Starting phenix.real_space_refine on Fri Jul 3 02:08:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hfy_34728/07_2026/8hfy_34728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfy_34728/07_2026/8hfy_34728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hfy_34728/07_2026/8hfy_34728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfy_34728/07_2026/8hfy_34728.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hfy_34728/07_2026/8hfy_34728.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hfy_34728/07_2026/8hfy_34728.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hfy_34728/07_2026/8hfy_34728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfy_34728/07_2026/8hfy_34728.cif" } resolution = 3.21 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= 0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6024 atoms to isotropic. 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 Zn 1 6.06 5 S 38 5.16 5 C 4195 2.51 5 N 1075 2.21 5 O 1259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6568 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "A" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4886 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.05, per 1000 atoms: 0.16 Number of scatterers: 6568 At special positions: 0 Unit cell: (85, 88.4, 120.7, 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) Zn 1 29.99 S 38 16.00 O 1259 8.00 N 1075 7.00 C 4195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A 701 " - " ASN A 432 " " NAG A 702 " - " ASN A 299 " " NAG A 703 " - " ASN A 91 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 54 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 223.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 704 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 378 " 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 54.9% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.749A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 removed outlier: 4.090A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.508A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'A' and resid 21 through 54 removed outlier: 3.677A pdb=" N HIS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 39 " --> pdb=" O HIS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 82 removed outlier: 3.724A pdb=" N LYS A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 removed outlier: 3.559A pdb=" N GLN A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 4.243A pdb=" N VAL A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 removed outlier: 3.585A pdb=" N LYS A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 139 removed outlier: 3.831A pdb=" N GLN A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.705A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.959A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.647A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.110A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.948A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.909A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.687A pdb=" N ARG A 393 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 4.136A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 448 Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.194A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 516 through 533 removed outlier: 3.575A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 530 " --> pdb=" O HIS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.047A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.723A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.626A pdb=" N THR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 134 Processing sheet with id=AA6, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.114A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.368A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 843 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: 0.57 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2075 1.34 - 1.46: 1522 1.46 - 1.58: 3091 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6748 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.444 -0.031 2.00e-02 2.50e+03 2.33e+00 ... (remaining 6743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 8936 1.56 - 3.13: 179 3.13 - 4.69: 32 4.69 - 6.25: 7 6.25 - 7.82: 2 Bond angle restraints: 9156 Sorted by residual: angle pdb=" N ILE A 55 " pdb=" CA ILE A 55 " pdb=" C ILE A 55 " ideal model delta sigma weight residual 106.55 110.56 -4.01 1.45e+00 4.76e-01 7.66e+00 angle pdb=" C PHE B 375 " pdb=" N THR B 376 " pdb=" CA THR B 376 " ideal model delta sigma weight residual 122.41 118.51 3.90 1.47e+00 4.63e-01 7.04e+00 angle pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " pdb=" C5 NAG D 1 " ideal model delta sigma weight residual 113.21 121.03 -7.82 3.00e+00 1.11e-01 6.79e+00 angle pdb=" C ALA A 384 " pdb=" N TYR A 385 " pdb=" CA TYR A 385 " ideal model delta sigma weight residual 122.65 118.46 4.19 1.66e+00 3.63e-01 6.36e+00 angle pdb=" N GLY A 537 " pdb=" CA GLY A 537 " pdb=" C GLY A 537 " ideal model delta sigma weight residual 110.46 113.97 -3.51 1.43e+00 4.89e-01 6.04e+00 ... (remaining 9151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.10: 3574 14.10 - 28.20: 258 28.20 - 42.30: 65 42.30 - 56.40: 21 56.40 - 70.50: 3 Dihedral angle restraints: 3921 sinusoidal: 1591 harmonic: 2330 Sorted by residual: dihedral pdb=" CA ILE A 233 " pdb=" C ILE A 233 " pdb=" N LYS A 234 " pdb=" CA LYS A 234 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA THR A 608 " pdb=" C THR A 608 " pdb=" N GLU A 609 " pdb=" CA GLU A 609 " ideal model delta harmonic sigma weight residual -180.00 -163.66 -16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA LEU A 281 " pdb=" C LEU A 281 " pdb=" N THR A 282 " pdb=" CA THR A 282 " ideal model delta harmonic sigma weight residual -180.00 -164.31 -15.69 0 5.00e+00 4.00e-02 9.85e+00 ... (remaining 3918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 812 0.053 - 0.107: 146 0.107 - 0.160: 19 0.160 - 0.214: 1 0.214 - 0.267: 1 Chirality restraints: 979 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.58e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.48e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 976 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 373 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 444 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C LEU A 444 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 444 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 445 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO A 146 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.021 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 68 2.64 - 3.21: 5868 3.21 - 3.77: 9628 3.77 - 4.34: 13493 4.34 - 4.90: 22737 Nonbonded interactions: 51794 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 704 " model vdw 2.081 2.230 nonbonded pdb=" OG1 THR B 500 " pdb=" OH TYR A 42 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.224 3.040 nonbonded pdb=" OD1 ASP A 382 " pdb=" OH TYR A 385 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.257 3.040 ... (remaining 51789 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.580 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 : 0.003 0.073 6763 Z= 0.161 Angle : 0.565 7.817 9191 Z= 0.290 Chirality : 0.042 0.267 979 Planarity : 0.004 0.049 1166 Dihedral : 11.134 70.500 2413 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.44 % Allowed : 6.47 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.29 (0.30), residues: 785 helix: 1.41 (0.27), residues: 392 sheet: 0.52 (0.80), residues: 44 loop : -1.30 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.019 0.001 TYR A 385 PHE 0.017 0.001 PHE A 369 TRP 0.009 0.001 TRP A 606 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 ( 6748) covalent geometry : angle 0.55418 / 0.29 ( 9156) SS BOND : bond 0.00106 / 0.05 ( 4) SS BOND : angle 0.73216 / 0.42 ( 8) hydrogen bonds : bond 0.14669 / 10.03 ( 297) hydrogen bonds : angle 5.28726 / 3.63 ( 843) metal coordination : bond 0.00402 / 0.21 ( 2) link_BETA1-4 : bond 0.00615 / 0.29 ( 3) link_BETA1-4 : angle 2.40347 / 1.28 ( 9) link_NAG-ASN : bond 0.00311 / 0.22 ( 6) link_NAG-ASN : angle 1.90321 / 1.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7229 (t0) cc_final: 0.6988 (t0) REVERT: A 149 ASP cc_start: 0.8409 (t0) cc_final: 0.8132 (t0) REVERT: A 152 MET cc_start: 0.9148 (mmm) cc_final: 0.8650 (mmt) REVERT: A 153 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7967 (mt-10) outliers start: 10 outliers final: 3 residues processed: 130 average time/residue: 0.0769 time to fit residues: 12.9585 Evaluate side-chains 77 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.120983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.090815 restraints weight = 11889.106| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.76 r_work: 0.3113 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6763 Z= 0.215 Angle : 0.630 8.101 9191 Z= 0.324 Chirality : 0.046 0.302 979 Planarity : 0.005 0.057 1166 Dihedral : 5.170 46.976 874 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.16 % Allowed : 10.78 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.24 (0.30), residues: 785 helix: 1.37 (0.27), residues: 395 sheet: 0.34 (0.80), residues: 45 loop : -1.35 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.015 0.002 TYR B 423 PHE 0.019 0.002 PHE A 369 TRP 0.014 0.001 TRP A 168 HIS 0.008 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 ( 6748) covalent geometry : angle 0.62058 / 0.32 ( 9156) SS BOND : bond 0.00212 / 0.10 ( 4) SS BOND : angle 0.40666 / 0.21 ( 8) hydrogen bonds : bond 0.06084 / 4.03 ( 297) hydrogen bonds : angle 4.54247 / 3.10 ( 843) metal coordination : bond 0.00412 / 0.20 ( 2) link_BETA1-4 : bond 0.00643 / 0.30 ( 3) link_BETA1-4 : angle 1.96584 / 1.02 ( 9) link_NAG-ASN : bond 0.00457 / 0.28 ( 6) link_NAG-ASN : angle 2.20478 / 1.50 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7638 (t0) cc_final: 0.7283 (t0) REVERT: A 552 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7964 (mp-120) outliers start: 15 outliers final: 7 residues processed: 85 average time/residue: 0.0892 time to fit residues: 10.3890 Evaluate side-chains 71 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN A 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.122454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.092603 restraints weight = 11869.489| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.77 r_work: 0.3176 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6763 Z= 0.126 Angle : 0.542 7.605 9191 Z= 0.278 Chirality : 0.043 0.298 979 Planarity : 0.004 0.050 1166 Dihedral : 4.937 50.983 873 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.87 % Allowed : 11.78 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.35 (0.30), residues: 785 helix: 1.43 (0.27), residues: 386 sheet: 0.36 (0.80), residues: 45 loop : -1.17 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.014 0.001 TYR A 385 PHE 0.012 0.001 PHE A 369 TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 6748) covalent geometry : angle 0.53116 / 0.28 ( 9156) SS BOND : bond 0.00138 / 0.07 ( 4) SS BOND : angle 0.30473 / 0.16 ( 8) hydrogen bonds : bond 0.05163 / 3.41 ( 297) hydrogen bonds : angle 4.41798 / 3.04 ( 843) metal coordination : bond 0.00136 / 0.07 ( 2) link_BETA1-4 : bond 0.00599 / 0.28 ( 3) link_BETA1-4 : angle 1.80718 / 0.94 ( 9) link_NAG-ASN : bond 0.00346 / 0.23 ( 6) link_NAG-ASN : angle 2.16399 / 1.49 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7585 (t0) cc_final: 0.7253 (t0) REVERT: B 469 SER cc_start: 0.8385 (m) cc_final: 0.8016 (p) REVERT: A 408 MET cc_start: 0.9144 (mmt) cc_final: 0.8865 (mmt) outliers start: 13 outliers final: 9 residues processed: 79 average time/residue: 0.0551 time to fit residues: 6.1267 Evaluate side-chains 72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 34 optimal weight: 6.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.121553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091656 restraints weight = 11952.770| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.77 r_work: 0.3137 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6763 Z= 0.150 Angle : 0.539 7.420 9191 Z= 0.276 Chirality : 0.043 0.300 979 Planarity : 0.004 0.058 1166 Dihedral : 4.870 54.930 873 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.87 % Allowed : 11.93 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.34 (0.30), residues: 785 helix: 1.41 (0.27), residues: 385 sheet: 0.47 (0.81), residues: 45 loop : -1.16 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.014 0.001 TYR A 385 PHE 0.015 0.001 PHE A 369 TRP 0.011 0.001 TRP A 168 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 6748) covalent geometry : angle 0.52942 / 0.27 ( 9156) SS BOND : bond 0.00166 / 0.08 ( 4) SS BOND : angle 0.32743 / 0.18 ( 8) hydrogen bonds : bond 0.05171 / 3.41 ( 297) hydrogen bonds : angle 4.41614 / 3.03 ( 843) metal coordination : bond 0.00254 / 0.13 ( 2) link_BETA1-4 : bond 0.00590 / 0.27 ( 3) link_BETA1-4 : angle 1.65541 / 0.86 ( 9) link_NAG-ASN : bond 0.00317 / 0.20 ( 6) link_NAG-ASN : angle 2.11553 / 1.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7618 (t0) cc_final: 0.7299 (t0) REVERT: B 469 SER cc_start: 0.8376 (m) cc_final: 0.8050 (p) outliers start: 13 outliers final: 10 residues processed: 75 average time/residue: 0.0650 time to fit residues: 6.8643 Evaluate side-chains 72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.120641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.090678 restraints weight = 12095.836| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.77 r_work: 0.3113 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6763 Z= 0.178 Angle : 0.553 7.407 9191 Z= 0.283 Chirality : 0.044 0.305 979 Planarity : 0.004 0.055 1166 Dihedral : 4.954 59.739 873 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.87 % Allowed : 12.93 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.37 (0.30), residues: 785 helix: 1.35 (0.27), residues: 396 sheet: 0.64 (0.82), residues: 44 loop : -1.15 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 600 TYR 0.014 0.001 TYR A 385 PHE 0.016 0.002 PHE A 369 TRP 0.016 0.001 TRP A 168 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 6748) covalent geometry : angle 0.54242 / 0.28 ( 9156) SS BOND : bond 0.00204 / 0.10 ( 4) SS BOND : angle 0.34384 / 0.19 ( 8) hydrogen bonds : bond 0.05438 / 3.58 ( 297) hydrogen bonds : angle 4.41500 / 3.02 ( 843) metal coordination : bond 0.00301 / 0.15 ( 2) link_BETA1-4 : bond 0.00586 / 0.27 ( 3) link_BETA1-4 : angle 1.64956 / 0.87 ( 9) link_NAG-ASN : bond 0.00338 / 0.21 ( 6) link_NAG-ASN : angle 2.21599 / 1.51 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7574 (t0) cc_final: 0.7279 (t0) REVERT: B 469 SER cc_start: 0.8323 (m) cc_final: 0.8020 (p) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.0655 time to fit residues: 7.2379 Evaluate side-chains 73 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 36 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.122973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093072 restraints weight = 11951.825| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.78 r_work: 0.3164 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6763 Z= 0.113 Angle : 0.502 7.340 9191 Z= 0.256 Chirality : 0.042 0.298 979 Planarity : 0.005 0.083 1166 Dihedral : 4.562 47.355 873 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.58 % Allowed : 12.79 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.50 (0.30), residues: 785 helix: 1.52 (0.27), residues: 384 sheet: 0.67 (0.81), residues: 44 loop : -1.06 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 600 TYR 0.014 0.001 TYR A 385 PHE 0.010 0.001 PHE A 315 TRP 0.013 0.001 TRP A 168 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 6748) covalent geometry : angle 0.49344 / 0.25 ( 9156) SS BOND : bond 0.00106 / 0.05 ( 4) SS BOND : angle 0.27022 / 0.16 ( 8) hydrogen bonds : bond 0.04587 / 3.02 ( 297) hydrogen bonds : angle 4.29798 / 2.96 ( 843) metal coordination : bond 0.00130 / 0.07 ( 2) link_BETA1-4 : bond 0.00548 / 0.25 ( 3) link_BETA1-4 : angle 1.50339 / 0.79 ( 9) link_NAG-ASN : bond 0.00359 / 0.24 ( 6) link_NAG-ASN : angle 1.91534 / 1.32 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7535 (t0) cc_final: 0.7258 (t0) REVERT: B 375 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.6859 (t80) REVERT: A 151 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8511 (mp) REVERT: A 408 MET cc_start: 0.9140 (mmt) cc_final: 0.8890 (mmt) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.0658 time to fit residues: 7.2302 Evaluate side-chains 74 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.121115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.090294 restraints weight = 12114.103| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.85 r_work: 0.3104 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6763 Z= 0.136 Angle : 0.517 7.294 9191 Z= 0.264 Chirality : 0.043 0.304 979 Planarity : 0.005 0.070 1166 Dihedral : 4.186 29.831 871 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.29 % Allowed : 13.65 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.58 (0.30), residues: 785 helix: 1.58 (0.27), residues: 384 sheet: 0.74 (0.81), residues: 44 loop : -1.02 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 600 TYR 0.014 0.001 TYR A 385 PHE 0.013 0.001 PHE A 369 TRP 0.013 0.001 TRP A 168 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6748) covalent geometry : angle 0.50818 / 0.26 ( 9156) SS BOND : bond 0.00149 / 0.07 ( 4) SS BOND : angle 0.31134 / 0.18 ( 8) hydrogen bonds : bond 0.04820 / 3.17 ( 297) hydrogen bonds : angle 4.27377 / 2.93 ( 843) metal coordination : bond 0.00218 / 0.11 ( 2) link_BETA1-4 : bond 0.00545 / 0.25 ( 3) link_BETA1-4 : angle 1.49874 / 0.79 ( 9) link_NAG-ASN : bond 0.00334 / 0.22 ( 6) link_NAG-ASN : angle 1.98811 / 1.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7525 (t0) cc_final: 0.7251 (t0) REVERT: A 151 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8482 (mp) REVERT: A 365 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7943 (p) REVERT: A 408 MET cc_start: 0.9138 (mmt) cc_final: 0.8837 (mmt) outliers start: 9 outliers final: 7 residues processed: 73 average time/residue: 0.0606 time to fit residues: 6.2949 Evaluate side-chains 73 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.120853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090018 restraints weight = 12160.519| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.85 r_work: 0.3094 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6763 Z= 0.153 Angle : 0.535 7.240 9191 Z= 0.273 Chirality : 0.043 0.309 979 Planarity : 0.005 0.065 1166 Dihedral : 4.090 17.396 869 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.58 % Allowed : 13.51 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.54 (0.30), residues: 785 helix: 1.52 (0.27), residues: 391 sheet: 0.74 (0.81), residues: 44 loop : -1.06 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 600 TYR 0.014 0.001 TYR A 385 PHE 0.014 0.001 PHE A 369 TRP 0.013 0.001 TRP A 168 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 6748) covalent geometry : angle 0.52551 / 0.27 ( 9156) SS BOND : bond 0.00162 / 0.08 ( 4) SS BOND : angle 0.30128 / 0.17 ( 8) hydrogen bonds : bond 0.05067 / 3.34 ( 297) hydrogen bonds : angle 4.30012 / 2.94 ( 843) metal coordination : bond 0.00267 / 0.13 ( 2) link_BETA1-4 : bond 0.00521 / 0.23 ( 3) link_BETA1-4 : angle 1.52752 / 0.81 ( 9) link_NAG-ASN : bond 0.00356 / 0.23 ( 6) link_NAG-ASN : angle 2.08995 / 1.43 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7543 (t0) cc_final: 0.7266 (t0) REVERT: B 375 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6853 (t80) REVERT: A 151 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8436 (mp) REVERT: A 365 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.8040 (p) outliers start: 11 outliers final: 6 residues processed: 75 average time/residue: 0.0601 time to fit residues: 6.2247 Evaluate side-chains 71 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.0040 chunk 15 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.0070 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.2210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.122501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.092585 restraints weight = 11986.329| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.66 r_work: 0.3115 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6763 Z= 0.103 Angle : 0.503 7.722 9191 Z= 0.257 Chirality : 0.041 0.298 979 Planarity : 0.004 0.062 1166 Dihedral : 3.903 17.916 869 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.15 % Allowed : 14.37 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.66 (0.30), residues: 785 helix: 1.75 (0.27), residues: 376 sheet: 0.78 (0.80), residues: 44 loop : -1.05 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 600 TYR 0.019 0.001 TYR A 183 PHE 0.010 0.001 PHE A 540 TRP 0.013 0.001 TRP A 566 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 6748) covalent geometry : angle 0.49509 / 0.26 ( 9156) SS BOND : bond 0.00089 / 0.04 ( 4) SS BOND : angle 0.28870 / 0.17 ( 8) hydrogen bonds : bond 0.04210 / 2.75 ( 297) hydrogen bonds : angle 4.25496 / 2.94 ( 843) metal coordination : bond 0.00064 / 0.03 ( 2) link_BETA1-4 : bond 0.00567 / 0.27 ( 3) link_BETA1-4 : angle 1.40671 / 0.74 ( 9) link_NAG-ASN : bond 0.00389 / 0.27 ( 6) link_NAG-ASN : angle 1.80421 / 1.26 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7485 (t0) cc_final: 0.7262 (t0) REVERT: B 375 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6603 (t80) REVERT: B 396 TYR cc_start: 0.8426 (m-10) cc_final: 0.8203 (m-10) REVERT: A 151 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8480 (mp) REVERT: A 365 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7921 (p) REVERT: A 408 MET cc_start: 0.9139 (mmt) cc_final: 0.8910 (mmt) outliers start: 8 outliers final: 4 residues processed: 76 average time/residue: 0.0678 time to fit residues: 7.2454 Evaluate side-chains 71 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 27 optimal weight: 0.3980 chunk 42 optimal weight: 0.3980 chunk 72 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.122607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.092625 restraints weight = 11872.436| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.65 r_work: 0.3123 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6763 Z= 0.109 Angle : 0.520 9.432 9191 Z= 0.268 Chirality : 0.042 0.301 979 Planarity : 0.005 0.084 1166 Dihedral : 3.826 17.371 869 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.01 % Allowed : 14.51 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.67 (0.30), residues: 785 helix: 1.75 (0.27), residues: 376 sheet: 0.87 (0.80), residues: 44 loop : -1.05 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 600 TYR 0.018 0.001 TYR A 183 PHE 0.010 0.001 PHE A 315 TRP 0.011 0.001 TRP A 168 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 6748) covalent geometry : angle 0.51332 / 0.27 ( 9156) SS BOND : bond 0.00114 / 0.06 ( 4) SS BOND : angle 0.27497 / 0.16 ( 8) hydrogen bonds : bond 0.04279 / 2.79 ( 297) hydrogen bonds : angle 4.27173 / 2.96 ( 843) metal coordination : bond 0.00097 / 0.05 ( 2) link_BETA1-4 : bond 0.00526 / 0.24 ( 3) link_BETA1-4 : angle 1.38110 / 0.73 ( 9) link_NAG-ASN : bond 0.00358 / 0.25 ( 6) link_NAG-ASN : angle 1.78568 / 1.23 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7454 (t0) cc_final: 0.7239 (t0) REVERT: A 151 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8495 (mp) REVERT: A 249 MET cc_start: 0.8304 (tpp) cc_final: 0.8043 (tpt) REVERT: A 365 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7946 (p) REVERT: A 408 MET cc_start: 0.9137 (mmt) cc_final: 0.8926 (mmt) outliers start: 7 outliers final: 5 residues processed: 76 average time/residue: 0.0718 time to fit residues: 7.6413 Evaluate side-chains 73 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.122572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.092077 restraints weight = 12235.048| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.82 r_work: 0.3135 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6763 Z= 0.178 Angle : 0.568 7.521 9191 Z= 0.293 Chirality : 0.044 0.311 979 Planarity : 0.005 0.081 1166 Dihedral : 4.035 17.050 869 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.44 % Allowed : 14.22 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.52 (0.30), residues: 785 helix: 1.46 (0.27), residues: 390 sheet: 0.90 (0.80), residues: 44 loop : -1.03 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.014 0.001 TYR A 385 PHE 0.015 0.001 PHE A 369 TRP 0.013 0.001 TRP A 168 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 6748) covalent geometry : angle 0.55964 / 0.29 ( 9156) SS BOND : bond 0.00210 / 0.10 ( 4) SS BOND : angle 0.33791 / 0.19 ( 8) hydrogen bonds : bond 0.05283 / 3.48 ( 297) hydrogen bonds : angle 4.38308 / 3.03 ( 843) metal coordination : bond 0.00366 / 0.18 ( 2) link_BETA1-4 : bond 0.00477 / 0.21 ( 3) link_BETA1-4 : angle 1.50761 / 0.80 ( 9) link_NAG-ASN : bond 0.00350 / 0.22 ( 6) link_NAG-ASN : angle 2.09831 / 1.43 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1513.14 seconds wall clock time: 26 minutes 36.90 seconds (1596.90 seconds total)