Starting phenix.real_space_refine on Thu Jul 2 03:52:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fdi_31544/07_2026/7fdi_31544.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fdi_31544/07_2026/7fdi_31544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fdi_31544/07_2026/7fdi_31544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fdi_31544/07_2026/7fdi_31544.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fdi_31544/07_2026/7fdi_31544.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fdi_31544/07_2026/7fdi_31544.cif" model { file = "/net/cci-nas-00/data/ceres_data/7fdi_31544/07_2026/7fdi_31544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fdi_31544/07_2026/7fdi_31544.cif" } resolution = 3.12 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= 0.003 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4097 2.51 5 N 1058 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 6403 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4802 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 594, 4795 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 594, 4795 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 4922 Chain: "E" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1531 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 183} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" 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 Time building chain proxies: 1.60, per 1000 atoms: 0.25 Number of scatterers: 6403 At special positions: 0 Unit cell: (113.36, 88.4, 79.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1212 8.00 N 1058 7.00 C 4097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 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 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 NAG-ASN " NAG A 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 53 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 391.6 milliseconds 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: 1484 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 58.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.647A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.908A pdb=" N MET A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.609A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.529A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.699A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.836A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.556A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 253 through 256 removed outlier: 4.198A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' 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 removed outlier: 3.552A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.567A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.540A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.881A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.797A 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 466 removed outlier: 3.732A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.625A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.265A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.668A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.808A pdb=" N VAL 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 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.859A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 385 through 390 Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.457A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.552A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.691A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 324 hydrogen bonds defined for protein. 908 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: 0.61 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2055 1.35 - 1.47: 1740 1.47 - 1.59: 2735 1.59 - 1.71: 0 1.71 - 1.84: 56 Bond restraints: 6586 Sorted by residual: bond pdb=" CB TRP A 478 " pdb=" CG TRP A 478 " ideal model delta sigma weight residual 1.498 1.452 0.046 3.10e-02 1.04e+03 2.20e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG A 704 " pdb=" O5 NAG A 704 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" CG MET A 455 " pdb=" SD MET A 455 " ideal model delta sigma weight residual 1.803 1.773 0.030 2.50e-02 1.60e+03 1.48e+00 bond pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.38e+00 ... (remaining 6581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 8711 1.70 - 3.39: 214 3.39 - 5.09: 31 5.09 - 6.78: 4 6.78 - 8.48: 2 Bond angle restraints: 8962 Sorted by residual: angle pdb=" C LEU A 529 " pdb=" N CYS A 530 " pdb=" CA CYS A 530 " ideal model delta sigma weight residual 122.65 118.39 4.26 1.66e+00 3.63e-01 6.58e+00 angle pdb=" CB MET A 152 " pdb=" CG MET A 152 " pdb=" SD MET A 152 " ideal model delta sigma weight residual 112.70 120.23 -7.53 3.00e+00 1.11e-01 6.30e+00 angle pdb=" N LYS A 234 " pdb=" CA LYS A 234 " pdb=" C LYS A 234 " ideal model delta sigma weight residual 109.81 115.33 -5.52 2.21e+00 2.05e-01 6.25e+00 angle pdb=" CA LEU A 266 " pdb=" CB LEU A 266 " pdb=" CG LEU A 266 " ideal model delta sigma weight residual 116.30 124.78 -8.48 3.50e+00 8.16e-02 5.87e+00 angle pdb=" CA GLU A 435 " pdb=" CB GLU A 435 " pdb=" CG GLU A 435 " ideal model delta sigma weight residual 114.10 118.90 -4.80 2.00e+00 2.50e-01 5.77e+00 ... (remaining 8957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3465 17.97 - 35.94: 304 35.94 - 53.92: 42 53.92 - 71.89: 10 71.89 - 89.86: 10 Dihedral angle restraints: 3831 sinusoidal: 1517 harmonic: 2314 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual -86.00 -17.03 -68.97 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CA CYS A 530 " pdb=" C CYS A 530 " pdb=" N GLN A 531 " pdb=" CA GLN A 531 " ideal model delta harmonic sigma weight residual 180.00 149.60 30.40 0 5.00e+00 4.00e-02 3.70e+01 dihedral pdb=" CA CYS A 344 " pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 3828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 753 0.054 - 0.108: 181 0.108 - 0.162: 18 0.162 - 0.216: 2 0.216 - 0.269: 1 Chirality restraints: 955 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA CYS A 530 " pdb=" N CYS A 530 " pdb=" C CYS A 530 " pdb=" CB CYS A 530 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CB ILE A 468 " pdb=" CA ILE A 468 " pdb=" CG1 ILE A 468 " pdb=" CG2 ILE A 468 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 952 not shown) Planarity restraints: 1162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 478 " 0.040 2.00e-02 2.50e+03 3.06e-02 2.34e+01 pdb=" CG TRP A 478 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP A 478 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 478 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 478 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 478 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 478 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 478 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 478 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 478 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 252 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO A 253 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 347 " -0.016 2.00e-02 2.50e+03 1.48e-02 3.84e+00 pdb=" CG PHE E 347 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE E 347 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE E 347 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE E 347 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 347 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 347 " -0.002 2.00e-02 2.50e+03 ... (remaining 1159 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 127 2.67 - 3.23: 6444 3.23 - 3.78: 10606 3.78 - 4.34: 14672 4.34 - 4.90: 23636 Nonbonded interactions: 55485 Sorted by model distance: nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.109 3.040 nonbonded pdb=" NH1 ARG A 460 " pdb=" O TYR A 510 " model vdw 2.133 3.120 nonbonded pdb=" O ASN E 439 " pdb=" OG SER E 443 " model vdw 2.181 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR E 500 " model vdw 2.182 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.208 3.120 ... (remaining 55480 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=0.50 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: 1.520 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.080 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 : 0.005 0.046 6598 Z= 0.220 Angle : 0.662 8.479 8991 Z= 0.349 Chirality : 0.046 0.269 955 Planarity : 0.005 0.070 1157 Dihedral : 14.053 89.858 2326 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.15 % Allowed : 0.00 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.19 (0.30), residues: 785 helix: 0.41 (0.25), residues: 397 sheet: 0.28 (0.79), residues: 48 loop : -0.74 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 582 TYR 0.021 0.002 TYR E 495 PHE 0.034 0.002 PHE E 347 TRP 0.082 0.003 TRP A 478 HIS 0.003 0.001 HIS E 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 ( 6586) covalent geometry : angle 0.64306 / 0.34 ( 8962) SS BOND : bond 0.00530 / 0.29 ( 7) SS BOND : angle 2.41379 / 1.35 ( 14) hydrogen bonds : bond 0.13468 / 9.04 ( 324) hydrogen bonds : angle 6.36841 / 4.61 ( 908) link_NAG-ASN : bond 0.00348 / 0.24 ( 5) link_NAG-ASN : angle 3.21182 / 1.95 ( 15) *********************** 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 86 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.6717 (t80) cc_final: 0.6350 (t80) REVERT: A 156 LEU cc_start: 0.8305 (mp) cc_final: 0.7830 (tt) REVERT: A 480 MET cc_start: 0.5237 (ptm) cc_final: 0.4998 (ptt) REVERT: A 557 MET cc_start: 0.8818 (tmm) cc_final: 0.8514 (tmm) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.0520 time to fit residues: 6.2309 Evaluate side-chains 68 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN A 239 HIS ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.143314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.118135 restraints weight = 17798.169| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.75 r_work: 0.3536 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6598 Z= 0.144 Angle : 0.605 10.967 8991 Z= 0.309 Chirality : 0.044 0.211 955 Planarity : 0.005 0.053 1157 Dihedral : 4.691 26.513 855 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.59 % Allowed : 4.58 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.39 (0.31), residues: 785 helix: 0.80 (0.25), residues: 400 sheet: 0.50 (0.78), residues: 50 loop : -0.33 (0.37), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 177 TYR 0.023 0.002 TYR A 385 PHE 0.017 0.001 PHE E 347 TRP 0.050 0.002 TRP A 478 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6586) covalent geometry : angle 0.59227 / 0.31 ( 8962) SS BOND : bond 0.00453 / 0.24 ( 7) SS BOND : angle 2.04845 / 1.13 ( 14) hydrogen bonds : bond 0.04597 / 3.05 ( 324) hydrogen bonds : angle 5.00494 / 3.55 ( 908) link_NAG-ASN : bond 0.00187 / 0.12 ( 5) link_NAG-ASN : angle 2.36381 / 1.48 ( 15) *********************** 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 82 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.6915 (t80) cc_final: 0.6379 (t80) outliers start: 4 outliers final: 3 residues processed: 81 average time/residue: 0.0529 time to fit residues: 6.2281 Evaluate side-chains 68 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.142512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.117273 restraints weight = 9859.943| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.27 r_work: 0.3599 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6598 Z= 0.144 Angle : 0.601 11.285 8991 Z= 0.299 Chirality : 0.043 0.199 955 Planarity : 0.005 0.049 1157 Dihedral : 4.559 25.701 855 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.74 % Allowed : 7.09 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.59 (0.31), residues: 785 helix: 0.97 (0.26), residues: 398 sheet: 0.56 (0.78), residues: 50 loop : -0.23 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 460 TYR 0.020 0.001 TYR A 385 PHE 0.017 0.001 PHE A 369 TRP 0.030 0.002 TRP A 478 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6586) covalent geometry : angle 0.59107 / 0.30 ( 8962) SS BOND : bond 0.00388 / 0.21 ( 7) SS BOND : angle 1.74974 / 0.96 ( 14) hydrogen bonds : bond 0.04389 / 2.92 ( 324) hydrogen bonds : angle 4.80850 / 3.41 ( 908) link_NAG-ASN : bond 0.00219 / 0.16 ( 5) link_NAG-ASN : angle 2.27889 / 1.41 ( 15) *********************** 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 78 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.6950 (t80) cc_final: 0.6342 (t80) REVERT: A 408 MET cc_start: 0.8506 (mmt) cc_final: 0.8200 (mmt) REVERT: A 435 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7617 (mp0) outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 0.0484 time to fit residues: 5.3584 Evaluate side-chains 74 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 373 HIS E 501 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.144211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.119811 restraints weight = 14794.529| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.06 r_work: 0.3596 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6598 Z= 0.128 Angle : 0.579 11.649 8991 Z= 0.286 Chirality : 0.042 0.188 955 Planarity : 0.004 0.048 1157 Dihedral : 4.383 24.905 855 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.03 % Allowed : 8.42 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.82 (0.31), residues: 785 helix: 1.09 (0.26), residues: 397 sheet: 0.60 (0.78), residues: 50 loop : -0.00 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.021 0.001 TYR A 385 PHE 0.016 0.001 PHE A 369 TRP 0.042 0.002 TRP A 478 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 6586) covalent geometry : angle 0.57039 / 0.28 ( 8962) SS BOND : bond 0.00377 / 0.20 ( 7) SS BOND : angle 1.56206 / 0.86 ( 14) hydrogen bonds : bond 0.04175 / 2.79 ( 324) hydrogen bonds : angle 4.68342 / 3.32 ( 908) link_NAG-ASN : bond 0.00186 / 0.13 ( 5) link_NAG-ASN : angle 2.08186 / 1.30 ( 15) *********************** 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 83 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.6981 (t80) cc_final: 0.6320 (t80) REVERT: A 150 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6955 (mm-30) REVERT: A 376 MET cc_start: 0.8407 (tpp) cc_final: 0.8097 (mmm) REVERT: A 408 MET cc_start: 0.8490 (mmt) cc_final: 0.8219 (mmt) REVERT: A 435 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: E 346 ARG cc_start: 0.7060 (mtm180) cc_final: 0.6221 (ptt180) outliers start: 7 outliers final: 4 residues processed: 80 average time/residue: 0.0458 time to fit residues: 5.4025 Evaluate side-chains 76 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.2980 chunk 64 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.147817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.121794 restraints weight = 12441.040| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.97 r_work: 0.3628 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6598 Z= 0.123 Angle : 0.572 12.201 8991 Z= 0.283 Chirality : 0.042 0.172 955 Planarity : 0.004 0.049 1157 Dihedral : 4.310 24.463 855 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.89 % Allowed : 9.45 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.86 (0.31), residues: 785 helix: 1.09 (0.26), residues: 399 sheet: 0.52 (0.77), residues: 50 loop : 0.09 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.020 0.001 TYR A 385 PHE 0.011 0.001 PHE A 369 TRP 0.031 0.001 TRP A 478 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 6586) covalent geometry : angle 0.56421 / 0.28 ( 8962) SS BOND : bond 0.00343 / 0.18 ( 7) SS BOND : angle 1.43822 / 0.79 ( 14) hydrogen bonds : bond 0.04089 / 2.73 ( 324) hydrogen bonds : angle 4.63554 / 3.29 ( 908) link_NAG-ASN : bond 0.00172 / 0.12 ( 5) link_NAG-ASN : angle 1.98712 / 1.24 ( 15) *********************** 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 81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.7095 (t80) cc_final: 0.6375 (t80) REVERT: A 150 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6860 (mm-30) REVERT: A 156 LEU cc_start: 0.8824 (mp) cc_final: 0.8126 (tt) REVERT: A 435 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: E 346 ARG cc_start: 0.7138 (mtm180) cc_final: 0.6290 (ptt180) outliers start: 6 outliers final: 4 residues processed: 79 average time/residue: 0.0492 time to fit residues: 5.7263 Evaluate side-chains 76 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 55 optimal weight: 0.0670 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.141589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.116437 restraints weight = 17873.896| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.87 r_work: 0.3509 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6598 Z= 0.186 Angle : 0.623 12.084 8991 Z= 0.309 Chirality : 0.044 0.192 955 Planarity : 0.004 0.048 1157 Dihedral : 4.563 25.378 855 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.89 % Allowed : 9.16 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.69 (0.31), residues: 785 helix: 0.94 (0.26), residues: 400 sheet: 0.50 (0.76), residues: 49 loop : -0.01 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 403 TYR 0.021 0.002 TYR A 385 PHE 0.016 0.001 PHE E 347 TRP 0.038 0.002 TRP A 165 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 ( 6586) covalent geometry : angle 0.61394 / 0.31 ( 8962) SS BOND : bond 0.00351 / 0.19 ( 7) SS BOND : angle 1.49113 / 0.82 ( 14) hydrogen bonds : bond 0.04422 / 2.95 ( 324) hydrogen bonds : angle 4.76151 / 3.39 ( 908) link_NAG-ASN : bond 0.00230 / 0.16 ( 5) link_NAG-ASN : angle 2.37277 / 1.46 ( 15) *********************** 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 79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.7179 (t80) cc_final: 0.6457 (t80) REVERT: A 156 LEU cc_start: 0.8830 (mp) cc_final: 0.8126 (tt) REVERT: A 429 GLN cc_start: 0.6810 (tp-100) cc_final: 0.6296 (tp-100) REVERT: A 435 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: E 346 ARG cc_start: 0.7207 (mtm180) cc_final: 0.6387 (ptt180) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 0.0456 time to fit residues: 5.1446 Evaluate side-chains 77 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 0.0000 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.145383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.121220 restraints weight = 14301.549| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.93 r_work: 0.3616 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6598 Z= 0.118 Angle : 0.574 12.516 8991 Z= 0.285 Chirality : 0.042 0.167 955 Planarity : 0.004 0.045 1157 Dihedral : 4.317 24.420 855 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.89 % Allowed : 9.75 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.85 (0.31), residues: 785 helix: 1.07 (0.26), residues: 400 sheet: 0.40 (0.76), residues: 50 loop : 0.11 (0.37), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.019 0.001 TYR A 385 PHE 0.013 0.001 PHE E 392 TRP 0.053 0.002 TRP A 478 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 6586) covalent geometry : angle 0.56637 / 0.28 ( 8962) SS BOND : bond 0.00333 / 0.18 ( 7) SS BOND : angle 1.33808 / 0.73 ( 14) hydrogen bonds : bond 0.04077 / 2.74 ( 324) hydrogen bonds : angle 4.61740 / 3.27 ( 908) link_NAG-ASN : bond 0.00173 / 0.12 ( 5) link_NAG-ASN : angle 1.96819 / 1.23 ( 15) *********************** 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 78 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6851 (mm-30) REVERT: A 156 LEU cc_start: 0.8809 (mp) cc_final: 0.8101 (tt) REVERT: A 408 MET cc_start: 0.8443 (mmt) cc_final: 0.8207 (mmt) REVERT: A 435 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: E 346 ARG cc_start: 0.7074 (mtm180) cc_final: 0.6228 (ptt180) REVERT: E 457 ARG cc_start: 0.8033 (ttt-90) cc_final: 0.7632 (ttt180) outliers start: 6 outliers final: 4 residues processed: 76 average time/residue: 0.0558 time to fit residues: 6.1038 Evaluate side-chains 75 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 0.0770 chunk 26 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 chunk 12 optimal weight: 0.0070 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN E 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.148795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.124194 restraints weight = 17546.459| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.71 r_work: 0.3610 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6598 Z= 0.104 Angle : 0.554 12.670 8991 Z= 0.273 Chirality : 0.041 0.151 955 Planarity : 0.004 0.039 1157 Dihedral : 4.072 22.841 855 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.74 % Allowed : 10.04 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.97 (0.31), residues: 785 helix: 1.13 (0.26), residues: 401 sheet: 0.37 (0.76), residues: 50 loop : 0.23 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.029 0.001 TYR A 243 PHE 0.011 0.001 PHE A 369 TRP 0.033 0.002 TRP A 478 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 6586) covalent geometry : angle 0.54816 / 0.27 ( 8962) SS BOND : bond 0.00328 / 0.17 ( 7) SS BOND : angle 1.27594 / 0.70 ( 14) hydrogen bonds : bond 0.03840 / 2.60 ( 324) hydrogen bonds : angle 4.46589 / 3.16 ( 908) link_NAG-ASN : bond 0.00174 / 0.11 ( 5) link_NAG-ASN : angle 1.62261 / 1.03 ( 15) *********************** 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 88 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6831 (mm-30) REVERT: A 408 MET cc_start: 0.8496 (mmt) cc_final: 0.7971 (mmt) REVERT: A 429 GLN cc_start: 0.6623 (tp-100) cc_final: 0.6375 (tp-100) REVERT: A 435 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: A 557 MET cc_start: 0.8755 (tmm) cc_final: 0.8412 (tmm) REVERT: E 346 ARG cc_start: 0.6946 (mtm180) cc_final: 0.6345 (ptt180) REVERT: E 457 ARG cc_start: 0.8104 (ttt-90) cc_final: 0.7764 (ttt180) outliers start: 5 outliers final: 4 residues processed: 86 average time/residue: 0.0586 time to fit residues: 6.8370 Evaluate side-chains 80 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 501 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 586 ASN E 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.146929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.123045 restraints weight = 12538.338| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.88 r_work: 0.3636 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6598 Z= 0.120 Angle : 0.588 11.610 8991 Z= 0.285 Chirality : 0.042 0.156 955 Planarity : 0.004 0.039 1157 Dihedral : 4.124 23.049 855 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.74 % Allowed : 11.37 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.00 (0.31), residues: 785 helix: 1.15 (0.26), residues: 400 sheet: 0.25 (0.76), residues: 50 loop : 0.28 (0.37), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 403 TYR 0.024 0.002 TYR A 243 PHE 0.013 0.001 PHE A 369 TRP 0.035 0.002 TRP A 478 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6586) covalent geometry : angle 0.58179 / 0.28 ( 8962) SS BOND : bond 0.00317 / 0.17 ( 7) SS BOND : angle 1.28946 / 0.71 ( 14) hydrogen bonds : bond 0.03948 / 2.65 ( 324) hydrogen bonds : angle 4.47278 / 3.17 ( 908) link_NAG-ASN : bond 0.00174 / 0.12 ( 5) link_NAG-ASN : angle 1.77107 / 1.11 ( 15) *********************** 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 79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6765 (mm-30) REVERT: A 252 TYR cc_start: 0.6071 (m-80) cc_final: 0.5702 (m-10) REVERT: A 408 MET cc_start: 0.8441 (mmt) cc_final: 0.7952 (mmt) REVERT: A 429 GLN cc_start: 0.6554 (tp-100) cc_final: 0.6287 (tp-100) REVERT: A 435 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: A 557 MET cc_start: 0.8797 (tmm) cc_final: 0.8502 (tmm) REVERT: E 346 ARG cc_start: 0.6952 (mtm180) cc_final: 0.6284 (ptt180) REVERT: E 457 ARG cc_start: 0.8019 (ttt-90) cc_final: 0.7620 (ttt180) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.0613 time to fit residues: 6.4767 Evaluate side-chains 77 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 68 optimal weight: 0.4980 chunk 64 optimal weight: 5.9990 chunk 30 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN E 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.147490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.122658 restraints weight = 12421.850| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.55 r_work: 0.3652 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6598 Z= 0.115 Angle : 0.585 12.301 8991 Z= 0.283 Chirality : 0.041 0.162 955 Planarity : 0.004 0.039 1157 Dihedral : 4.127 22.858 855 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.89 % Allowed : 11.67 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.00 (0.31), residues: 785 helix: 1.18 (0.26), residues: 400 sheet: 0.24 (0.76), residues: 50 loop : 0.25 (0.37), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.022 0.001 TYR A 243 PHE 0.012 0.001 PHE A 369 TRP 0.032 0.002 TRP A 478 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 6586) covalent geometry : angle 0.57884 / 0.28 ( 8962) SS BOND : bond 0.00316 / 0.17 ( 7) SS BOND : angle 1.27981 / 0.70 ( 14) hydrogen bonds : bond 0.03889 / 2.61 ( 324) hydrogen bonds : angle 4.45241 / 3.16 ( 908) link_NAG-ASN : bond 0.00177 / 0.12 ( 5) link_NAG-ASN : angle 1.76460 / 1.11 ( 15) ********************** 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 81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6764 (mm-30) REVERT: A 408 MET cc_start: 0.8451 (mmt) cc_final: 0.7902 (mmt) REVERT: A 429 GLN cc_start: 0.6597 (tp-100) cc_final: 0.6332 (tp-100) REVERT: A 435 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: A 557 MET cc_start: 0.8804 (tmm) cc_final: 0.8491 (tmm) REVERT: E 346 ARG cc_start: 0.6966 (mtm180) cc_final: 0.6318 (ptt180) REVERT: E 457 ARG cc_start: 0.8007 (ttt-90) cc_final: 0.7623 (ttt180) outliers start: 6 outliers final: 4 residues processed: 79 average time/residue: 0.0672 time to fit residues: 7.3396 Evaluate side-chains 78 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 0.0980 chunk 58 optimal weight: 0.6980 chunk 17 optimal weight: 0.0870 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.147671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.122368 restraints weight = 17659.512| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 3.87 r_work: 0.3585 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6598 Z= 0.117 Angle : 0.594 13.316 8991 Z= 0.288 Chirality : 0.041 0.156 955 Planarity : 0.004 0.039 1157 Dihedral : 4.107 22.848 855 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.89 % Allowed : 11.67 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.03 (0.31), residues: 785 helix: 1.21 (0.26), residues: 400 sheet: 0.23 (0.76), residues: 50 loop : 0.27 (0.37), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.022 0.001 TYR A 243 PHE 0.013 0.001 PHE A 369 TRP 0.032 0.002 TRP A 478 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6586) covalent geometry : angle 0.58862 / 0.29 ( 8962) SS BOND : bond 0.00312 / 0.17 ( 7) SS BOND : angle 1.27436 / 0.70 ( 14) hydrogen bonds : bond 0.03876 / 2.59 ( 324) hydrogen bonds : angle 4.45243 / 3.16 ( 908) link_NAG-ASN : bond 0.00172 / 0.12 ( 5) link_NAG-ASN : angle 1.74816 / 1.10 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1334.33 seconds wall clock time: 23 minutes 30.60 seconds (1410.60 seconds total)