1.46 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 379 TYR 0.010 0.002 TYR C 582 PHE 0.020 0.002 PHE A 407 TRP 0.011 0.002 TRP C 303 HIS 0.008 0.002 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00614 (10030) covalent geometry : angle 0.61767 (13620) SS BOND : bond 0.00255 ( 6) SS BOND : angle 0.85140 ( 12) hydrogen bonds : bond 0.05156 ( 275) hydrogen bonds : angle 4.44353 ( 741) link_NAG-ASN : bond 0.01197 ( 8) link_NAG-ASN : angle 3.78203 ( 24) *********************** 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 119 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 265 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7350 (t70) REVERT: A 381 MET cc_start: 0.9254 (ttt) cc_final: 0.8954 (ttt) REVERT: A 415 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7203 (mmp) REVERT: A 610 MET cc_start: 0.8419 (mmm) cc_final: 0.8050 (mpt) REVERT: A 619 ARG cc_start: 0.8160 (mtp-110) cc_final: 0.7734 (mmm-85) REVERT: A 628 ASP cc_start: 0.7991 (m-30) cc_final: 0.7507 (m-30) REVERT: A 653 LYS cc_start: 0.8832 (ptpp) cc_final: 0.8447 (mtmt) REVERT: C 415 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7349 (mmp) REVERT: C 574 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7856 (mtp-110) REVERT: C 610 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7920 (mtm) REVERT: C 663 ARG cc_start: 0.8379 (mtt180) cc_final: 0.7936 (mmm160) outliers start: 33 outliers final: 18 residues processed: 112 average time/residue: 0.5453 time to fit residues: 65.9278 Evaluate side-chains 103 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 500 ILE 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 312 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 574 ARG 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 664 ASP 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 97 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.092497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.069826 restraints weight = 16385.624| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.44 r_work: 0.2745 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 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 : 0.004 0.035 10044 Z= 0.188 Angle : 0.562 9.683 13656 Z= 0.292 Chirality : 0.046 0.306 1494 Planarity : 0.004 0.049 1740 Dihedral : 6.606 47.895 1478 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.45 % Allowed : 16.57 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.24), residues: 1184 helix: 0.53 (0.30), residues: 300 sheet: -1.62 (0.44), residues: 148 loop : -1.33 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 619 TYR 0.009 0.001 TYR C 582 PHE 0.016 0.002 PHE C 407 TRP 0.010 0.001 TRP A 303 HIS 0.006 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00443 (10030) covalent geometry : angle 0.54791 (13620) SS BOND : bond 0.00122 ( 6) SS BOND : angle 0.78482 ( 12) hydrogen bonds : bond 0.04395 ( 275) hydrogen bonds : angle 4.25745 ( 741) link_NAG-ASN : bond 0.00366 ( 8) link_NAG-ASN : angle 2.98451 ( 24) *********************** 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 : 0.386 Fit side-chains revert: symmetry clash REVERT: A 265 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.7364 (t70) REVERT: A 381 MET cc_start: 0.9247 (ttt) cc_final: 0.9002 (ttt) REVERT: A 415 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7172 (mmp) REVERT: A 610 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7923 (mpt) REVERT: A 619 ARG cc_start: 0.8187 (mtp-110) cc_final: 0.7821 (mmm-85) REVERT: A 628 ASP cc_start: 0.8032 (m-30) cc_final: 0.7498 (m-30) REVERT: A 653 LYS cc_start: 0.8810 (ptpp) cc_final: 0.8451 (mtmt) REVERT: C 265 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.6808 (t70) REVERT: C 415 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7245 (mmp) REVERT: C 663 ARG cc_start: 0.8444 (mtt180) cc_final: 0.7905 (mmm160) outliers start: 37 outliers final: 25 residues processed: 115 average time/residue: 0.4736 time to fit residues: 59.5427 Evaluate side-chains 109 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 261 ASN 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 500 ILE 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 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 580 VAL Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 664 ASP 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 74 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 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 201 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 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 = 0.3289 r_free = 0.3289 target = 0.093233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.070500 restraints weight = 16685.571| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.46 r_work: 0.2757 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10044 Z= 0.162 Angle : 0.543 9.635 13656 Z= 0.284 Chirality : 0.045 0.280 1494 Planarity : 0.004 0.047 1740 Dihedral : 6.141 46.048 1474 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.17 % Allowed : 17.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.24), residues: 1184 helix: 0.67 (0.30), residues: 300 sheet: -1.63 (0.43), residues: 148 loop : -1.23 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 619 TYR 0.010 0.001 TYR C 582 PHE 0.014 0.001 PHE C 407 TRP 0.010 0.001 TRP C 303 HIS 0.005 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00378 (10030) covalent geometry : angle 0.53130 (13620) SS BOND : bond 0.00207 ( 6) SS BOND : angle 0.70825 ( 12) hydrogen bonds : bond 0.04117 ( 275) hydrogen bonds : angle 4.17561 ( 741) link_NAG-ASN : bond 0.00397 ( 8) link_NAG-ASN : angle 2.71588 ( 24) *********************** 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 121 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.257 Fit side-chains REVERT: A 265 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7386 (t70) REVERT: A 336 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8707 (mt) REVERT: A 381 MET cc_start: 0.9231 (ttt) cc_final: 0.8996 (ttt) REVERT: A 415 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7162 (mmp) REVERT: A 610 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7913 (mpt) REVERT: A 619 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7799 (mmm-85) REVERT: A 628 ASP cc_start: 0.8015 (m-30) cc_final: 0.7413 (m-30) REVERT: A 653 LYS cc_start: 0.8817 (ptpp) cc_final: 0.8463 (mtmt) REVERT: C 265 HIS cc_start: 0.7265 (OUTLIER) cc_final: 0.6859 (t70) REVERT: C 336 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8746 (mt) REVERT: C 415 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7302 (mmp) REVERT: C 653 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8189 (mttt) REVERT: C 663 ARG cc_start: 0.8374 (mtt180) cc_final: 0.7811 (mmm160) outliers start: 34 outliers final: 21 residues processed: 112 average time/residue: 0.5003 time to fit residues: 60.8658 Evaluate side-chains 113 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 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 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 664 ASP 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 25 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 59 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** C 524 ASN ** C 578 HIS ** 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 = 0.3270 r_free = 0.3270 target = 0.092013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.069186 restraints weight = 16467.753| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.43 r_work: 0.2737 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10044 Z= 0.208 Angle : 0.594 12.172 13656 Z= 0.307 Chirality : 0.048 0.307 1494 Planarity : 0.004 0.054 1740 Dihedral : 6.148 46.923 1472 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.89 % Allowed : 17.50 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.24), residues: 1184 helix: 0.66 (0.30), residues: 298 sheet: -1.52 (0.48), residues: 132 loop : -1.31 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 619 TYR 0.009 0.001 TYR C 682 PHE 0.016 0.002 PHE C 407 TRP 0.010 0.001 TRP A 303 HIS 0.006 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00490 (10030) covalent geometry : angle 0.57916 (13620) SS BOND : bond 0.00247 ( 6) SS BOND : angle 0.82561 ( 12) hydrogen bonds : bond 0.04498 ( 275) hydrogen bonds : angle 4.23975 ( 741) link_NAG-ASN : bond 0.01136 ( 8) link_NAG-ASN : angle 3.15393 ( 24) *********************** 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 116 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.415 Fit side-chains REVERT: A 265 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7380 (t70) REVERT: A 381 MET cc_start: 0.9215 (ttt) cc_final: 0.8985 (ttt) REVERT: A 415 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7250 (mmp) REVERT: A 610 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7921 (mpt) REVERT: A 619 ARG cc_start: 0.8161 (mtp-110) cc_final: 0.7817 (mmm-85) REVERT: A 628 ASP cc_start: 0.8004 (m-30) cc_final: 0.7426 (m-30) REVERT: A 653 LYS cc_start: 0.8827 (ptpp) cc_final: 0.8476 (mtmt) REVERT: C 265 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6861 (t70) REVERT: C 415 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7388 (mmp) REVERT: C 610 MET cc_start: 0.8748 (mpp) cc_final: 0.8545 (mtm) REVERT: C 653 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8211 (mttt) REVERT: C 663 ARG cc_start: 0.8353 (mtt180) cc_final: 0.7721 (mmm160) outliers start: 31 outliers final: 21 residues processed: 110 average time/residue: 0.5284 time to fit residues: 63.4410 Evaluate side-chains 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 490 VAL 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 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 312 SER 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 25 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** ** C 578 HIS ** 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 = 0.3294 r_free = 0.3294 target = 0.093712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.071023 restraints weight = 16482.596| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.45 r_work: 0.2766 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10044 Z= 0.137 Angle : 0.525 9.704 13656 Z= 0.276 Chirality : 0.044 0.265 1494 Planarity : 0.003 0.057 1740 Dihedral : 5.840 44.856 1472 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.42 % Allowed : 17.78 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.24), residues: 1184 helix: 0.82 (0.30), residues: 302 sheet: -1.59 (0.43), residues: 148 loop : -1.21 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 619 TYR 0.010 0.001 TYR C 582 PHE 0.013 0.001 PHE A 407 TRP 0.009 0.001 TRP A 303 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00315 (10030) covalent geometry : angle 0.51574 (13620) SS BOND : bond 0.00155 ( 6) SS BOND : angle 0.61922 ( 12) hydrogen bonds : bond 0.03819 ( 275) hydrogen bonds : angle 4.09025 ( 741) link_NAG-ASN : bond 0.00348 ( 8) link_NAG-ASN : angle 2.44017 ( 24) *********************** 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 111 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.413 Fit side-chains REVERT: A 265 HIS cc_start: 0.7612 (OUTLIER) cc_final: 0.7325 (t70) REVERT: A 381 MET cc_start: 0.9199 (ttt) cc_final: 0.8991 (ttt) REVERT: A 415 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7017 (mmp) REVERT: A 610 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7929 (mpt) REVERT: A 619 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7706 (ttm110) REVERT: A 653 LYS cc_start: 0.8814 (ptpp) cc_final: 0.8481 (mtmt) REVERT: C 265 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6833 (t70) REVERT: C 415 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7214 (mmp) REVERT: C 653 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8193 (mttt) REVERT: C 663 ARG cc_start: 0.8348 (mtt180) cc_final: 0.7787 (mmm160) outliers start: 26 outliers final: 20 residues processed: 108 average time/residue: 0.5064 time to fit residues: 59.9006 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 : 0.407 ------------------------------------------------------------------------------- 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 605 LEU 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 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 420 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.094147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.071434 restraints weight = 16474.705| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.45 r_work: 0.2778 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10044 Z= 0.127 Angle : 0.515 11.924 13656 Z= 0.269 Chirality : 0.044 0.250 1494 Planarity : 0.004 0.061 1740 Dihedral : 5.542 43.236 1471 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.42 % Allowed : 17.97 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.25), residues: 1184 helix: 1.02 (0.31), residues: 298 sheet: -1.58 (0.43), residues: 148 loop : -1.14 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 619 TYR 0.010 0.001 TYR C 682 PHE 0.013 0.001 PHE C 407 TRP 0.010 0.001 TRP A 431 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00289 (10030) covalent geometry : angle 0.50768 (13620) SS BOND : bond 0.00288 ( 6) SS BOND : angle 0.54900 ( 12) hydrogen bonds : bond 0.03728 ( 275) hydrogen bonds : angle 4.04691 ( 741) link_NAG-ASN : bond 0.00405 ( 8) link_NAG-ASN : angle 2.12954 ( 24) *********************** 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: 26 poor density : 87 time to evaluate : 0.431 Fit side-chains REVERT: A 265 HIS cc_start: 0.7644 (OUTLIER) cc_final: 0.7349 (t70) REVERT: A 381 MET cc_start: 0.9171 (ttt) cc_final: 0.8963 (ttt) REVERT: A 415 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7015 (mmp) REVERT: A 610 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7932 (mpt) REVERT: A 619 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7676 (ttm110) REVERT: A 628 ASP cc_start: 0.8078 (m-30) cc_final: 0.7523 (m-30) REVERT: A 653 LYS cc_start: 0.8841 (ptpp) cc_final: 0.8524 (mtmt) REVERT: A 663 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7209 (mmp80) REVERT: C 265 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6937 (t70) REVERT: C 415 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7164 (mmp) REVERT: C 653 LYS cc_start: 0.8755 (mtpp) cc_final: 0.8208 (mttt) REVERT: C 663 ARG cc_start: 0.8348 (mtt180) cc_final: 0.7777 (mmm160) outliers start: 26 outliers final: 18 residues processed: 108 average time/residue: 0.5060 time to fit residues: 59.4772 Evaluate side-chains 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 660 THR Chi-restraints excluded: chain A residue 663 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 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 420 SER Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 664 ASP 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 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.0040 chunk 26 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.095480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.072971 restraints weight = 16335.958| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.46 r_work: 0.2804 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10044 Z= 0.103 Angle : 0.492 9.680 13656 Z= 0.259 Chirality : 0.042 0.236 1494 Planarity : 0.003 0.063 1740 Dihedral : 5.205 41.201 1471 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.77 % Allowed : 18.53 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.25), residues: 1184 helix: 1.21 (0.31), residues: 298 sheet: -1.57 (0.43), residues: 148 loop : -1.10 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 619 TYR 0.010 0.001 TYR A 682 PHE 0.012 0.001 PHE C 407 TRP 0.010 0.001 TRP C 431 HIS 0.003 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00225 (10030) covalent geometry : angle 0.48654 (13620) SS BOND : bond 0.00139 ( 6) SS BOND : angle 0.44136 ( 12) hydrogen bonds : bond 0.03358 ( 275) hydrogen bonds : angle 3.93679 ( 741) link_NAG-ASN : bond 0.00443 ( 8) link_NAG-ASN : angle 1.86930 ( 24) ********************** 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 109 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.462 Fit side-chains REVERT: A 96 SER cc_start: 0.6104 (OUTLIER) cc_final: 0.5720 (t) REVERT: A 265 HIS cc_start: 0.7625 (OUTLIER) cc_final: 0.7335 (t70) REVERT: A 415 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.6910 (mmp) REVERT: A 610 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7906 (mpt) REVERT: A 619 ARG cc_start: 0.8137 (mtp-110) cc_final: 0.7696 (ttm110) REVERT: A 628 ASP cc_start: 0.8123 (m-30) cc_final: 0.7573 (m-30) REVERT: A 653 LYS cc_start: 0.8820 (ptpp) cc_final: 0.8517 (mtpt) REVERT: C 415 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7001 (mmp) REVERT: C 653 LYS cc_start: 0.8754 (mtpp) cc_final: 0.8214 (mttt) REVERT: C 663 ARG cc_start: 0.8358 (mtt180) cc_final: 0.7778 (mmm160) outliers start: 19 outliers final: 13 residues processed: 104 average time/residue: 0.5051 time to fit residues: 57.3091 Evaluate side-chains 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 415 MET Chi-restraints excluded: chain A residue 610 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 111 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 654 ASN 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 34 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 88 optimal weight: 0.9980 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 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 = 0.3329 r_free = 0.3329 target = 0.095533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.073009 restraints weight = 16526.644| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.47 r_work: 0.2806 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10044 Z= 0.106 Angle : 0.491 11.646 13656 Z= 0.256 Chirality : 0.043 0.213 1494 Planarity : 0.004 0.063 1740 Dihedral : 4.872 41.102 1470 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.77 % Allowed : 18.81 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.25), residues: 1184 helix: 1.28 (0.30), residues: 298 sheet: -1.57 (0.43), residues: 148 loop : -1.06 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 619 TYR 0.010 0.001 TYR C 682 PHE 0.012 0.001 PHE C 407 TRP 0.011 0.001 TRP C 431 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00236 (10030) covalent geometry : angle 0.48590 (13620) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.45348 ( 12) hydrogen bonds : bond 0.03369 ( 275) hydrogen bonds : angle 3.87961 ( 741) link_NAG-ASN : bond 0.00402 ( 8) link_NAG-ASN : angle 1.72262 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.02 seconds wall clock time: 59 minutes 0.14 seconds (3540.14 seconds total)