Starting phenix.real_space_refine on Fri Sep 11 14:25:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6yuz_10936/09_2026/6yuz_10936.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yuz_10936/09_2026/6yuz_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6yuz_10936/09_2026/6yuz_10936.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6yuz_10936/09_2026/6yuz_10936.cif" model { file = "/net/cci-nas-00/data/ceres_data/6yuz_10936/09_2026/6yuz_10936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yuz_10936/09_2026/6yuz_10936.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yuz_10936/09_2026/6yuz_10936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yuz_10936/09_2026/6yuz_10936.map" } 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-2.2.1-6174/lib/python3.11/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 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 chiralities: 4 Time building chain proxies: 2.23, per 1000 atoms: 0.23 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: 1.09 Conformation dependent library (CDL) restraints added in 345.6 milliseconds 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: 0.35 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: 1.17 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 - 17.74: 5354 17.74 - 35.48: 395 35.48 - 53.22: 77 53.22 - 70.97: 26 70.97 - 88.71: 6 Dihedral angle restraints: 5858 sinusoidal: 2374 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 5855 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: 3.500 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.870 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 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 : 13.444 88.707 3600 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 are 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/Z covalent geometry : bond 0.00606 / 0.33 (10030) covalent geometry : angle 0.57613 / 0.33 (13620) SS BOND : bond 0.01938 / 0.94 ( 6) SS BOND : angle 1.60833 / 0.80 ( 12) hydrogen bonds : bond 0.30368 / 19.88 ( 275) hydrogen bonds : angle 8.82422 / 6.14 ( 741) link_NAG-ASN : bond 0.01196 / 0.52 ( 8) link_NAG-ASN : angle 4.96484 / 3.09 ( 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 : 0.386 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: 0.5820 time to fit residues: 99.6807 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 : 0.350 ------------------------------------------------------------------------------- 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... A 195 ASN 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 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 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.095626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.072784 restraints weight = 16284.280| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.43 r_work: 0.2816 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 10044 Z= 0.196 Angle : 0.596 7.425 13656 Z= 0.311 Chirality : 0.046 0.220 1494 Planarity : 0.004 0.040 1740 Dihedral : 5.734 56.926 1319 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.49 % Favored : 94.34 % Rotamer: Outliers : 3.35 % Allowed : 15.36 % Favored : 81.28 % 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 are not related in a simple way. whole: -2.22 (0.22), residues: 1184 helix: -1.03 (0.25), residues: 304 sheet: -1.61 (0.45), residues: 124 loop : -1.69 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 456 TYR 0.013 0.002 TYR C 166 PHE 0.020 0.002 PHE C 407 TRP 0.012 0.001 TRP C 303 HIS 0.009 0.002 HIS C 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (10030) covalent geometry : angle 0.58070 / 0.31 (13620) SS BOND : bond 0.00327 / 0.17 ( 6) SS BOND : angle 0.78251 / 0.42 ( 12) hydrogen bonds : bond 0.04926 / 3.14 ( 275) hydrogen bonds : angle 4.80337 / 3.34 ( 741) link_NAG-ASN : bond 0.00498 / 0.27 ( 8) link_NAG-ASN : angle 3.22104 / 2.18 ( 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 129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.7352 (t70) REVERT: A 415 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6729 (mmp) REVERT: A 435 MET cc_start: 0.9256 (ttp) cc_final: 0.8926 (ttp) REVERT: A 574 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7745 (ptt90) REVERT: A 619 ARG cc_start: 0.8129 (mtp-110) cc_final: 0.7621 (mmm-85) REVERT: C 415 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.6967 (mmp) REVERT: C 437 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8202 (mt-10) REVERT: C 610 MET cc_start: 0.8064 (mtp) cc_final: 0.7819 (mtm) outliers start: 36 outliers final: 18 residues processed: 119 average time/residue: 0.5079 time to fit residues: 65.6939 Evaluate side-chains 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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: 10.0000 chunk 83 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 44 optimal weight: 0.0170 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 354 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.094920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.072448 restraints weight = 16406.508| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.43 r_work: 0.2801 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10044 Z= 0.145 Angle : 0.529 8.448 13656 Z= 0.277 Chirality : 0.044 0.228 1494 Planarity : 0.004 0.039 1740 Dihedral : 5.451 54.594 1314 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.65 % Favored : 95.19 % Rotamer: Outliers : 3.17 % Allowed : 15.27 % Favored : 81.56 % 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 are not related in a simple way. whole: -1.52 (0.23), residues: 1184 helix: 0.12 (0.29), residues: 306 sheet: -1.27 (0.51), residues: 108 loop : -1.51 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 619 TYR 0.008 0.001 TYR A 682 PHE 0.016 0.001 PHE C 407 TRP 0.011 0.001 TRP C 303 HIS 0.005 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (10030) covalent geometry : angle 0.51471 / 0.27 (13620) SS BOND : bond 0.00240 / 0.13 ( 6) SS BOND : angle 0.61248 / 0.34 ( 12) hydrogen bonds : bond 0.04288 / 2.74 ( 275) hydrogen bonds : angle 4.35652 / 3.03 ( 741) link_NAG-ASN : bond 0.00451 / 0.26 ( 8) link_NAG-ASN : angle 2.93749 / 1.97 ( 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 124 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.7378 (t70) REVERT: A 415 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.6894 (mmp) REVERT: A 435 MET cc_start: 0.9293 (ttp) cc_final: 0.9000 (ttp) REVERT: A 574 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7817 (ptm160) REVERT: A 610 MET cc_start: 0.8357 (mmm) cc_final: 0.7766 (mpt) REVERT: A 619 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7619 (mmm-85) REVERT: A 628 ASP cc_start: 0.7991 (m-30) cc_final: 0.7534 (m-30) REVERT: A 653 LYS cc_start: 0.8793 (ptpp) cc_final: 0.8408 (mtmt) REVERT: C 333 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8465 (mptp) REVERT: C 415 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7024 (mmp) REVERT: C 449 ASP cc_start: 0.7586 (m-30) cc_final: 0.7081 (p0) REVERT: C 574 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7761 (mtp-110) REVERT: C 619 ARG cc_start: 0.7702 (ttp-110) cc_final: 0.7361 (mmm-85) outliers start: 34 outliers final: 19 residues processed: 115 average time/residue: 0.5038 time to fit residues: 63.0510 Evaluate side-chains 109 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 312 SER 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 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 261 ASN Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 415 MET 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 23 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 ASN ** 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 = 0.3265 r_free = 0.3265 target = 0.091590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.068897 restraints weight = 16529.003| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.40 r_work: 0.2741 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: 0.9079 moved from start: 0.3937 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= 0.257 Angle : 0.618 9.594 13656 Z= 0.325 Chirality : 0.049 0.268 1494 Planarity : 0.004 0.040 1740 Dihedral : 6.012 51.555 1314 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.91 % Favored : 93.92 % Rotamer: Outliers : 2.98 % Allowed : 17.04 % Favored : 79.98 % 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 are not related in a simple way. whole: -1.47 (0.24), residues: 1184 helix: 0.19 (0.29), residues: 308 sheet: -1.42 (0.52), residues: 122 loop : -1.45 (0.22), residues: 754 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 0.018 0.002 PHE C 407 TRP 0.011 0.001 TRP A 303 HIS 0.008 0.002 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.26 (10030) covalent geometry : angle 0.60651 / 0.32 (13620) SS BOND : bond 0.00145 / 0.09 ( 6) SS BOND : angle 0.93030 / 0.53 ( 12) hydrogen bonds : bond 0.05030 / 3.20 ( 275) hydrogen bonds : angle 4.43927 / 3.09 ( 741) link_NAG-ASN : bond 0.00257 / 0.14 ( 8) link_NAG-ASN : angle 2.79688 / 1.89 ( 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 120 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 HIS cc_start: 0.7669 (OUTLIER) cc_final: 0.7328 (t70) REVERT: A 381 MET cc_start: 0.9250 (ttt) cc_final: 0.8970 (ttt) REVERT: A 415 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7260 (mmp) REVERT: A 574 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7857 (ptm160) REVERT: A 610 MET cc_start: 0.8369 (mmm) cc_final: 0.7985 (mpt) REVERT: A 619 ARG cc_start: 0.8145 (mtp-110) cc_final: 0.7700 (mmm-85) REVERT: A 653 LYS cc_start: 0.8825 (ptpp) cc_final: 0.8454 (mtmt) REVERT: C 415 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7283 (mmp) REVERT: C 574 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7849 (mtp-110) REVERT: C 610 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8063 (mtm) outliers start: 32 outliers final: 18 residues processed: 112 average time/residue: 0.5166 time to fit residues: 62.7861 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 : 0.388 ------------------------------------------------------------------------------- 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 574 ARG 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 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 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: 2.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.073259 restraints weight = 16404.745| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.45 r_work: 0.2813 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10044 Z= 0.103 Angle : 0.492 8.922 13656 Z= 0.255 Chirality : 0.042 0.204 1494 Planarity : 0.003 0.050 1740 Dihedral : 5.168 43.766 1314 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.98 % Allowed : 17.32 % 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 are not related in a simple way. whole: -1.10 (0.24), residues: 1184 helix: 0.86 (0.30), residues: 294 sheet: -1.41 (0.45), residues: 142 loop : -1.29 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 619 TYR 0.009 0.001 TYR C 582 PHE 0.012 0.001 PHE A 407 TRP 0.010 0.001 TRP A 431 HIS 0.003 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (10030) covalent geometry : angle 0.47657 / 0.25 (13620) SS BOND : bond 0.00326 / 0.17 ( 6) SS BOND : angle 0.42163 / 0.23 ( 12) hydrogen bonds : bond 0.03455 / 2.20 ( 275) hydrogen bonds : angle 4.04360 / 2.80 ( 741) link_NAG-ASN : bond 0.00401 / 0.23 ( 8) link_NAG-ASN : angle 2.92944 / 1.95 ( 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 118 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.382 Fit side-chains REVERT: A 265 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.7384 (t70) REVERT: A 381 MET cc_start: 0.9222 (ttt) cc_final: 0.9002 (ttt) REVERT: A 415 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.6908 (mmp) REVERT: A 610 MET cc_start: 0.8286 (mmm) cc_final: 0.7937 (mpt) REVERT: A 619 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7760 (mmm-85) REVERT: A 653 LYS cc_start: 0.8766 (ptpp) cc_final: 0.8421 (mtmt) REVERT: A 663 ARG cc_start: 0.7498 (mmm160) cc_final: 0.7280 (mmp80) REVERT: C 265 HIS cc_start: 0.7203 (OUTLIER) cc_final: 0.6908 (t70) REVERT: C 415 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7069 (mmp) REVERT: C 449 ASP cc_start: 0.8071 (m-30) cc_final: 0.7799 (p0) REVERT: C 610 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7991 (mtm) outliers start: 32 outliers final: 17 residues processed: 110 average time/residue: 0.5208 time to fit residues: 62.3205 Evaluate side-chains 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 334 THR 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 334 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 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: 9.9990 chunk 81 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 HIS ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS C 215 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.093377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.070642 restraints weight = 16680.867| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.46 r_work: 0.2756 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10044 Z= 0.177 Angle : 0.567 10.283 13656 Z= 0.293 Chirality : 0.046 0.266 1494 Planarity : 0.004 0.046 1740 Dihedral : 4.931 29.765 1306 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.26 % Allowed : 17.69 % Favored : 79.05 % 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 are not related in a simple way. whole: -1.06 (0.24), residues: 1184 helix: 0.82 (0.30), residues: 296 sheet: -1.49 (0.46), residues: 138 loop : -1.22 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 619 TYR 0.010 0.001 TYR C 582 PHE 0.016 0.001 PHE C 407 TRP 0.010 0.001 TRP C 303 HIS 0.006 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (10030) covalent geometry : angle 0.54990 / 0.29 (13620) SS BOND : bond 0.00235 / 0.13 ( 6) SS BOND : angle 0.72644 / 0.41 ( 12) hydrogen bonds : bond 0.04190 / 2.66 ( 275) hydrogen bonds : angle 4.13987 / 2.87 ( 741) link_NAG-ASN : bond 0.01559 / 0.99 ( 8) link_NAG-ASN : angle 3.29958 / 2.34 ( 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 122 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.401 Fit side-chains REVERT: A 265 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7346 (t70) REVERT: A 381 MET cc_start: 0.9216 (ttt) cc_final: 0.8992 (ttt) REVERT: A 415 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7129 (mmp) REVERT: A 610 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7879 (mpt) REVERT: A 619 ARG cc_start: 0.8103 (mtp-110) cc_final: 0.7705 (ttm110) REVERT: A 653 LYS cc_start: 0.8808 (ptpp) cc_final: 0.8451 (mtmt) REVERT: C 265 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6895 (t70) REVERT: C 415 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7215 (mmp) REVERT: C 610 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8123 (mtm) REVERT: C 653 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8158 (mttt) outliers start: 35 outliers final: 24 residues processed: 112 average time/residue: 0.4815 time to fit residues: 59.0101 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 : 0.336 ------------------------------------------------------------------------------- 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 312 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 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 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: 4.9990 chunk 71 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.091645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.068877 restraints weight = 16552.888| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.44 r_work: 0.2721 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.4176 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= 0.234 Angle : 0.599 10.692 13656 Z= 0.315 Chirality : 0.048 0.294 1494 Planarity : 0.004 0.055 1740 Dihedral : 5.271 30.202 1306 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.07 % Allowed : 18.25 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.24), residues: 1184 helix: 0.67 (0.30), residues: 298 sheet: -1.36 (0.51), residues: 122 loop : -1.35 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 619 TYR 0.010 0.001 TYR C 582 PHE 0.017 0.002 PHE C 407 TRP 0.010 0.001 TRP C 303 HIS 0.007 0.002 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.23 (10030) covalent geometry : angle 0.58691 / 0.31 (13620) SS BOND : bond 0.00254 / 0.15 ( 6) SS BOND : angle 0.90748 / 0.50 ( 12) hydrogen bonds : bond 0.04652 / 2.96 ( 275) hydrogen bonds : angle 4.26850 / 2.95 ( 741) link_NAG-ASN : bond 0.00291 / 0.16 ( 8) link_NAG-ASN : angle 2.86442 / 1.81 ( 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 117 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 0.413 Fit side-chains REVERT: A 265 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.7095 (t70) REVERT: A 336 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8785 (mt) REVERT: A 381 MET cc_start: 0.9206 (ttt) cc_final: 0.8987 (ttt) REVERT: A 415 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7268 (mmp) REVERT: A 610 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7888 (mpt) REVERT: A 619 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7753 (ttm110) REVERT: A 653 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8473 (mtmt) REVERT: C 265 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.6898 (t70) REVERT: C 336 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8796 (mt) REVERT: C 415 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7383 (mmp) REVERT: C 610 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8172 (mtm) REVERT: C 653 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8178 (mttt) REVERT: C 665 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7994 (ptm160) outliers start: 33 outliers final: 24 residues processed: 108 average time/residue: 0.4884 time to fit residues: 57.6722 Evaluate side-chains 116 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 336 ILE Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 543 THR 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 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 334 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 664 ASP Chi-restraints excluded: chain C residue 665 ARG 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: 1.9990 chunk 107 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 95 optimal weight: 0.0010 chunk 73 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 0.0270 chunk 9 optimal weight: 0.6980 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3325 r_free = 0.3325 target = 0.095342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.072933 restraints weight = 16598.053| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.46 r_work: 0.2809 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.4056 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= 0.102 Angle : 0.487 9.155 13656 Z= 0.258 Chirality : 0.042 0.209 1494 Planarity : 0.003 0.055 1740 Dihedral : 4.668 28.766 1306 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.51 % Allowed : 18.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.24), residues: 1184 helix: 1.14 (0.30), residues: 294 sheet: -1.45 (0.45), residues: 138 loop : -1.18 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 619 TYR 0.009 0.001 TYR C 582 PHE 0.011 0.001 PHE A 407 TRP 0.009 0.001 TRP A 431 HIS 0.016 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (10030) covalent geometry : angle 0.48104 / 0.26 (13620) SS BOND : bond 0.00153 / 0.09 ( 6) SS BOND : angle 0.42945 / 0.22 ( 12) hydrogen bonds : bond 0.03350 / 2.14 ( 275) hydrogen bonds : angle 4.01694 / 2.77 ( 741) link_NAG-ASN : bond 0.00425 / 0.24 ( 8) link_NAG-ASN : angle 1.83756 / 1.11 ( 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 113 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.525 Fit side-chains REVERT: A 265 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.7263 (t70) REVERT: A 415 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.6976 (mmp) REVERT: A 610 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7897 (mpt) REVERT: A 619 ARG cc_start: 0.8118 (mtp-110) cc_final: 0.7731 (ttm110) REVERT: A 653 LYS cc_start: 0.8806 (ptpp) cc_final: 0.8487 (mtmt) REVERT: A 664 ASP cc_start: 0.8029 (p0) cc_final: 0.7572 (p0) REVERT: C 265 HIS cc_start: 0.7207 (OUTLIER) cc_final: 0.6929 (t70) REVERT: C 415 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7058 (mmp) REVERT: C 610 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8156 (mtm) REVERT: C 653 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8134 (mttt) outliers start: 27 outliers final: 14 residues processed: 105 average time/residue: 0.5132 time to fit residues: 58.5926 Evaluate side-chains 102 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 664 ASP 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: 5.9990 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 0.0970 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.092222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.069464 restraints weight = 16423.315| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.42 r_work: 0.2740 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.4194 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= 0.187 Angle : 0.558 10.723 13656 Z= 0.293 Chirality : 0.045 0.237 1494 Planarity : 0.004 0.063 1740 Dihedral : 4.924 27.769 1304 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.33 % Allowed : 18.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.24), residues: 1184 helix: 0.96 (0.30), residues: 296 sheet: -1.48 (0.46), residues: 138 loop : -1.17 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 619 TYR 0.011 0.001 TYR C 682 PHE 0.015 0.001 PHE C 407 TRP 0.010 0.001 TRP C 303 HIS 0.006 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (10030) covalent geometry : angle 0.55034 / 0.29 (13620) SS BOND : bond 0.00244 / 0.14 ( 6) SS BOND : angle 0.79886 / 0.46 ( 12) hydrogen bonds : bond 0.04285 / 2.73 ( 275) hydrogen bonds : angle 4.17945 / 2.89 ( 741) link_NAG-ASN : bond 0.00245 / 0.13 ( 8) link_NAG-ASN : angle 2.19946 / 1.32 ( 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 112 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.304 Fit side-chains REVERT: A 265 HIS cc_start: 0.7547 (OUTLIER) cc_final: 0.7128 (t70) REVERT: A 415 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7167 (mmp) REVERT: A 610 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7887 (mpt) REVERT: A 619 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7733 (ttm110) REVERT: A 628 ASP cc_start: 0.8100 (m-30) cc_final: 0.7547 (m-30) REVERT: A 653 LYS cc_start: 0.8833 (ptpp) cc_final: 0.8502 (mtmt) REVERT: A 664 ASP cc_start: 0.7992 (p0) cc_final: 0.7518 (p0) REVERT: C 265 HIS cc_start: 0.7279 (OUTLIER) cc_final: 0.6893 (t70) REVERT: C 415 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7362 (mmp) REVERT: C 653 LYS cc_start: 0.8804 (mtpp) cc_final: 0.8183 (mttt) REVERT: C 663 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7213 (mmp80) outliers start: 25 outliers final: 16 residues processed: 104 average time/residue: 0.4926 time to fit residues: 55.8581 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 : 0.403 ------------------------------------------------------------------------------- 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 543 THR 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 265 HIS 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 660 THR Chi-restraints excluded: chain C residue 663 ARG 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: 2.9990 chunk 16 optimal weight: 0.0010 chunk 26 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 95 optimal weight: 0.0070 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3337 r_free = 0.3337 target = 0.096066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.073749 restraints weight = 16392.882| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.45 r_work: 0.2821 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10044 Z= 0.096 Angle : 0.479 9.294 13656 Z= 0.254 Chirality : 0.042 0.191 1494 Planarity : 0.003 0.063 1740 Dihedral : 4.404 26.551 1304 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.77 % Allowed : 19.55 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.24), residues: 1184 helix: 1.36 (0.31), residues: 294 sheet: -1.08 (0.47), residues: 128 loop : -1.20 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 619 TYR 0.009 0.001 TYR C 579 PHE 0.011 0.001 PHE C 407 TRP 0.010 0.001 TRP A 431 HIS 0.015 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (10030) covalent geometry : angle 0.47510 / 0.25 (13620) SS BOND : bond 0.00154 / 0.10 ( 6) SS BOND : angle 0.31077 / 0.18 ( 12) hydrogen bonds : bond 0.03198 / 2.05 ( 275) hydrogen bonds : angle 3.95369 / 2.72 ( 741) link_NAG-ASN : bond 0.00393 / 0.22 ( 8) link_NAG-ASN : angle 1.57909 / 0.92 ( 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 108 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.414 Fit side-chains REVERT: A 265 HIS cc_start: 0.7413 (OUTLIER) cc_final: 0.7046 (t70) REVERT: A 415 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.6866 (mmp) REVERT: A 619 ARG cc_start: 0.8107 (mtp-110) cc_final: 0.7716 (ttm110) REVERT: A 628 ASP cc_start: 0.8097 (m-30) cc_final: 0.7543 (m-30) REVERT: A 653 LYS cc_start: 0.8799 (ptpp) cc_final: 0.8486 (mtpt) REVERT: A 663 ARG cc_start: 0.7478 (mmm160) cc_final: 0.7179 (mmm160) REVERT: C 96 SER cc_start: 0.6227 (OUTLIER) cc_final: 0.5856 (t) REVERT: C 265 HIS cc_start: 0.7170 (OUTLIER) cc_final: 0.6922 (t70) REVERT: C 334 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8800 (p) REVERT: C 415 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7009 (mmp) REVERT: C 663 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7140 (mmp80) outliers start: 19 outliers final: 9 residues processed: 102 average time/residue: 0.5187 time to fit residues: 57.6761 Evaluate side-chains 102 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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 334 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 663 ARG 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: 1.9990 chunk 96 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 ASN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.092026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.069334 restraints weight = 16547.456| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.43 r_work: 0.2731 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10044 Z= 0.207 Angle : 0.569 9.880 13656 Z= 0.301 Chirality : 0.046 0.230 1494 Planarity : 0.004 0.066 1740 Dihedral : 4.899 27.026 1303 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.86 % Allowed : 19.83 % Favored : 78.31 % 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 are not related in a simple way. whole: -0.90 (0.24), residues: 1184 helix: 1.09 (0.30), residues: 294 sheet: -1.48 (0.46), residues: 138 loop : -1.15 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 619 TYR 0.012 0.001 TYR A 682 PHE 0.017 0.002 PHE A 407 TRP 0.010 0.001 TRP C 303 HIS 0.006 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (10030) covalent geometry : angle 0.56170 / 0.30 (13620) SS BOND : bond 0.00225 / 0.12 ( 6) SS BOND : angle 0.82998 / 0.48 ( 12) hydrogen bonds : bond 0.04391 / 2.80 ( 275) hydrogen bonds : angle 4.19457 / 2.90 ( 741) link_NAG-ASN : bond 0.00169 / 0.09 ( 8) link_NAG-ASN : angle 2.18505 / 1.31 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3277.03 seconds wall clock time: 56 minutes 44.19 seconds (3404.19 seconds total)